WO2014036314A2 - Diagnosis of rheumatoid arthritis (ra) using differentially methylated loci identified in peripheral blood mononuclear cells, t-cells, b-cells and monocytes - Google Patents

Diagnosis of rheumatoid arthritis (ra) using differentially methylated loci identified in peripheral blood mononuclear cells, t-cells, b-cells and monocytes Download PDF

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WO2014036314A2
WO2014036314A2 PCT/US2013/057375 US2013057375W WO2014036314A2 WO 2014036314 A2 WO2014036314 A2 WO 2014036314A2 US 2013057375 W US2013057375 W US 2013057375W WO 2014036314 A2 WO2014036314 A2 WO 2014036314A2
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methylation
loci
dna
panel
dml
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PCT/US2013/057375
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WO2014036314A3 (en
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Jonathan Lim
Robert Shoemaker
Louis Bookbinder
David Anderson
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Ignyta, Inc.
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 are included in the specification of this application.
  • the claimed subject matter of the present application was made by or on behalf of parties to a joint research agreement that was in effect on or before the date the claimed invention was made; the claimed invention was made as a result of activities undertaken within the scope of the joint research agreement; and the parties to the joint research agreement include: The Regents of the University of California and Ignyta, Inc. (formerly NexDx, Inc.).
  • the joint research agreement was a written contract, grant or cooperative agreement entered into by the above-mentioned parties for the performance of experimental, developmental or research work in the field of the claimed invention.
  • Embodiments of the present invention include methods, compositions and kits for the diagnosis or prognosis of a subject with an autoimmune disorder such as Rheumatoid Arthritis. Some embodiments include identifying a therapeutic agent or selecting or monitoring a treatment for treating a disorder such as Rheumatoid Arthritis. BACKGROUND OF THE INVENTION
  • Rheumatoid arthritis is an autoimmune disease characterized by chronic, systemic inflammation, especially involving the synovial joints (Harris et al., 2009. "Clinical features of rheumatoid arthritis, ' " In: Firestein et al., eds. Kelley's Textbook of Rheumatology. 8 th ed. Philadelphia, Pa: Saunders Elsevier; Chapter 66; Firestein, 2003. "Evolving concepts of rheumatoid arthritis,” Nature 423:356-61; Klareskog et al, 2009. “Rheumatoid arthritis " Lancet 373:659-72).
  • RA is the most common chronic inflammatory joint disease with an estimated incidence of ⁇ 1% of the US population, and a 2 to 3 times higher prevalence in women than in men (Helmick et al. 2008. "Estimates of the prevalence of arthritis and other rheumatic conditions in the United States, " Part I. Arthritis Rheum. 58:15-25). RA poses a substantial burden on public health with the overall costs estimated to exceed $30 billion annually in the U.S. (Birnbaum et al., 2010. "Societal cost of rheumatoid arthritis patients in the US, " Curr Med Res Opin. 26:77-90). Treatment with DMARDs can often ameliorate the disease and improve the clinical outcome.
  • RA osteoarthritis
  • lupus lupus
  • ankylosing spondylitis other connective tissue disease
  • fibromyalgia connective tissue disease
  • the methylome approaches for global DNA methylation profiling, " Trends in Genetics 24:231-237). Methylation of promoters within CpG islands increase or decrease gene expression (hypomethylation and hypermethylation patterns, respectively) (Portela et al., 2010. “Epigenetic modifications and human disease, “ Nature Biotechnology 28(10): 1057-1068; Feinberg et al., 2007. “Phenotypic plasticity and the epigenetics of human disease, " Nature 447:433-40). Environmental factors and lifestyle factors can modify the epigenome and in some cases lead to gene dysregulation and disease (Lu a et al., 2006.
  • DNA methylation may play an important role in the pathogenesis of RA, suggesting that multiplexed methylation biomarkers could be developed as a valuable diagnostic tool (Laird, 2003. "The power and the promise of DNA methylation markers, " Nature Rev. Cancer 3:253-266).
  • the DNA methylation signatures within cells are considered to be a novel and important source of biomarkers to better diagnose RA and other autoimmune diseases (Brooks et al., 2010. "Epigenetics and autoimmunity. Journal of Autoimmunity; 34:J207-J219; Huber et al., 2007.
  • DNA methylation biomarkers They reflect past environmental influences leading to persistent changes in cellular transcription and function with consequences for disease risk, diagnosis, prognosis, and potential response to therapy.
  • the prevalence of DNA methylation biomarkers is higher than most genetic markers of disease, can be associated with multiple loci within a cell potentially affecting several genes or other regulatory molecules (Laird, 2003. "The power and the promise of DNA methylation markers, " Nature Rev. Cancer 3:253-266), and can be detected with very high sensitivity and specificity, including blood-based tests, making methylation biomarkers for RA attractive for a clinical diagnostic laboratory (Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526).
  • DML differentially methylated loci
  • the methods, reagents and kits comprise one or more panels of DML that may be used to distinguish rheumatoid arthritis (RA) from osteoarthritis (OA), systemic lupus erythematosus (SLE), other autoimmune diseases, other rheumatic diseases, or normal healthy control (HC) patients.
  • RA rheumatoid arthritis
  • OA osteoarthritis
  • SLE systemic lupus erythematosus
  • HC normal healthy control
  • Panels of DML may comprise three or more DML, and may comprise one or more DML selected from the following Tables. In each table the following data are provided: the position of the DML; identity of any associated gene; the sample source from which a DML was identified; and the condition corresponding to the sample with which an RA sample was compared to identify the DML is indicated.
  • the sample sources are PBMCs, T-cells, B-cells and Monocytes.
  • DML were identified by comparing RA sample methylation patters with those of SLE samples, OA samples, or healthy control (HC) samples, individually or in combination, and a larger "not RA" category that includes samples taken from individuals having a number of autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
  • autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
  • Tables 1A, IB, 2A, 2B, 3A and 3B disclose DMLs corresponding to methylation sites at which the inventors have discovered a diagnostically relevant association between methylation status and RA status.
  • Table 1A and IB DML reported in Tables 1A and IB identify loci corresponding to sites for which a previously-reported association between methylation status and RA exists, but which were independently identified and reported herein. Importantly, the list of sites for which a previously-reported association between methylation status and RA exists is substantially greater than the list of DML in Table 1. That is, Tables 1A and IB represent a specific subset of DML which, although previously reported as methylation sites related to RA, have been affirmed herein to have a diagnostic value not uniformly present in RA-associated sites reported in the literature.
  • Tables 2 A and 2B DML reported in Tables 2 A and 2B identify loci for which no previous association between methylation status at the listed sites and RA was reported, and for which no previous association between the associated loci and RA was reported. That is, Tables 2A and 2B report novel DML that identify novel loci in the context of RA.
  • Tables 3A and 3B DML reported in Tables 3A and 3B identify loci for which no previous association between methylation status at the listed sites and RA was reported, but for which a previous association between the associated loci and RA has been reported.
  • Panels comprising DML selected at random from Tables 1A-3B have been generated and are reported herein to demonstrate performance characteristics substantially above the performance characteristics of randomly selected panels of methylation sites that are not known to be differentially methylated in the context of RA. Accordingly, a randomly selected panel of DML from any of Tables 1A, IB, 2A, 2B, 3A and 3B will substantially outperform a random panel of DML not known to be implicated in RA diagnosis in an assay for the presence of an RA methylation signature in an individual.
  • Table 4 DML reported in Table 4 represent a subset of the DML reported in Tables 1A, IB, 2A, 2B, 3A, 3B, above that most robustly discriminate RA from other conditions ("not RA"). DML listed in Table 4 have been cross-validated across data sets. Table 4 DML are observed in some embodiments to contribute to panels having performance characteristics substantially above the performance characteristics of randomly selected panels of loci selected from one or more of Tables 1A, IB, 2A, 2B, 3A and 3B, which in turn have performance characteristics substantially above the performance characteristics of randomly selected panels of loci not associated with RA diagnosis.
  • Tables 1A, 2 A, and 3 A were generated from DML identified from analysis of PBMC samples from 39 patients (13 RA, 11 SLE, 10 OA, and 5 HC patients), and T-cell, B-cell, and Monocyte DML were generated from 23 patients (7 RA, 5 SLE, 6 OA, and 5 HC). These samples came from a single source in the US.
  • Tables IB, 2B, and 3B were generated from DML identified from analysis of PBMC samples from 937 patients (431 RA, 32 SLE, 13 OA, 371 HC, 48 autoimmune and rheumatic diseases, and 42 other). These samples came from 15 sources worldwide.
  • DML panels in sample assessment for a disease status such as RA disease status.
  • panels may comprise from one to hundreds of DML, such as the DML listed herein, and may further comprise other DML and other non-DML indicia of disease status, such as single nucleotide polymorphisms, other alleles, transcript accumulation levels, protein accumulation levels or activities, antibody levels, clinical data or other data relevant to the assessment of an individual or a sample from an individual regarding RA status.
  • the assessment involves steps performed on a computer to analyze large arrays of data, such as data related to DML methylation levels for one or more than one sample.
  • a method of characterizing a potential autoimmune disease in a subject comprises ascertaining the methylation status of a panel comprising at least 3 differentially- methylated loci (DML) in DNA of peripheral blood mononuclear cells (PBMCs) from a mammalian subject.
  • DML differentially- methylated loci
  • PBMCs peripheral blood mononuclear cells
  • a method comprises electronically comparing in a computer values reflective of said methylation status of said panel of DMLs with stored information reflective of methylation status of DMLs in at least one standard population, generating a report based on the comparison relative to the potential autoimmune disease; and providing the report to a caregiver or to a subject; wherein the at least 3 DML are selected from the DML listed.
  • the autoimmune disease is RA.
  • the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from PBMCs of said subject.
  • the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from circulating cells of a subject comprising PBMC cells. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of said subject comprising PBMC DNA.
  • the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of a subject. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from T-cells of a subject. In some aspects of these embodiments ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from B-cells of said subject. In some aspects of these embodiments ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from monocytes of said subject. In some aspects of these embodiments an ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from whole blood of said subject.
  • a laboratory analysis comprises chemical treatment of DNA extracted from said sample that differentially affects methylated and unmethylated bases.
  • the treatment comprises bisulfite treatment.
  • the fragments comprise 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb on either side of DML.
  • the laboratory analysis further comprises contacting said amplified DNA with a reagent that distinguishes between bisulfite-treated methylated and bisulfite -treated unmethylated DNA.
  • the reagent is an oligonucleotide probe.
  • the reagent is a protein that differentially binds DNA according to its methylation status.
  • the panel comprises at least 1, at least 2, at least 3, at least 4, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
  • a standard population comprises individuals not having said autoimmune disease, or having said autoimmune disease.
  • the standard populations comprise individuals with RA, OA, SLE, HC, or a collection of rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
  • rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
  • the ascertaining step further comprises ascertaining values reflective of one or more additional non-DML characteristics of the subject, and wherein said electronically comparing step further comprises comparing those non-DML values with non-DML values from one or more standard populations in a computer.
  • the non-DML values are selected from the group consisting of: SNP or gene variation status, levels of autoantibodies such as anti-dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
  • autoantibodies such as anti-dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
  • the methylation events are detected at loci set forth in Tables 1A, IB, 2A, 2B, 3A, 3B or 4 in this disclosure.
  • the method comprises subjecting a sample from a human individual comprising DNA to treatment that differentially affects methylated bases of said human sample, and ascertaining the extent of methylation of a panel of loci, wherein a plurality of said loci are listed in one or more of Tables 1A, IB, 2A, 2B, 3A, 3B and 4 .
  • the sample comprises circulating DNA, DNA from circulating blood cells, or comprises DNA from PBMCs or from whole blood.
  • the sample comprises B-cell DNA, T-cell DNA, or Monocyte DNA, or DNA selected from the list of DNA sources consisting of T-cell DNA, B-cell DNA and monocyte DNA.
  • the method further comprises comparing the methylation status of the loci of the panel with methylation status indicative of RA, OA, HC, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or and HC individuals.
  • the treatment comprises contacting said locus with bisulfite.
  • the panel comprises at least 5, 10, 20, 50, 200, 250 or more than 250 loci.
  • the method further comprises determining the status of one or more of the traits from the individual selected from the list comprising: SNP or gene variation status, levels of auto-antibodies such as anti- dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
  • auto-antibodies such as anti- dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
  • a method is disclosed of diagnosis of a disorder in a mammalian subject comprising the steps of: isolating PBMCs from a patient; determining an accumulation level of transcripts from at least two genes identified from said PBMCs; and diagnosing whether the patient has a disorder based on said determination.
  • the panel comprises at least two genes associated with DML of Tables 1A, IB, 2A, 2B, 3A, and 3B, and optionally also listed in Table 4.
  • the gene is within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in a table above.
  • a PBMC comprises at least on cell selected from the list of cells consisting of T-cells, B-cells and monocytes.
  • accumulation levels of a panel of transcripts are determined, such as a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109
  • the oligonucleotides anneal within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Table 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
  • the method involves comparing the accumulation levels to those of corresponding transcripts in a cell of an individual or population not suffering from RA, OA, SLE, HC individuals, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
  • rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
  • a method is disclosed of diagnosis of a disorder in a mammalian subject comprising the steps of: isolating at least one circulating cell from a patient; determining a protein accumulation level or activity level of proteins from genes identified from said at least one cell; and diagnosing whether the patient has a disorder based on said determination; wherein said genes are genes associated with DML in one or more of Tables 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4; and wherein said disorder is RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
  • At least one circulating cells is a PBMC. In some aspects of these embodiments at least one circulating cells is a B-cell, T-cell or Monocyte. [0047] In some aspects of these embodiments the circulating cells comprise PBMCs. In some aspects of these embodiments the said gene is within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Table 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
  • the accumulation levels or activity levels of a panel of proteins are determined, such as a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
  • the method involves comparing the accumulation levels or activities to those of corresponding transcripts in a cell of an individual or population not suffering from RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or from an individual or population suffering from RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
  • the detection comprises differential antibody binding.
  • a method is disclosed of evaluation of differential methylation in a subject comprising: (a) determining the extent of methylation at a plurality of DNA loci selected from the loci in the tables above in a sample comprising PBMC DNA taken from the subject; (b) evaluating values reflective of the extent of methylation at said loci; and (c) providing a report based on the evaluation of step (b).
  • the evaluating step comprises processing values reflective of methylation at said loci in a computer and comparing said processed values to values known to be reflective of an autoimmune disorder status.
  • the report further discusses a treatment regimen for said autoimmune disorder based on said evaluating step.
  • the loci comprise a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113
  • a set of PCR primers capable of amplifying loci of human chromosomal DNA in a PCR reaction are disclosed.
  • the loci are selected from the DML identified in the tables above.
  • the loci comprise DNA within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
  • kits for the diagnosis of a disorder selected from the group of disorders consisting of RA, OA, SLE, or other rheumatic diseases and other autoimmune diseases in a mammalian subject comprising a plurality of DNA reagents.
  • the reagents may be capable of distinguishing between methylated and unmethylated DNA from loci listed in the Tables above upon subjecting said DNA to a treatment that differentially affects methylated bases.
  • the reagents comprise oligonucleotides.
  • the treatment is a chemical modification.
  • the treatment comprises bisulfite mapping.
  • the kit comprises a plurality of different reagents, each capable of distinguishing between methylated and unmethylated DNA at a respective locus listed in the Tables above.
  • an isolated DNA molecule having a sequence spanning a DML of a Table above is disclosed.
  • DNA at said DML has been chemically modified as a result of the presence of methylation at said DML, resulting in a detectable moiety reflective of methylation at said DML.
  • the DNA molecule has a sequence which anticipates the sequence of the vicinity of a DML of a Table above upon chemical modification to identify methylation status.
  • the modified form is an expected product of a reaction whereby an isolated DNA molecule mentioned above having a methylation signature characteristic of a disorder selected from the list of disorders consisting of RA, OA, SLE, or other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis in DNA isolated from blood is subjected to treatment that differentially affects methylated bases.
  • the DNA isolated from blood is isolated from at least one PBMC cell.
  • the PBMC is a T-cell, a B-cell or a monocyte.
  • the treatment comprises contacting said isolated DNA molecule with bisulfite.
  • the molecule comprises at least 14 bases.
  • Some embodiments comprise a panel of different DNA molecules mentioned above.
  • treatment of the molecules comprises contact with bisulfite.
  • the panel comprises of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107,
  • a method is disclosed of treating a patient with symptoms of RA comprising: ascertaining the methylation status of loci of the patient's DNA, wherein the loci are selected from the loci listed in the Tables above; ascertaining that the loci are differentially methylated consistent with RA; selecting an autoimmune disorder treatment from among available treatment options; and treating the patient for said autoimmune disorder.
  • the panel comprises 1 , 2, 3, 4, 5, 10, 20, 50, 200, 250 or more than 250 loci.
  • the treatment alters the methylation status of loci in said panel.
  • the said treatment affects the activity of gene products of loci listed in said panel or the genes regulated by methylation of the loci in said panel.
  • a method is disclosed of developing an assay for the detection of a methylation profile comprising the steps of: selecting a plurality of DML from the DML listed in the Tables above; analyzing with a computer the extent of methylation at said loci; and ascertaining a methylation pattern at said loci that correlates with a positive diagnosis indicative of a status of an autoimmune disorder selected from the list comprising RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
  • Figures 1A-D Diagnostic Error Rate versus Number of DML included.
  • a sliding window moved along a list of 51 CpGs and the diagnostic accuracy of the CpGs captured in each window was measured using leave-one-out cross validation.
  • the size of the window corresponded to the diagnostic panel size, which was 1, 2, 3, 5, 10 or 25 CpGs.
  • Leave-one-out cross validation involved randomly selecting one sample from each phenotype (i.e., RA, OA, SLE, or HC) and placing it into a test set.
  • the diagnostic model was then trained on the remaining data. Once trained, the model predicted the phenotypes of the test set samples. This process was repeated 100 times for each window.
  • a computer algorithm was used as the diagnostic model.
  • the averaged diagnostic accuracies for each window size were graphed and an error bar represents a single standard deviation of diagnostic error.
  • Figure 1 A Diagnostic Error Rate versus number of DML Included for B-cell DML.
  • Figure IB Diagnostic Error Rate versus number of DML Included for T-cell DML.
  • Figure 1C Diagnostic Error Rate versus number of DML Included for Monocyte DML.
  • Figure ID Diagnostic Error Rate versus number of DML Included for PBMC DML.
  • FIGS 2A-B Larger DML panels have lower error rates. Typical 10- member and 25 -member DML panels from the analysis above were selected for presentation. The two 25-membered DML panels shown have error rates, specificities and sensitivities substantially improved over those of typical 10-member panels.
  • Figure 2A presents error rates, sensitivity and specificity for a selection of 10-member DML panels.
  • Figure 2B presents error rates, sensitivity and specificity for a selection of 25-member DML panels.
  • Figure 3 presents True Positive Rates as a function of False Positive Rates for a Randomly Selected DML panel, a ranked DML panel selected from Tables 2A and 2B ("Enriched Panel"), and a ranked DML panel selected from Table 4 (“Optimized Panel”).
  • the Randomly Selected DML panel shows an approximately equal True Positive and False Positive rate, while both the Enriched Panel, and, even more so, the Optimized Panel, are skewed towards identification of True Positives.
  • a minimally-invasive blood-based RA diagnostic is desired for RA diagnostic tests to rule in RA definitively and to rule out other conditions which have arthritic symptoms (e.g., OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.).
  • OA OA
  • SLE Ankylosing Spondylitis
  • Crohn's Disease Multiple Sclerosis
  • Psoriasis Psoriatic Arthritis
  • Reactive Arthritis Reactive Arthritis
  • Spondyloarthropathy Type I Diabetes, or Ulcerative Colitis.
  • PBMCs peripheral blood mononuclear cells
  • enriched PBMC subsets performed to assess the potential of a blood-based RA diagnostic test identified new RA associated DML, demonstrating an RA methylation signature in blood unique from that identified in FLS (Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526).
  • Bioinformatics and computational algorithms have been used to determine the strongest methylation signature set that most accurately identifies RA phenotypes from either any circulating nucleic acid or nucleic acid reservoir including those isolated from the blood of a human subject, such as PBMC samples or from more homogeneous PBMC subsets.
  • Embodiments of the present disclosure involve panels of DML.
  • Said DML were obtained by determining methylation patterns of Whole blood, PBMCs, T- cells, B-cells and Monocytes derived from individuals suffering from RA, OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis or from HC individuals suffering from none of the above ailments or disorders, and comparing these methylation patterns to identify DML relevant to distinguishing each disease class.
  • the additional statistical power from PBMC subsets has allowed for the identification of significantly differentially methylated CpGs and allowed a more confident assessment of the RA methylation signature in PBMCs and PBMC subsets such as T-cells, B-cells and Monocytes.
  • the methylation signatures of whole blood, isolated PBMCs, T-cells, B-cells, and monocytes from RA, OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC patient PBMC samples were investigated.
  • methylation patterns particularly 5-methylcytosine methylation patterns, of the nucleic acids of certain cells or cell populations, or other DNA reservoirs may be determined.
  • a number of methods for the determination of cytosine methylation status are known to one of skill in the art. For example, bisulfite mapping may be used. Through this process, extracted DNA is treated with a bisulfite as part of a process that differentially converts cytosine unmethylated at the C5 position to uracil, while leaving 5 -methyl cytosine unaffected.
  • Other methods for the determination of methylation status at one or more cytosine positions are also known in the art, and embodiments disclosed herein are not limited to any particular method of determining methylation status at a particular locus to the exclusion of any other method.
  • an array such as an ILLUMINA HumanMethylation 450 BeadChip may be used to determine a methylation status (Sandoval, et al., (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6:6, 692-702).
  • the sequencing method may comprise one or more technologies such as pyrosequencing, e.g., 'the '454' method (Margulies et al., (2005) Genome sequencing in microfabricated high- density picolitre reactors. Nature 437:376-380; Ronaghi, et al. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal.
  • methods for assaying the methylation status, particularly the 5 -methyl cytosine methylation status, at one or more loci may include randomly shearing or fragmenting genomic DNA, cutting with a methylation-dependent or methylation sensitive restriction endonuclease, of which many are known to one of skill in the art, and analyzing the resultant DNA fragments.
  • analysis may involve amplification of nucleic acids. In some embodiments this amplification can be performed using gene or locus specific primers, or using primers specific to, for example, adapters that may be added to the ends of fragmented DNA.
  • the DNA may be amplified using a quantitative PCR protocol, such as one that allows for real time quantification of amplification products. See, e.g., U.S. Patent No. 7,186,512; U.S. Patent Application Ser. Nos. 10/971,986; 11/071,013; and 10/971,339; U.S. Pat. Nos.
  • methods for detecting DNA methylation may involve genomic sequencing before and after treatment that differentially affects methylated bases.
  • a methylation assay may be run to obtain data for use in some embodiments.
  • One set of methods are predicated upon methylation-specific changes in hybridization efficiency that result from bisulfite treatment.
  • a PCR primer that specifically anneals to a differentially methylated site may be used in a PCR amplification reaction wherein the amplification efficiency is dependent upon either the methylation status or the identity of the base following bisulfite treatment.
  • Amplification efficiency may be assayed by the generation of a signal, such as light, in proportion to the concentration of double-stranded DNA during the course of a PCR reaction.
  • a signal may be generated by the binding of an oligonucleotide probe, such as a labeled probe, to a region spanning a differentially methylated site of interest.
  • Alternate methods of assaying for the outcome of bisulfite treatment on a sample may be used. For example, chemical differences between methylated and unmethylated DNA that manifest themselves after bisulfite treatment may be indicative of substrate sequence after bisulfite treatment and, by inference, methylation status before treatment.
  • the melting temperature of a double-stranded DNA molecule may be assayed using, for example, high-resolution melt analysis using techniques known in the art (White HE, et ah, 2007. "Methylation sensitive high resolution melt curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes, " Clin Chem. 2007 Nov; 53(11): 1960-2; Dahl C. and Guldberg P. 2007. "High-resolution melting for accurate assessment of DNA methylation, " Clin Chem. 2007 Nov; 53(11) 1877-1878 ).
  • DNA to be assayed may, for example, be contacted with proteins that preferentially bind methylated or unmethylated sequences (e.g., methyl binding domain [MBD] binding proteins such as MECP2, MBD1, MBD2, MBD3, and MBD4, other methylation-distinguishing proteins, or antibodies such as MeDIP).
  • MBD methyl binding domain
  • DNA sequences may be sequenced directly, either after bisulfite treatment or after methylation-based separation as discussed above. Any of the sequencing methods known in the art may be used, including those mentioned above. Embodiments are not limited by the sequencing method used, and sequencing innovations may be incorporated into various embodiments as the sequencing innovations become available to those of skill in the art.
  • Sequencing methods which assay for methylation directly on input sequences may also be used. For example, measurable transcription rate changes may be used to determine methylation status at specific bases (e.g., single molecule real time (SMRT) sequencing), or spectrographic or electric field measurements may be used to discriminate between methylated and unmethylated bases during single molecule sequencing such as nanopore sequencing.
  • SMRT single molecule real time
  • Sequencing methods may target individual methylation sites or loci to assay. Targeted regions may be amplified or preserved in processes that degrade sequences not of interest. Alternately, methylation sites of interest may be sequenced as part of whole-genome sequencing efforts whereby all or substantially all sequence information in a DNA sample is determined.
  • DNA to be analyzed may be obtained from a number of sources.
  • DNA may be obtained from any circulating nucleic acid or nucleic acid reservoir including those isolated from the blood of a human subject.
  • the sample from which DNA is to be assayed is whole blood.
  • the cell population from which DNA is to be assayed is a whole blood cell population.
  • the cell population from which DNA is to be assayed is peripheral blood mononuclear cells (PBMCs).
  • PBMCs peripheral blood mononuclear cells
  • the cell population is selected from a group comprising T-cells, B-cells and monocytes.
  • the cell population from which DNA is to be assayed is a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) or a subset of monocytes (such as Ml and M2 monocytes and dendritic cells) [see Littman and Rudensky (2010) Thl 7 and regulating T- cells in mediating and restraining inflammation. Cell 140:845-858; Lo and Tsokos (2011) T- cells in Systemic Lupus Erythematosus. The Rheumatologists; Allman and Pillai (2008) Peripheral B- cell subsets. Curr. Opin. Immunol.
  • T-cells such as Thl, Th2, Thl7, T-regs, NK cells
  • B-cells such as Bl, B2
  • monocytes such as Ml and M2 monocytes and dendritic cells
  • DNA may be extracted from cells using any of a number of methods known in the art.
  • the DNA extraction method will preferably substantially preserve the methylation pattern of the extracted DNA and yield DNA of a purity and integrity suitable for downstream analysis, but is not otherwise limited. If peripheral blood mononuclear cells are used as a DNA source, the extraction method should be appropriate to these cells. Alternately, free circulating DNA from, for example, the blood, urine, other body fluid, or other tissue of a patient may be used as a sample source.
  • methylation patterns determined for one or more of the above cell populations may be compared to methylation patterns determined from similar cell types in one or more individuals with a known autoimmune disorder status, or from one or more different cell populations taken from the same or different individuals compared to the individual to be diagnosed.
  • an increase or decrease in the methylation state of loci from a cell or population of cells of an individual to be diagnosed may be indicative of that individual's autoimmune disorder status.
  • the methylation status of loci from a cell or population of cells of an individual to be diagnosed may be determined and then normalized to the methylation status of a control locus to control for error in detection methods that may otherwise impact a diagnosis as to the presence or absence of an autoimmune disorder. Appropriate control loci or control techniques are known to one of skill in the art.
  • the methylation patterns may be deduced by determining the methylation status, for example the presence of 5-methyl cytosine, of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105
  • a number of cell isolation protocols are contemplated in the present disclosure, and the subject matter does not require that any single cell isolation protocol be used to the exclusion of others.
  • the methylation status at DML disclosed herein may be assayed in cells isolated by these or other cell isolation protocols.
  • cell populations may be isolated as follows. Approximately 10 ml of blood is obtained from a patient. PBMCs are purified from whole blood using standard Ficoll gradient centrifugation (Ruitenberg JJ, Mulder CB, Maino VC, Landay AL, Ghanekar SA. "VACUTAINER CPT and Ficoll density gradient separation perform equivalently in maintaining the quality and function of PBMC from HIV seropositive blood samples.” BMC Immunol. 2006; 7: 11). Some embodiments additionally include a purification by Percoll gradient (Gutierrez C, Bernabe RR, Vega J, Kreisler M.
  • the PBMCs are further enriched for T-Cells, B-cells, and monocytes by magnetic beads with biotinylated monoclonal antibodies towards human cell surface markers (anti-huCD4, huCD19 and huCD68 or other appropriate CD-markers or other cytokine receptors) as described (Vallee I, Guillaumin JM, Thibault G, Gruel Y, Lebranchu Y, Bardos P, Watier H.
  • Some samples require no cell isolation prior to downstream sample processing such as DNA extraction.
  • whole blood samples are used to extract total nucleic acids from all cell sources and from extracellular sources, such as free circulating nucleic acids as well as cellular components of whole blood.
  • Some embodiments disclosed herein relate to the diagnosis, typing, or prognosis of an autoimmune disorder such as RA in an individual based in part on the methylation status at a set of loci, or a "panel,” from a restricted population of cells from that individual.
  • Tables of loci provided for the purpose of enabling the diagnosis of RA in an individual.
  • the Tables list Differentially Methylated Loci (hereinafter "DMLs”) corresponding to methylation sites at which the inventors have discovered a correlation between extent of status in an isolated cell population such as PBMCs, T Cells, B Cells, Monocytes, or cells from whole blood, and RA status.
  • DMLs Differentially Methylated Loci
  • Loci are sorted into tables as discussed in the summary of the invention, above.
  • Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 disclose Differentially Methylated Loci (hereinafter "DML") corresponding to methylation sites at which the inventors have discovered an association between methylation status and disorder status.
  • DML Differentially Methylated Loci
  • a set of loci where methylation status is relevant to an RA, diagnosis relative to OA, SLE, or other rheumatic and autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or relative to a HC is selected from among the loci listed in Tables 1A, IB, 2A, 2B, 3A, and 3B, and optionally also listed in Table 4. In some embodiments this set of loci may be additionally supplemented by at least one locus selected from an additional source.
  • Table 4 consists of methylation sites which also appear in at least one of Tables 1A, IB, 2A, 2B, 3A, or 3B. Accordingly, reference to "a DML of Tables 1A, IB, 2A, 2B, 3A, 3B, or 4" or "Tables 1A, IB, 2A, 2B, 3A, 3B and 4" is not to be read to indicate that a DML of Table 4 is not also included in one of the preceding Tables 1A, IB, 2A, 2B, 3A, or 3B. Table 4 consists of a subset of DML from tables 1A, IB, 2A, 2B, 3A, or 3B.
  • IB, 2A, 2B, 3A, 3B, and 4 may be used as guides to direct a researcher, medical professional or other interested party to determine the methylation status of loci marked by listed methylation sites.
  • these loci may comprise 20 bp, 40bp, 60bp, 80bp, lOObp, 500bp, lkb, 1.5 kb, 2kb, 2.5kb, 5kb, lOkb, or more than lOkb on either side of methylation sites listed in Table 1A, IB, 2A, 2B, 3A, or 3B, and optionally listed in Table 4.
  • a condition such as RA may be indicated by an extent of methylation of 0%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%
  • Methylation status is a matter of degree, wherein some bases at a particular locus will be methylated in one cell and unmethylated in another cell. Thus, a determination of methylation status not only includes ascertaining whether an individual locus on an individual chromosome is methylated, but also can include determining the extent of methylation at that locus across a population of cells. Although methylation status at a single locus has value in diagnosis and prognosis of an autoimmune disorder, combinations of loci have enhanced diagnostic and prognostic value. Thus, various embodiments include assays in which loci in Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 are analyzed, together with one or more additional loci.
  • FIG. 1 presents an example wherein combining information from multiple DML produces better performing models than do uncombined data sets.
  • DML panels of increasing size show a decrease in diagnostic error. Whereas individual DML show error up to 50% or more, a panel of 25 such DML shows an error below 5% representing a substantial increase in the accuracy and therefore the utility of the test.
  • Figure 1 illustrates that the incremental increase in DML panel size leads to an incremental decrease in the error rate. With the increase in panel size, the error rate decreases until the optimal DML panel size is reached.
  • RA Autoimmune diseases such as RA cover many clinical subtypes (e.g., disease stages, severity, organs involved in the pathology) and it is expected that a single locus may not be able to discriminate across these subtypes with acceptable sensitivity and specificity.
  • the multiplex design of the assay is due to the complex nature of the disease and the heterogeneity of disease within the patients.
  • Determining and evaluating the methylation status of panels of loci rather than single loci have a number of advantages. For example, an assay that uses a panel detects not only the single loci that may have strong prognostic or diagnostic value in comparing disorder presenting or pre-disorder presenting samples to non-disorder presenting samples, but it also detects the subtle deviations in methylation status at diagnostic loci that may not be individually statistically significant enough to warrant a diagnosis or to justify selection or administration of a course of treatment, but can cumulatively lead to a clear diagnosis of a disorder or a risk of developing a disorder.
  • Methylation status of a panel of loci from a selected cell type in an individual to be diagnosed may be compared to the methylation status of the same loci of a control individual, control tissue or a composite value derived from analysis of a control population of prior samples. Diagnosis may be based upon the extent of difference in methylation status at individual loci selected from within a panel, or may be based on deviations from the control methylation pattern in the aggregate. Thus, it is possible that a single locus, which shows a great difference in methylation status between a test sample and a control, may be sufficient to diagnose an autoimmune disorder or a risk of an autoimmune disorder. However, in most cases, a single locus will not provide adequate specificity and/or sensitivity.
  • Such a diagnosis may involve noting that a test sample presents a number of loci, which differ in methylation status only subtly, from a control, but where these differences collectively support a diagnosis of a disorder such as RA.
  • Statistical evaluation of the aggregate results of a panel assay may be performed using a complex algorithm and performed on a computer. This may include use of a weighting algorithm in which certain loci are weighted differently than others, or any other algorithm derived from analysis of patient data that gives the desired specificity and sensitivity.
  • a number of algorithms for combining results from multiple loci to reach a diagnosis may be used.
  • classification models may be used to assign probabilities of phenotypes to samples.
  • Each of these models is considered to be an algorithm and each is known in the art. This list is not limiting; other algorithms may be used to combine the results of multiple loci to reduce noise or improve specificity or sensitivity.
  • the model's input is a list of methylation values at a panel of methylation sites, transcript accumulation levels, or protein accumulation levels or activity levels.
  • the output is a list of phenotype-specific probabilities. The phenotype with the highest probability is assigned to the sample.
  • a variety of criteria may be used to determine which DML to include in a given panel.
  • a panel may comprise, for example, loci with methylation statuses that are individually strong indicators of an autoimmune disorder or a risk of an autoimmune disorder, for example due to a consistently large difference in methylation status between an individual having an autoimmune disorder and an unaffected individual.
  • Such a panel may be useful when a statistically very strong signal is needed (i.e., a statistical signal that may be generated from loci the methylation status of which differs greatly, such as from near zero to near 1 , in samples from affected or pre-affected cells compared to unaffected controls).
  • a strong signal may be needed, for example, when relatively little starting material is available or when there is reason to believe that a sample may have degraded to some extent.
  • a panel may advantageously include multiple loci that are not strong indicators of an autoimmune disorder on an individual basis, but which in combination produce a robust indication of (or correlation with) an autoimmune disorder and improve the clinical diagnostic utility.
  • a panel is selected based on population studies that in the aggregate can provide a desired level of sensitivity and specificity over the broad population, so that a single assay can be commercialized that is appropriate for all patients.
  • assays can be tailored for a particular population based on gender, age, ethnicity, or any other result-effective variable. Thus, there may be a panel of assays from which one may select the assay most appropriate for any particular patient.
  • a computer can be used to select an appropriate assay based on relevant patient data.
  • Methylation sites may also be selected for inclusion or exclusion based on criteria other than those above. For example, loci may be selected based in part on the degree of allelic variation at the site or in the immediate region of an identified methylation site. The presence of multiple alleles at or near a methylation site may complicate data acquisition or analysis by affecting the primers necessary for amplification, the probe sequence necessary to assay a site, or the sequence to be derived from a site, for example.
  • a methylation site at or near a locus wherein alleles of said locus correspond to differential diagnoses may be included in some panels because the assay technique, such as sequencing, may easily be able to obtain and incorporate any allelic information obtained into the data used to generate a final determination.
  • Methylation sites may be selected for inclusion based on their utility within a specific population or ethnic group rather than their utility among patients at large. Thus panels may be selected to maximize the diagnostic efficacy as to a specific patient demographic, such as women (for whom methylation sites located on the Y- Chromosome are unlikely to be informative), or specific genetically similar ethnic groups (which may present allelic frequencies at one or more given loci that differ from the frequencies of civilization as a whole, and which may affect the utility of one or more methylation sites as panel constituents). See, e.g., John Butler (2006) “Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing," J. Forensic Sci. 51(2): 253-265.
  • One or more control loci may be included in a panel. These loci are not known to demonstrate a change in methylation status in autoimmune disorder or pre- autoimmune disorder samples compared to non-disorder samples.
  • the assay of the methylation status of one or more control loci may be useful as a measure of the reliability of the results obtained from a given sample analysis.
  • External control loci that are not present in the human genome e.g., synthetic oligos
  • the methylation values of these control loci may change relative to autoimmune disorder or pre-autoimmune disorder patients' samples but since they are not from the human genome, they will not be mistaken as patient data.
  • the methylation patterns may be deduced by determining the methylation status, for example the presence of 5 -methyl cytosine, of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 300
  • the methylation patterns may be deduced by determining the methylation status, for example the presence of 5 -methyl cytosine, of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci from other sources in addition to the methylation patterns from the one or more loci of Tables
  • IB, 2A, 2B, 3A, 3B, and 4 may comprise a panel.
  • the panel may further comprise at least one locus elsewhere.
  • a panel may comprise at least two loci of Tables 1A, IB, 2A, 2B, 3 A, 3B, and 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or more than 23 loci elsewhere.
  • a panel may comprise at least three loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least four loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
  • a panel may comprise at least five loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least six loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
  • a panel may comprise at least seven loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5,
  • a panel may comprise at least eight loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least nine loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least ten loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6,
  • a panel may comprise at least eleven loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least twelve loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least thirteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4,
  • a panel may comprise at least fourteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least fifteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least sixteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5,
  • a panel may comprise at least seventeen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least eighteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least nineteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least twenty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least twenty-five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least thirty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least thirty- five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least forty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least forty-five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least fifty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least sixty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seventy loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least eighty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least ninety loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least one hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least two hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least three hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9,
  • a panel may comprise at least four hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
  • a panel may comprise at least six hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seven hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least eight hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least nine hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least one thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least one thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least two thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least two thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least three thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least three thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • a panel may comprise at least four thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least more than four thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
  • Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with SLE samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with OA samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with HC samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with SLE, OA and HC samples.
  • Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis samples.
  • autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis samples.
  • Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with SLE samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with OA samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with HC samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with SLE, OA and HC samples.
  • Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis samples.
  • Panels may comprise at least one locus identified in a comparison of methylation patterns of PBMC samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of T-cell samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of B-cell samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of monocyte samples.
  • Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of PBMC samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of T-cell samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of B-cell samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of monocyte samples.
  • an oligonucleotide primer or probe is disclosed.
  • probes or primers are designed having sequences that match those of loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or a locus listed elsewhere.
  • probes or primers are designed having sequences that span loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
  • the probes or primers are designed to base pair with nucleotide sequences that are predicted to result from the treatment of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere with a reagent that alters nucleotide base identity in a manner that is methylation-sensitive.
  • this treatment is bisulfite treatment as part of a process that selectively transforms cytosine but not 5 -methyl cytosine to uracil, thus changing the base pairing properties of the molecule treated.
  • a population of oligonucleotide probes is synthesized such that the population comprises one or more of the possible probes corresponding to each possible methylation pattern for a given locus given the known methylation patterns of the loci selected from Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere.
  • these probes may distinguish between DNA that was methylated at a given base or bases prior to a chemical treatment which differentially affects methylated DNA as compared to unmethylated DNA from DNA that was not methylated at a given base or bases prior to chemical treatment which differentially affects methylated DNA as compared to unmethylated DNA.
  • the oligonucleotides are designed to anneal to templates comprising the methylation loci selected from the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
  • the oligonucleotides are designed to anneal to cDNA molecules derived from the mRNA or other RNA product associated with loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere.
  • the oligonucleotide may comprise a panel of 2, 3, 4, 5, or more, 10 or more, 20 or more, 50 or more, 200 or more, 250 or more than 250 oligo probes.
  • said panel may comprise oligos spanning or related to loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4,.
  • the panel may further comprise an oligo spanning or related to a locus listed elsewhere.
  • the primers are designed to base pair with nucleotide sequences that are predicted to result from the treatment of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 or elsewhere with a reagent that alters nucleotide base identity in a manner that is methylation-sensitive.
  • this treatment is bisulfite treatment that selectively transforms cytosine but not 5-methyl cytosine to uracil, thus changing the base pairing properties of the molecule.
  • the oligonucleotide primers selectively anneal to specific DNA sequences corresponding to specific methylation patterns of loci of Tables 1A, IB, 2 A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere, or to a specific embodiment of one of the complete set of possible methylation patterns of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere.
  • primer pairs are designed to amplify loci comprising differentially methylated sites. In some embodiments primer pairs are designed to amplify segments of transcripts or cDNA molecules derived from transcripts the synthesis of which is directed from loci associated with differentially methylated sites, such as transcripts from the genes listed in Tables 2, 3, or 1.
  • primer pairs are synthesized in combination with one or more oligonucleotide probes.
  • these probes are labeled such that binding to a target sequence results in a detectable configuration change in a probe or detectably affects another probe.
  • these probes are specific to DNA that results from bisulfite-treated methylated DNA or to bisulfite treated unmethylated DNA or to untreated DNA.
  • an oligonucleotide is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or more than 35 bases long.
  • primer pair sets may be assembled wherein primer pair sets are capable of amplifying loci identified in Tables 1A, IB, 2 A, 2B, 3 A, 3B or 4 under standard PCR conditions known to one of skill in the art.
  • primer pairs may be able to direct the amplification of loci spanning differentially methylated sites, or additionally spanning 20 bp, 40bp, 60bp, 80bp, lOObp, 500bp, lkb, 1.5kb, 2kb, 2.5kb, 5kb, lOkb, or more than lOkb on either side of methylation sites listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere.
  • transcript accumulation levels for a gene or genes corresponding to one or more loci of one or more of Tables 1A, IB, 2 A, 2B, 3 A, or 3B, and optionally also listed in Table 4, may be determined. Additionally, transcript levels for at least one additional locus may be determined. Methylation sites from Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4were associated with gene promoters if they were located between 2.5 kb upstream and 500 bp downstream of a gene's transcription start site. Generally, an increase in methylation status at a methylation site indicates a decrease in the accumulation level of transcripts from loci corresponding to or near the methylation site.
  • transcript accumulation levels of each member of a panel discussed above may be assayed. Embodiments disclosed herein are not limited to any particular method of assaying transcript accumulation levels.
  • Transcripts to be used in performing an assay may be selected from transcripts that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within lOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 or from transcripts derived from genes that are located within 200bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts
  • transcript accumulation levels are assayed in one or more cell populations, for example a circulating cell population. In some embodiments transcript accumulation levels are assayed in cell populations comprising whole blood. In some embodiments transcript accumulation levels are assayed in cell populations comprising peripheral blood mononuclear cells. In some embodiments the cell population is selected from a group comprising T-cells, B-cells and monocytes.
  • the cell population from which DNA is to be assayed is a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells).
  • T-cells such as Thl, Th2, Thl7, T-regs, NK cells
  • B-cells such as Bl, B2
  • monocytes such as Ml and M2 monocytes or dendritic cells
  • transcript accumulation patterns determined for one or more of the above cell populations may be compared to transcript accumulation or methylation patterns determined from similar cell types in one or more individuals with a known autoimmune disorder status or other disease state, or from one or more different cell populations taken from the same or different individuals compared to the individual to be diagnosed.
  • an increase or decrease in the transcript accumulation levels of genes corresponding to loci from a cell or population of cells of an individual to be diagnosed may be indicative of that individual's autoimmune disorder status.
  • the transcript accumulation levels of genes corresponding to loci from a cell or population of cells of an individual to be diagnosed may be determined and then normalized to the transcript accumulation levels or methylation status of control transcripts or loci to control for error in detection methods that may otherwise impact a diagnosis as to the presence or absence or progression or regression of an autoimmune disorder.
  • Appropriate control loci, transcripts or techniques are known to one of skill in the art.
  • Transcript accumulation levels may be assayed using quantitative PCR, ribonucleic acid blot hybridization assays, microarray assays, DNase protection assays, or quantitative nucleic acid sequencing methods, for example. Embodiments disclosed herein are not limited to any particular method of transcript isolation or accumulation level assay to the exclusion of any other.
  • R A may be purified from an isolated cell or cells from, for example, a patient to be diagnosed, using methods known in the art.
  • the cell source may be a circulating cell, such as at least one whole blood cell or at least one peripheral blood mononuclear cell, or may specifically be at least one T- cell, B-cell or monocyte.
  • Transcripts may be isolated from any white blood cell type, or from circulating exosomes. In some embodiments, free circulating RNA transcripts may be used.
  • [0140] Accumulation levels of 2, 3, 4, 5 or more, 10 or more, 20 or more, 50 or more than 50 genes may be determined. [0141] Transcript accumulation levels may be used much like methylation status determinations. In each case, the set of values determined for a test sample is compared to the values from controls, and deviation from control values, either absolute or relative, may be used to assess the presence or risk or progression of an autoimmune disorder in an individual, and may be further used to suggest a course of treatment.
  • the activity or accumulation level of proteins encoded by genes at loci identified or associated with Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 is monitored.
  • the activity or accumulation levels of proteins encoded by genes at loci identified or associated with loci identified elsewhere is monitored.
  • the activity or accumulation level or both are measured in a protein population derived from peripheral blood mononuclear cells.
  • proteins are isolated from circulating white blood cells, exosomes or from free circulating proteins. Generally, an increase in methylation status at a methylation site indicates a decrease in the accumulation level and/or total activity of proteins encoded by loci corresponding to or near methylation sites.
  • the protein population is selected from a group comprising proteins corresponding to T-cells, B-cells and monocytes. In some embodiments the protein population is selected from a group comprising proteins corresponding to a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells).
  • T-cells such as Thl, Th2, Thl7, T-regs, NK cells
  • B-cells such as Bl, B2
  • monocytes such as Ml and M2 monocytes or dendritic cells
  • T-cells such as Thl, Th2, Thl7, T-regs, NK cells
  • subset of B-cells such as Bl, B2
  • monocytes such as Ml and M2 monocytes or dendritic cells
  • activity or accumulation levels of protein populations comprising proteins encoded by genes associated with loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 corresponding to a non- autoimmune disorder individual are compared to similar levels from similar protein populations corresponding to an individual having an autoimmune disorder or an individual presenting a methylation profile corresponding to an autoimmune disorder or an individual for which the presence of an autoimmune disorder or early signs of an autoimmune disorder are to be diagnosed.
  • the above protein populations comprise purified proteins selected from the list of proteins encoded by genes at the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
  • Proteins to be used in an assay may be selected from proteins encoded by genes that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within lOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 200bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 300bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 400bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally
  • Proteins may be assayed by accumulation level, using protein-specific antibodies, mass-spectrometric methods, nonspecific staining techniques, purification techniques, or a combination of the above. Proteins may also be quantified by measuring their activity levels in a sample extract by, for example, measuring the rate at which they metabolize or otherwise modify a substrate. Method of measuring protein accumulation levels and activity are known to those of skill in the art.
  • a panel of proteins is assayed. Accumulation levels of 2, 3, 4, 5 or more, 10 or more, 20 or more, 50 or more than 50 proteins may be determined.
  • the panel comprises proteins encoded by genes associated with the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
  • the panel may additionally comprise at least one protein from the proteins encoded by genes at loci identified elsewhere.
  • the activity or accumulation level or both of proteins selected from the list of proteins taught in Tables 1 A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 is measured.
  • these proteins are taken from a population of an individual's circulating cells, such as an individual's whole blood cells, peripheral blood mononuclear cells, or T-cells, B-cells or monocytes or a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells).
  • this measurement is compared to a reference measurement made from a similar cellular protein source (i.e., circulating cell such as whole blood cells, peripheral blood mononuclear cells, or T-cells, B-cells or monocytes, or a subset of T- cells (such as Thl, Th2, Thl 7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells) from a healthy individual.
  • a similar cellular protein source i.e., circulating cell such as whole blood cells, peripheral blood mononuclear cells, or T-cells, B-cells or monocytes, or a subset of T- cells (such as Thl, Th2, Thl 7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2
  • Protein activity or accumulation levels may be used much like methylation status determinations.
  • the set of values determined for a test sample is compared to the values from controls, and deviation from control values, either absolute or relative, may be used to assess the presence or risk or progression of an autoimmune disorder in an individual, and may be further used to suggest a course of treatment.
  • any of the foregoing assays in which methylation status of one or more markers is evaluated can be supplemented by additional data, because the methylation state of DML may be informative when integrated with other non- methylation data such as transcription profiles and genomic profiles.
  • additional data such as transcription profiles and genomic profiles.
  • biomarkers may be used in combination with any of the forgoing assays.
  • SNPs or other allelic data relating to, for example, PTPN2; ITGAM- ITGAX; IRF5; IRF8; the FcRy genes; CTLA-4; STAT-4; BANK; IRAKI; FCRL3; Clq; C2; C4; C5aR; Complement Factor H and Factor H-Related Genes, MECP2; IKZF3; TMEM39a BLK; KIAA1542; PXK; or the MHC alleles HLA DR2, DR3, DR5, or HLA- DQ may be used.
  • protein levels markers including but not limited to blood or serum chemical, biochemical, or protein markers, antibodies or auto-antibodies associated with RA or other autoimmune disease
  • a non-limiting list of examples comprises the antibodies ACPAs and Anti-CCP, Rheumatoid Factor, anti-dsDNA; anti- nuclear antibodies; anti-phospholipids; anti-cardiolipin; anti-P2glycoprotein; anti-Ro anti- La; anti-snRNP (Ul-RNP); anti-ribonuclear protein; anti-histone; anti-nucleosome; anti- N-methyl-D-aspartate (NR2); anti-Clq; cell surface molecules such as CD27; CD 154; CD95; levels of cytokine and chemokine such as a-interferon; IL-1, IL-6, IL-17, IL-23; TNFSF13B/BAFF;CXCL10;CCL2;CCL19; enzymes such as neutrophil gelatinas
  • miRNA microRNA
  • any of the foregoing assays in which methylation status of markers is evaluated can be supplemented by additional data.
  • biomarkers such as Human Leukocyte Antigens (e.g. HLA-DR4 and HLA-DRB1; Wagner U, Kaltenhauser S, Sauer H et al. "HLA markers and prediction of clinical course and outcome in rheumatoid arthritis. " Arthritis Rheum 1997; 40:341-51), CD (cluster of differentiation) cell surface markers on leukocytes (Mo YQ, Dai L, Zheng DH, Zhu LJ, Wei XN, Pessler F, Shen J, Zhang BY.
  • markers including but not limited to blood or serum chemical, biochemical, or protein panels of markers (such as C-reactive protein [CRP], Serum Amyloid A Protein [SAA], or Haptoglobin ), antibodies or auto-antibodies including Rheumatoid Factors [RF] and Anti-Citrullinated Protein Antibodies [ACPA]; Lee DM, Schur PH.
  • markers including but not limited to blood or serum chemical, biochemical, or protein panels of markers (such as C-reactive protein [CRP], Serum Amyloid A Protein [SAA], or Haptoglobin ), antibodies or auto-antibodies including Rheumatoid Factors [RF] and Anti-Citrullinated Protein Antibodies [ACPA]; Lee DM, Schur PH.
  • CRP C-reactive protein
  • SAA Serum Amyloid A Protein
  • ACPA Anti-Citrullinated Protein Antibodies
  • RA or autoimmune disease such as Anti-nuclear antibodies [ANA] or Anti-double stranded DNA
  • cytokines such as Anti-nuclear antibodies [ANA] or Anti-double stranded DNA
  • cytokines such as Anti-nuclear antibodies [ANA] or Anti-double stranded DNA
  • chemokines such as cytokines, chemokines, or growth factors (e.g., Tumor necrosis factor-a [TNF-a], Interleukin-1 [IL-1], Interleukine-6 [L-6] or Interleukin-17 ⁇ IL-17]) as mediators of inflammation, (David S. Gibson, Madeleine E. Rooney, Sorcha Finnegan, Ji Qiu, David C. Thompson, Joshua LaBaer, Stephen R. Pennington and Mark W. Duncan.
  • TNF-a Tumor necrosis factor-a
  • IL-1 Interleukin-1
  • IL-17 ⁇ IL-17 Interleukin-17
  • metabolic biomarkers (Rasmus K Madsen; Torbjorn Lundstedt; Jon Gabrielsson; Carl-Johan Sennbro; Gerd- Marie Alenius; Thomas Moritz; Solbritt Rantapaa-Dahlqvist; Johan Trygg. "Diagnostic Properties of Metabolic Perturbations in Rheumatoid Arthritis.” Arthritis Research & Therapy. 2011;13(1)), microRNAs (Filkova M, Jungel A, Gay RE, Gay S. "MicroRNAs in rheumatoid arthritis: potential role in diagnosis and therapy.” BioDrugs. 2012 Jun 1 ;26(3): 131-41.) or other markers can be used in combination with the methylation information to further enhance the diagnosis of RA or the classification of patients and their prognosis.
  • a methylation profile for a DNA region or portion thereof, or multiple regions or portions thereof selected from regions corresponding to the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and optionally additionally including regions corresponding to loci identified elsewhere can, for example, be given a value reflective of methylation status that may be compared by a computer to a threshold value or standard values, including values embedded in an algorithm, as described herein, or each methylation site may be evaluated individually. Ratios or degrees of methylation of certain loci within an individual patient sample may be compared. Values reflective of methylation status need not be methylation values themselves, but can include values generated by processing methylation status of an individual DML or a panel of DMLs together, with or without weighting.
  • an activity profile or an accumulation profile or both for a set or proteins taught by Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 can, for example, be given a value reflective of activity or an accumulation that may be compared by a computer to a threshold value or standard values, as described herein, or each value may be evaluated individually.
  • Evaluation of the results of a panel assay may be accomplished using a computer-based algorithm.
  • Such an algorithm may evaluate the methylation status of the loci evaluated in comparison to known or measured values generated from standard populations to generate a signal indicative of the presence or absence or progression of an autoimmune disorder. As above, ratios or degrees of methylation of certain loci within an individual patient sample may be compared.
  • Standard populations can include individuals without a target disease (e.g., without RA, OA, SLE, or other rheumatic and autoimmune disease, such as autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis), as well as individuals with one such disease and not another. It is preferred that a differential diagnosis be performed, ruling out particular disease states or the absence of particular disease states, as the case may be. Thus, a dataset can be generated comparing RA to any of the diseases or the HC condition as reported herein. .
  • a target disease e.g., without RA, OA, SLE, or other rheumatic and autoimmune disease, such as autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease,
  • An algorithm may assess the absolute or relative difference in methylation status between loci, and may weigh all loci equally or may give greater or lesser significance to certain loci based on, for example, prior knowledge of the significance of these loci in diagnosis, or redundancy of certain loci in comparison to other loci assayed.
  • Evaluation of the results obtained by assaying to obtain a panel of data from a sample taken from an individual may involve evaluating individual or combined values reflective of the extent of methylation at said loci or perturbations in gene product accumulation or activity. This evaluation may involve calculating the difference between values for samples in terms of absolute or normalized values obtained, or may involve calculating the ratio of values obtained in comparison to reference or control values, for example.
  • the results of such an evaluation may be collected into a report that may contain values for the assay results, information regarding autoimmune disorder status of the individual, progression or regression of disease, or all of the aforementioned.
  • the report may, for example, contain a metric indicating the number of methylation sites showing a methylation status indicative of an autoimmune disorder, or the aggregate deviation from an autoimmune disorder-free methylation pattern or from an autoimmune disorder pattern.
  • the report may contain a statistical probability, or a simple yes/no assessment of the presence of an autoimmune disorder methylation pattern.
  • Reports may be generated providing information mentioned above resulting from an assay of transcript accumulation level panels, protein accumulation level panels, or protein activity panels as well.
  • a panel used to generate a report such as those described above may involve loci selected from Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
  • a panel involving an assay of methylation status may be comprised of loci from more than one table.
  • a panel involving transcript or protein accumulation levels or protein activity levels may be comprised exclusively of levels taught in Table 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or may also comprise levels associated with loci identified elsewhere.
  • the panel assessed may comprise at least 5, at least 10, at least 20, at least 50 or more than 50 loci or loci associated levels.
  • an increase in methylation at a methylation site within the promoter region of a gene indicates a decrease in transcript accumulation level, protein accumulation level and, subsequently, total protein activity of a gene product corresponding to or adjacent to a methylation site.
  • a change in methylation status may, for example, affect RNA processing such as splicing, may affect chromatin structure, or regulate the production of microRNAs, either increasing or decreasing transcription all of which can be measured using standard biochemical techniques.
  • the methylation levels, transcript accumulation levels, protein accumulation levels or protein activity levels may serve as the input for a classification model, which may generate a list of phenotype-specific probabilities. In some embodiments, the highest probability phenotype will be assigned to the sample. In some embodiments, a classification model will be trained on samples with known phenotypes. Using these training samples, some models may automatically weigh the loci's methylation levels to maximize its ability to correctly predict these training samples. For example, if one locus is more informative than the others, its methylation value will have a stronger influence in the assignment of phenotype probabilities. Loci can be considered independently or combinatorially by the classification model. Other methods of evaluation are contemplated, and embodiments are not limited to a specific method of analysis.
  • the tools are advantageously provided in the form of computer programs that are executable, for example, by a general purpose computer system (referred to herein as a "host computer").
  • the host computer may be of conventional design.
  • the host computer may be made in any number of dimensions and styles (e.g., desktop PC, laptop, Tablet PC, handheld computer, server, workstation, mainframe) and may be configured with many different hardware components. Standard components, such as disk drives, CD and/or DVD drives, monitors, and keyboards, for example, may be included in some configurations.
  • the connections may be effected via any suitable transport media (e.g., wired, optical, and/or wireless media) and any suitable communication protocol (e.g., TCP/IP).
  • the host computer may include suitable networking hardware (e.g., modem, Ethernet card, WiFi card).
  • Data accessible by the computer can include local RAM, local nonvolatile memory (e.g., optical storage or Flash memory), network-accessible storage, internet storage, and the like. Predetermined or standard population values can be stored in any such location that is accessible by the computer.
  • the host computer may implement any of a variety of operating systems, including UNIX, Linux, Microsoft Windows, MacOS, or any other commercially available operating system. Embodiments disclosed herein are not limited to any particular hardware or software.
  • aspects of the present invention may be implemented using any of a variety of computer code languages, including PERL, Python, R, MATLAB, C, C++, Java, JavaScript, VBScript, Bash or any other scripting or programming language that can be executed on the host computer or that can be compiled to execute on the host computer. Code may also be written or distributed in low level languages such as assembler languages or machine languages. Embodiments disclosed herein are not limited to any particular computer language.
  • the host computer system advantageously provides an interface through which the user directs operation of the tools.
  • commands can be adapted to a number of operating systems as appropriate.
  • a graphical user interface may be provided, which allows the user to control operations using a pointing device.
  • embodiments of the present invention are not limited to any particular user interface.
  • Programs or scripts for incorporating various features of the present invention may be encoded on various computer readable media for storage and/or transmission.
  • Storage or transmission media such as magnetic disk or tape, optical storage media such as compact disk (CD) or digital versatile disk (DVD), flash memory, and carrier signals adapted for transmission via wired, optical, and/or wireless networks conforming to a variety of protocols, including the Internet are contemplated.
  • Embodiments disclosed herein are not limited to any particular storage or transmission medium.
  • an analysis platform is used to analyze bisulfite converted sequences.
  • exemplary analysis platforms include: (1) Illumina BeadChips and (2) next generation sequencing (NGS), although other platforms are contemplated and no platform should be perceived as limiting.
  • the first step in either platform is the bisulfite conversion of sample DNA. This forms an artificial oligonucleotide (i.e., not found in nature) where every unmethylated cytosine is transformed into a uracil.
  • Illumina BeadChips there are two probe types. For type I probes, the bisulfite converted sample sequences hybridize to BeadChip- oligonucleotides in a methylation state specific matter.
  • a sample sequence is hybridized to a BeadChip-bound oligonucleotide
  • an artificially marked nucleotide is added to the BeadChip-bound oligonucleotide.
  • bisulfite converted sequences hybridize to BeadChip-attached oligonucleotides, independent of methylation status.
  • An artificially marked nucleotide is then selectively added. The identity of the added nucleotide is dependent on the methylation status of the sample sequence.
  • the methylation states of the sample sequences for both type I and type II probes result read by red and green light intensities, generated by a BeadChip scanner. The ratio of these captured intensities estimates the degree of methylation for each CpG.
  • NGS targeted CpGs in the bisulfite converted sample sequence are selectively PCR amplified for NGS processing. Determining which CpGs are amplified is not obvious (described below). Due to the artificial nature of the generated sequences, special experimental conditions are required to amplify our targeted regions. For example, one must use a DNA polymerase that properly reads uracil nucleotides, and one must be mindful that bisulfite converted DNA is single stranded and thus more unstable relative to natural DNA. In some NGS configurations, one will need to make further adjustments to account for the lower GC content of bisulfite converted sequences.
  • the NGS platform produces sequence read-outs of targeted regions. One may transform these sequences via in silico demethylation so that one can accurately map them back to an unmethylated bisulfite converted genome. Once mapped to the genome, one may identify the nucleotides present at methylation sites on the sequence. Due to bisulfite conversion, unmethylated cytosines are artificially transformed into another base (i.e., uracil), and as a result, unmethylated cytosines are read as a different base than methylated cytosines.
  • another base i.e., uracil
  • the output from both BeadChip and NGS platforms may be formatted, for example into an n x m matrix, where n represents the number of interrogated CpGs and m represents the number of samples.
  • a BeadChip matrix may consist of 480,000 CpGs across 48 samples, representing a total of 23 million data points. Each data point may represent a degree of methylation (e.g., methylation frequency).
  • a classification model is trained on a static data set that contains methylation frequency profiles for samples of known phenotypes.
  • a methylation profile consists of an arbitrary number of methylation frequency values.
  • This statistical algorithm transforms methylation frequencies so that their statistical importance can be measured. An example entails transforming these methylation frequencies into phenotype-specific methylation frequency distributions and assessing the similarity of these distributions.
  • methylation frequency profiles Prior to analysis by a classification model, methylation frequency profiles may be transformed. An example is subtracting each methylation frequency in a methylation profile by the profile's methylation frequency average and dividing by the standard deviation.
  • the classification model determines which methylation signature across all input CpGs best identifies each phenotype.
  • the classification model may perform additional transformations. For example, a methylation profile containing 25 CpG methylation frequency values may be transformed via a kernel function into a unitless profile containing 30 values. While training, the classification model analyzes the CpGs in the methylation profile simultaneously and may use CpGs independently or in various combinations to classify phenotypes.
  • the assignment of phenotypes is arbitrary. Samples may be partitioned into two phenotype groups (e.g., disease and no-disease). A multi-disease data set may be partitioned such that each disease is assigned a distinct phenotype or subtypes of a disease is represented as individual phenotypes (e.g., disease subtype I, disease subtype II, and disease subtype III, and no disease).
  • a test methylation profile is inputted into the classification model and it is compared against the patterns learned from the training data set.
  • the model outputs a classification value per phenotype included in the training set.
  • these classification values can directly represent classification probabilities.
  • the output values are not probabilistic and may be further transformed to represent probabilistic values (via linear regression, for example).
  • the output values are then compared against thresholds determined based on the training data to classify the sample. These classification threshold values are not obvious.
  • the training data set may be used in combination with cross validation algorithms to assess an optimal cutoff value that best identifies a phenotype of interest relative to all other phenotypes.
  • the resultant classification may be further transformed so that it is more interpretable to the data recipient.
  • classification information can show sensitivity and specificity numbers, or recite a probability that the patient has RA.
  • kits comprising reagents disclosed herein.
  • Said reagents may comprise oligonucleotide probes or primers, a gene chip, an antibody, a panel list or any other reagents disclosed herein provided that the kit comprises reagents specific for loci disclosed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
  • this kit provides reagents that facilitate the determination of the methylation status of loci selected from the list of loci in Tables 1A, IB, 2A, 2B, 3A, 3B or 4, or of a panel of loci that may further comprise at least one locus identified elsewhere.
  • kits may comprise reagents for the determination of the methylation state of loci selected from Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
  • the kit also includes oligonucleotide primers each comprising a sequence hybridizing to at least a portion of a locus selected from the group consisting of the loci listed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
  • the kit can include one or more of methylation-sensitive restriction endonucleases, amplification reagents such as PCR reagents, probes and/or primers.
  • a "DNA reservoir” is any source of DNA that may be informative in diagnosis, such as DNA from an individual or individuals, DNA from a cell population taken from an individual or individuals, or extracellular DNA found within an individual, such as free circulating DNA.
  • a "Differentially Methylated Locus” or “DML” is a methylation site of Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
  • locus is a specific place on a chromosome where a base (nucleic acid residue) or a consecutive set of bases is located.
  • a locus may be a methylation site, or it may be a consecutive set of bases comprising a methylation site and adjacent sequence.
  • It may comprise, for example a methylation site as well as 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 750 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb, or more than 10 kb on either side of the methylation site.
  • methylation refers to the addition of a methyl (CH 3 ) moiety, for example onto a cytosine base at positions C5 or N4, onto an adenine at the N6 position, or onto any other molecular structure capable of forming a covalent bond with CH 3 .
  • methylation refers to cytosine methylation at positions C5 to produce 5-methyl cytosine.
  • unmethylated DNA or “methylated DNA” can also be used informally to refer to a segment of DNA having at least one base capable of being methylated and wherein said at least one base is unmethylated or methylated, respectively.
  • a "methylation pattern" refers to the set of methylation states of two or more bases in a genome.
  • the profile can include the methylation state of every base in a cell, tissue or individual, or can comprise any subset thereof comprising more than one base.
  • a “methylation state” or “methylation status” refers to the presence, absence or extent of methylation at a particular base or set of bases, or nucleotides within a portion of DNA, or other molecule capable of being methylated.
  • Determination of the methylation status of a particular DNA sequence can involve determination of the methylation state of every cytosine C5 position in the sequence or can involve determination of the methylation state of a subset of the cytosine C5 positions (such as the methylation state of cytosines in one or more specific restriction enzyme recognition sequences) within the sequence, or can involve determining regional methylation density within the sequence without providing precise information of where in the sequence the methylation occurs, or can refer to the determination of the methylation status at other positions along a given molecule.
  • a "methylation site” is a specific base that is known to be differentially methylated in one cell, population of cells or individuals as compared to another cell, population of cells or individuals (i.e., cells of individuals suffering from an autoimmune disorder or rheumatic disorder such as RA, in comparison to cells of individuals suffering from OA or SLE, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC indiviauals, or pre-autoimmune or autoimmune- like symptoms in comparison to cells of autoimmune disorder- free or rheumatic disorder- free individuals).
  • a methylation site need not be methylated under all conditions - for example, a methylation site may be completely unmethylated in some individuals or cell populations
  • a "p-value" represents the probability of finding a test statistic that is at least as extreme as the one reported.
  • q-value represents the false discovery rate (FDR) to account for multiple hypothesis testing.
  • a "panel" is a set of loci, genes or proteins whose methylation states, transcript accumulation levels, or activities or accumulation levels, respectively.
  • a panel may be used to diagnose a condition, such as an autoimmune disorder, determine a cell type, determine a cell fate or otherwise evaluate a cell, cell population or individual from which a cell, cell population, DNA sample, transcript sample or protein sample is derived.
  • a "primer” is a probe which is used to provide a 3 ⁇ moiety to which a nucleotide triphosphate may be added in a DNA synthesis reaction such as, for example, a polymerase chain reaction.
  • a "probe” is an oligonucleotide which specifically binds a given DNA sequence. Probes may be modified so that binding to a substrate differentially affects an assayable output.
  • a "protein accumulation level” is the aggregate amount of that protein which is present in a sample from a cell or cell population. It represents the net effects of translation and degradation on a given protein population, and is often colloquially referred to as 'expression level' of a protein.
  • a "protein accumulation profile” is the measure of accumulation levels for a panel of proteins.
  • a "protein activity” is a measure of the rate at which a reaction in which the protein participates occurs in a sample from a cell or cell population comprising a given protein. It represents the net effects of translation, degradation, post- translational modification and substrate availability for a given protein population, and is often colloquially referred to as 'expression level' of a protein.
  • a "protein activity profile” is the measure of protein activities for a panel of proteins.
  • an isolated DNA molecule having a sequence "spanning" a differentially methylated site has a sequence which base pairs with the sequence immediately on either side of the differentially methylated site.
  • a "standard population” is any population of DML data used as a basis for comparison of a given result.
  • a standard population can comprise DML data from a set of individuals with known disease status, or from a set of cells having a known or expected DML pattern.
  • a standard population may be compared to sample DML data, such as a result obtained from a patient sample.
  • a "transcript accumulation level" of a related gene is the aggregate amount of R A derived from that gene which is present in a sample from a cell or cell population. It represents the net effects of transcription and transcript degradation on a given transcript population, and is often colloquially referred to as 'expression level' of a transcript.
  • a "transcript accumulation pattern" is the set of transcript accumulation levels for each member of a gene panel.
  • DNA from peripheral blood mononuclear cells or other cells found in blood are extracted using techniques known to those of skill in the art.
  • the protocols of Mallone (Mallone, R. et al., (2010) Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T- cell responses: position statement of the T-cell Workshop Committee of the Immunology of Diabetes Society, Clin. Exp. Immunol. 163:33-49) and Al-Moundhri (Al-Moundhri, et al., (2010) The prognostic significance of whole blood global and specific DNA methylation levels in gastric adenocarcinoma. PloS one 5:el5585) are among the protocols known in the art.
  • Circulating cell-free DNA is extracted with methods from Li, M et al. (Li, M. et al., (2009) "Sensitive digital quantification of DNA methylation in clinical samples," Nat Biotechnol (27)9: 858-863). Up to 18 ml of blood is collected into standard blood collection tubes containing EDTA. The tubes are immediately chilled to 8 °C and processed within 30 min of collection. The blood cells are pelleted for 15 min at 200g in a Leucosep tube (Greiner) filled with 15 ml of Ficoll-Paque solution.
  • Greiner Leucosep tube
  • the supernatant that is, plasma
  • the supernatant is transferred into 1.5 ml tubes, immediately frozen, and stored at -80 °C.
  • the plasma samples are then thawed at 25 °C for 5 min, and any remaining debris is pelleted at 16,000g for 5 min.
  • the supernatant is transferred to a new tube.
  • Total genomic DNA is then purified from aliquots of 2 ml plasma supernatant using the QIAamp MinElute Virus Vacuum Kit (Qiagen) as recommended by the manufacturer.
  • the DNA is finally eluted in elution buffer (Qiagen), and stored at -20 °C.
  • Peripheral blood mononuclear cells are extracted using techniques known to those of skill in the art.
  • the protocol of Mallone (Mallone, R. et al., (2010) Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T- cell responses: position statement of the T-cell Workshop Committee of the Immunology of Diabetes Society, Clin. Exp. Immunol. 163:33-49) is among the protocols known in the art.
  • total PBMCs obtained from RA, OA, SLE, other autoimmune disease, or other rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and normal patient blood samples are prepared by Ficoll gradient. (Langevin et al., 2012. "Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: An epigenome-wide association study, " Epigenetics. 7(3):291-9).
  • the isolated cell subsets are further enriched for T-Cells, B-cells, and Monocytes by magnetic beads pre -bound with biotinylated monoclonal antibodies towards human cell surface markers (including nonlimiting examples such as anti-huCD4, huCD19 and huCD68) as described.
  • human cell surface markers including nonlimiting examples such as anti-huCD4, huCD19 and huCD68.
  • Extracted DNA is treated largely following the protocol of Frommer et al., (1992) A genomic sequencing protocol that yields a positive display of 5- methylcytosine residues in individual DNA strands. Proc. Nat. Acad. Sci. USA 89. 2 ⁇ g of human DNA and 8 ⁇ g of carrier plasmid DNA are sheared through a fine needle, alkali denatured, neutralized, and precipitated. DNA is then incubated in a total volume of 1.2mL with freshly prepared 3.1M Sodium bisulfite / 0.5mM hydroquinone, pH 5.0 for 16 hours at 50°C under mineral oil.
  • the solution is dialyzed at 4°C in an excess volume of 5mM Sodium acetate / 0.5mM hydroquinone, pH 5.2, and then at 4°C in an excess volume of 5mM Sodium acetate, pH 5.2, and finally in an excess of deionized water.
  • the solution is dried under a vacuum and the solid residue is resuspended in 100 ⁇ , of lOOmM Tris/HCl, 01. mM EDTA, pH 7.5 buffer. NaOH is added to a final concentration of 0.3mM and the reaction is allowed to stand at room temperature for 10 minutes. Ammonium acetate is then added to a final concentration of 3M.
  • the DNA is then precipitated, washed and resuspended in lOOuL of lOmM Tris/HCl, 0.1 mM EDTA pH 7.5 buffer, and used immediately or stored at -20°C.
  • Commercial kits for bisulfite conversion are also readily available and can be used in place of the foregoing procedure.
  • l-5uL of bisulfite-treated DNA is amplified for 25-30 cycles using specific primers under standard cycling conditions. Amplified fragments are purified. Optionally, fragments are cloned into a vector of interest, which is transformed into a host organism wherein the vector is replicated, and then purified from the host for sequencing.
  • Sequencing is performed using dideoxy chain-termination methods and position extension products are visualized using electrophoretic methods appropriate to the label for each dideoxy nucleotide (other sequencing techniques, such as pyrosequencing, single strand sequencing, or NGS can also be used.)
  • ddCTP and ddGTP (dideoxy"-) nucleotides to be incorporated are labeled with biotin, while the ddATP and ddTTP are labeled with 2,4-dinitrophenol.
  • the hybridized chip is subjected to repeated rounds of antibody staining to apply fluorophores.
  • the hybridized chips are placed in an Illumina HiScan SQ scanner, a two-color laser (532 nm/660 nm) fluorescent scanner with a 0.375 ⁇ spatial resolution, which is capable of exciting the fluorophores generated during the staining step of the protocol.
  • Image intensities are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software, scored as 0 (unmethylated) to 1 (fully methylated).
  • Methylation patterns were determined in whole blood, purified PBMC and subsets comprising T-cells, B-cells and Monocytes obtained from individuals suffering from RA, OA, SLE, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals suffering from none of the above disorders.
  • rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals suffering from none of the above disorders.
  • DML associated CD 160 a cell surface glycoprotein expression of which is tightly associated with peripheral blood NK cells and CD8 T lymphocytes with cytolytic effector activity
  • CXCL17 a chemokine ligand (CXC motif) ligand 17-CXCL17 that attracts dendritic cells and monocytes
  • DUSP22 Dual specificity protein phosphatase 22, which regulates focal adhesion kinase (FAK) and controls cell motility and adhesion
  • IL17RB a receptor on lymphocytes that binds to interleukin- 17B and E regulators of autoimmune diseases
  • IL6R Receptor for Interleukin-6, a mediator of inflammation in RA which is antagonistic to regulatory T- cells that shut down autoimmunity
  • ITGAM Integrin alpha M receptor which binds C3
  • Mirl46b which regulates inflammatory cytokines and immune cells
  • ADAMTS14 a partial list includes DML associated CD 160, a cell surface glycoprotein expression
  • DML DML associated with CD40LG, CD40 ligand-expressed on activated B-cells
  • CD84 which functions in adhesion interactions between T lymphocytes and accessory cells and enhances cytokine synthesis
  • Interleukin-21 receptor which is important for the proliferation and differentiation of T-cells, B-cells, and natural killer (NK) cells
  • Interleukin-6 receptor which plays a role in B-cell activation and immunoglobulin synthesis
  • Interleukin-27 which plays an important function in regulating the activity of B- and T-lymphocytes and which is found in RA synovium
  • Interleukin-7 which causes expansion of T and B- cells, is associated with increased levels of proinflammatory mediators, and drives B-cell development
  • BCL2L14 which regulates B-cell proliferation, survival and apoptosis
  • IL13 DML associated with CD40LG, CD40 ligand-expressed on activated
  • DML identified in Monocytes a partial list includes DML associated with CD226, which mediates cellular adhesion to other cells bearing its ligands, CD112 and CD155 confers the risk of RA in certain populations; CD59, Protectin, a complement regulatory protein which inhibits the complement membrane attack complex, and decrease of which is associated with increase inflammation and tissue damage; CXCR-4, an alpha-chemokine receptor specific for stromal-derived- factor-1 (SDF-1 also called CXCL12), a molecule endowed with potent chemotactic activity for lymphocytes, and which is important for angiogenesis in RA synovium; Interleukin-1 beta (IL- ⁇ ) also known as catabolin, is a cytokine that is an important mediator of the inflammatory response, and is involved in a variety of cellular activities, including cell proliferation, differentiation, and apoptosis, and which induces Cyclooxygenase 2; Interleukin 1 receptor-like 1, a member of the Toll
  • each locus in the diagnostic panel multiple sets of candidate primers are designed to efficiently amplify the 50-200 bp bisulfite converted region covering the locus.
  • the best performing primer pair is used in the final diagnostic.
  • Taqman probes are used during this amplification process to determine methylation values.
  • the amplified regions are sequenced to determine methylation values.
  • the DML panels are used to screen patient samples based on their disease state and response or lack of response to treatment to develop diagnostic, predictive or therapeutic selection tests, disease monitoring tests, and prognostic tests.
  • DML Differentially methylated loci identified by methylation- specific, arbitrarily primed PCR and methylated CpG island amplification were scored and prioritized using the following scoring variables: (a) appearance using multiple discovery methods; (b) appearance in multiple pools of like samples; (c) located within a CpG island; (d) located within the promoter region of a gene; (e) located near or within predicted or known genes; (f) known to be associated with disease; (g) class of gene (transcription factor, growth factor, apoptosis gene, oncogene, cytokine gene; and (h) repetitive element.
  • DML Differentially methylated loci
  • DNA methylation patterns in key genes may serve as a biomarker for inflammation and RA in some embodiments of the methods and compositions disclosed herein.
  • Random DMLs were selected from Tables 1A and IB, Tables 2A and 2B, Tables 3A and 3B, and Table 4, below to constitute panels of 50 loci.
  • Control panels were selected comprising methylation sites known in related literature to be methylated independent of RA status. That is, control panels consisted of methylation sites that were randomly selected without consideration of RA status.
  • a first set of samples from individuals each having a known RA status were assayed for their relative methylation status at the loci in panels from the Tables disclosed herein and from the random methylation sites unrelated to RA.
  • a second set of samples from individuals each having a known RA status were assayed for their relative methylation status at each locus in the ranked panels and the control panels.
  • Sensitivity, or 'True Positive' and Specificity, or 'True Negative' metrics were generated by 1,000 rounds of leave -one-out cross validation using DML from the indicated table. Randomly selected DML were selected from a genome-wide set of 452,768 methylation sites.
  • the ranked DML panels and the control panels were evaluated for their ability to accurately identify RA status in the sample data set.
  • Panels were assessed as to their Sensitivity, which is their utility to identify True Positive RA samples, that is, to correctly identify RA positive samples relative to the total number of analyzed RA positive patient samples.
  • Panels were also evaluated as to their Specificity, which is their utility to identify True Negative RA samples, that is, to correctly call RA negative samples relative to the total number of analyzed RA negative samples.
  • both high sensitivity and high specificity values are required for a panel to have good performance.
  • An effective panel must be able to classify RA negative patients as RA negative and RA positive patients as RA positive.
  • Panels were also evaluated as to their overall Accuracy, which is a metric that includes measurement of both True Positive and True Negative call rates.
  • the randomly selected DML panels demonstrated a True Positive Rate of 19.4% a True Negative Rate of about 90.0%, and an accuracy of 54.3%.
  • Ranked Table 1 DML selected from Tables 1A and IB, demonstrated a True Positive Rate of 37.7%, a True Negative Rate of about 90.1%, and an accuracy of 63.5%.
  • Ranked Table 2 DML selected from Tables 2A and 2B, demonstrated a True Positive Rate of 48.8%, a True Negative Rate of about 90.3%, and an accuracy of 69.8%.
  • Ranked Table 3 DML, selected from Tables 3 A and 3B demonstrated a True Positive Rate of 85.9%, a True Negative Rate of about 90.1%, and an accuracy of 88.0%.
  • Example 10 Exemplary Panel Performance
  • DMLs were selected from Tables 1A, IB, 2A, 2B, 3A, and 3B for inclusion in diagnostic panels based upon their capacity to predict RA status, and included in Table 4.
  • Table 4 DML were ranked for further analysis. Ranked Table 4 DML, demonstrated a True Positive Rate of 85.1%, a True Negative Rate of about 90.5%, and an accuracy of 87.6%.
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (UCSC hgl9 genome build).
  • the DML coordinate is labeled according to its position on the + strand for simplicity but the DML refers to the CpG on the + and/or - strand.
  • position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • Table 2 A Data are listed as "DML coordinate, optional associated gene
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • PBMC OA_SLE_HC,PBMC:SLE; 11:132217395, PBMC:HC; 11:133782453, IGSF9B
  • Bcell OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:315118, IFITMl
  • PBMC OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 11:66362959, CCDC87
  • Enhancer 512367,LOC100292680
  • Enhancer 1351, SNORDl 15-15
  • PBMC OA_SLE_HC,PBMC:SLE; 16: 14394816, MIR193B
  • PBMC OA_SLE_HC,PBMC:SLE,PBMC:notRA; 16:34209247, Wholeblood:notRA; 16:34787597, PBMC:notRA; 16:3511787, NAA60
  • PBMC OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 17:74266574, FAM100B
  • PBMC OA_SLE_HC,PBMC:SLE,Tcell:HC; 19: 10206746, ANGPTL611 Exon 2 : 6679,C 19orf66113 ' Proximal Enhancer:9941, PBMC:OA_SLE_HC,PBMC:notRA; 19: 10223710, EIF3G
  • PBMC OA_SLE_HC,PBMC:SLE; 19:55688114, PTPRH
  • PBMC OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 19:55887799, IL11
  • Bcell OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 1:79085250, IFI44L
  • PBMC OA_SLE_HC,Tcell:OA_SLE_HC; 3: 122509111, DIRC2
  • PBMC OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 3:12595696, LOC100129480
  • Bcell OA_SLE_HC,Bcell:SLE,Mono:SLE; 5:72824251, Mono:HC; 5:7287160, PBMC:notRA; 5:72934606, RGNEF
  • Enhancer 10109,HISTlH4D
  • PBMC OA_SLE_HC; 6:32309323, C6orflO
  • PBMC OA_SLE_HC,PBMC:SLE,PBMC:notRA; 6:37616482, MDGAl
  • PBMC OA_SLE_HC,PBMC:SLE; 7: 107700124, LAMB4
  • Enhancer 11565,LRRC61
  • Enhancer 18603,RARRES2
  • position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
  • Bcell OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 10:91151885, IFITl
  • PBMC OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 2:37384523, EIF2AK2
  • DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.

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Abstract

Differentially methylated loci relevant to the diagnosis of autoimmune disorders such as RA, as well as related methods and reagents, are disclosed.

Description

DIAGNOSIS OF RHEUMATOID ARTHRITIS (RA) USING DIFFERENTIALLY METHYLATED LOCI IDENTIFIED IN PERIPHERAL BLOOD MONONUCLEAR CELLS, T-CELLS, B-CELLS AND MONOCYTES
REFERENCE TO SEQUENCE LISTING, TABLE, OR COMPUTER PROGRAM
LISTING
[0001] Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 are included in the specification of this application.
RELATED APPLICATIONS
[0002] The present application claims priority to U.S. Provisional Application Serial Nos. 61/695,685, filed August 31, 2012, 61/695,703, filed August 31, 2012, 61/776,731, filed March 11, 2013, and 61/777,680, filed March 12, 2013.
JOINT RESEARCH AGREEMENT
[0003] The claimed subject matter of the present application was made by or on behalf of parties to a joint research agreement that was in effect on or before the date the claimed invention was made; the claimed invention was made as a result of activities undertaken within the scope of the joint research agreement; and the parties to the joint research agreement include: The Regents of the University of California and Ignyta, Inc. (formerly NexDx, Inc.).
[0004] The joint research agreement was a written contract, grant or cooperative agreement entered into by the above-mentioned parties for the performance of experimental, developmental or research work in the field of the claimed invention.
[0005] The above-mentioned Joint Research Agreement was executed November 10, 2011 and amended May 25, 2012.
FIELD OF THE INVENTION
[0006] Embodiments of the present invention include methods, compositions and kits for the diagnosis or prognosis of a subject with an autoimmune disorder such as Rheumatoid Arthritis. Some embodiments include identifying a therapeutic agent or selecting or monitoring a treatment for treating a disorder such as Rheumatoid Arthritis. BACKGROUND OF THE INVENTION
[0007] Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic, systemic inflammation, especially involving the synovial joints (Harris et al., 2009. "Clinical features of rheumatoid arthritis,'" In: Firestein et al., eds. Kelley's Textbook of Rheumatology. 8th ed. Philadelphia, Pa: Saunders Elsevier; Chapter 66; Firestein, 2003. "Evolving concepts of rheumatoid arthritis," Nature 423:356-61; Klareskog et al, 2009. "Rheumatoid arthritis " Lancet 373:659-72). Progressive inflammation leads to erosion of the articular cartilage with subsequent bone erosion leading to pain, functional impairment, and, ultimately, disability. Systemic effects may include damage to organs and accelerated atherosclerosis with significant morbidity and mortality (del Rincon et al., 2005. "Relative contribution of cardiovascular risk factors and rheumatoid arthritis clinical manifestations to atherosclerosis " Arthritis Rheum 52:3413-23; Centers for Disease Control and Prevention www, cdc . gov/ arthri tis/basi cs/rh eurnatoi d.h tm) .
[0008] RA is the most common chronic inflammatory joint disease with an estimated incidence of ~1% of the US population, and a 2 to 3 times higher prevalence in women than in men (Helmick et al. 2008. "Estimates of the prevalence of arthritis and other rheumatic conditions in the United States, " Part I. Arthritis Rheum. 58:15-25). RA poses a substantial burden on public health with the overall costs estimated to exceed $30 billion annually in the U.S. (Birnbaum et al., 2010. "Societal cost of rheumatoid arthritis patients in the US, " Curr Med Res Opin. 26:77-90). Treatment with DMARDs can often ameliorate the disease and improve the clinical outcome. Thus, therapy should be initiated early in the course of the disease to minimize joint damage (Combe et al., 2007. "EULAR recommendations for the management of early arthritis: report of a task force of the European Standing Committee for International Clinical Studies Including Therapeutics (ESCISIT), " Ann Rheum Dis. 66:34-45; Finckh et al, 2006. "Long-term impact of early treatment on radiographic progression in rheumatoid arthritis: A metaanalysis, " Arthritis Rheum. 55:864-72). Early therapeutic intervention prior to progression prevents or minimizes irreversible joint damage and can result in disease remission in approximately 40% of RA patients and clinical improvement in 80% (Allaart et al., 2006. "Aiming at low disease activity in rheumatoid arthritis with initial combination therapy or initial monotherapy strategies: the BeSt study " Clin Exp Rheumatol 24:S-77-82). Because only about one-third of patients diagnosed with undifferentiated arthritis develop RA, making a definitive diagnosis of RA, especially early RA, is critical for appropriate patient management (van Aken et al., 2006. "Comparison of long term outcome of patients with rheumatoid arthritis presenting with undifferentiated arthritis or with rheumatoid arthritis: an observational cohort study, " Ann Rheum Dis 65(l):20-25; Hazes et al., 2011. "The epidemiology of early inflammatory arthritis, " Nature Reviews Rheumatology 7:7,381) and reduction of future morbidity and mortality.
[0009] Individuals who seek medical help for symptoms of inflammatory synovitis often cannot be categorized and are diagnosed as having undifferentiated arthritis (UA) (Allaart et al., 2006. "Aiming at low disease activity in rheumatoid arthritis with initial combination therapy or initial monotherapy strategies: the BeSt study," Clin Exp Rheumatol 24:S-77-82; Hazes et al., 2011. "The epidemiology of early inflammatory arthritis," Nature Reviews Rheumatology 7:7,381). Because 40-50% of these patients have spontaneous remission, an early diagnosis of RA is essential in order to obtain a differential diagnosis of RA versus other conditions (osteoarthritis [OA], lupus, ankylosing spondylitis, other connective tissue disease, fibromyalgia) so as to select the appropriate therapy and plan for patient management (Allaart et al., 2006. "Aiming at low disease activity in rheumatoid arthritis with initial combination therapy or initial monotherapy strategies: the BeSt study," Clin Exp Rheumatol 24:S-77-82; Hazes et al., 2011. "The epidemiology of early inflammatory arthritis," Nature Reviews Rheumatology 7:7,381). Currently available laboratory diagnostic tests for RA focus on measuring autoantibodies (i.e., Rheumatoid Factors [RF] and Anti-citrullinated protein antibodies (ACPA) or anti-cyclic citrullinated peptide antibodies (anti-CCP)]) (Lee et al., 2003. "Clinical utility of the anti-CCP assay in patients with rheumatic diseases," Ann Rheum Dis 62:870-4; Nishimura et al, 2007. "Meta-analysis: diagnostic accuracy of anti-cyclic citrullinated peptide antibody and rheumatoid factor for rheumatoid arthritis," Ann Intern Med 146:797-808; De et al, 2004. "Rheumatoid factor and anticitrullinated protein antibodies in rheumatoid arthritis: diagnostic value, associations with radiological progression rate, and extra-articular manifestations," Ann Rheum Dis. 63: 1587-1593; Greiner et al, 2005. "Association of anti-cyclic citrullinated peptide antibodies, anti-citrullin antibodies, and IgM and IgA rheumatoid factors with serological parameters of disease activity in rheumatoid arthritis," Ann NY Acad Sci. 1050:295-303). These tests assist in diagnosis, can sometimes help identify patients who are likely to benefit from disease-modifying anti-rheumatic drugs (DMARDs) therapy and can often correlate with disease severity. However, specificity and sensitivity are highly variable (70-98%) and 30-88%), respectively) and the tests frequently cannot detect early disease (Nishimura et al., 2007. "Meta-analysis: diagnostic accuracy of anti-cyclic citrullinated peptide antibody and rheumatoid factor for rheumatoid arthritis " Ann Intern Med 146:797-808; Aggarwal et al, 2009. "Anti-citrullinated peptide antibody assays and their role in the diagnosis of rheumatoid arthritis," Arthritis Rheum. 61(11): 1472-1483; Nielen et al, 2005. "Antibodies to citrullinated human fibrinogen (ACF) have diagnostic and prognostic value in early arthritis " Ann Rheum Dis. 64: 1199-204). Furthermore, results vary based on the stage of the disease (Nielen et al, 2005. "Antibodies to citrullinated human fibrinogen (ACF) have diagnostic and prognostic value in early arthritis " Ann Rheum Dis. 64: 1199-204; Goldbach-Mansky et al., 2000. "Rheumatoid arthritis associated autoantibodies in patients with synovitis of recent onset " Arthritis Res 2:236-43; Visser et al, 2002. "How to diagnose rheumatoid arthritis early: a prediction model for persistent (erosive) arthritis " Arthritis Rheum 46:357-65), and ACPA autoantibodies are not detected in the blood of -30% of RA patients and are present in only about 50% of RA patients at the initial onset of symptoms (Hazes et al., 2011. "The epidemiology of early inflammatory arthritis " Nature Reviews Rheumatology 7:7,381). These issues can preclude a definitive diagnosis, making it difficult to differentiate RA from other rheumatic diseases. Composite scoring systems for diagnosis of RA have been developed, but rely on variable, non-objective criteria, which can lead to delay or inaccurate diagnosis or inappropriate treatment of patients with expensive and dangerous drugs with significant side effects (Gartlehner et al, 2006. "The comparative efficacy and safety of biologies for the treatment of rheumatoid arthritis: a systematic review and meta-analysis " J Rheumatol 33:2398-408; Donahue et al., 2008. "Lohr Systematic Review: Comparative Effectiveness and Harms of Disease-Modifying Medications for Rheumatoid Arthritis " Ann Intern Med 148(2): 124-134; Keyser, 2011. "De Choice of Biologic Therapy for Patients with Rheumatoid Arthritis: The Infection Perspective Current Rheumatology Reviews " 7:77-87; Wolfe et al. 2004. "Lymphoma in rheumatoid arthritis: the effect of methotrexate and ant-tumor necrosis factor therapy in 18,572 patients " Arthritis Rheum 501740-1751). New diagnostic tests are needed to overcome these problems (Gibson et al, 2012. "Biomarkers in rheumatology, now and in the future " Rheumatology 51 :423-433). Cytokines and growth factors (Deane et al, 2010. "The number of elevated cytokines and chemokines in preclinical seropositive rheumatoid arthritis predicts time to diagnosis in an age-dependent manner " Arthritis Rheum. 62(11):3161-72; Kokkonen et al, 2010. "Up-regulation of cytokines and chemokines predates the onset of rheumatoid arthritis " Arthritis Rheum. 62(2):383-91; Hitchon et al., 2004. "A distinct multicytokine profile is associated with anti-cyclical citrullinated peptide antibodies in patients with early untreated inflammatory arthritis J Rheumatol. 31(12):2336-46) are highly non-specific, vary widely in concentration between individuals, and rapidly change in response to a wide variety of different stimuli (Gibson et al., 2012. "Biomarkers in rheumatology, now and in the future,'" Rheumatology 51 :423-433; Bruunsgaard et al, 2003. "Age-related inflammatory cytokines and disease. Immunology and Allergy Clinics of North America,'" 23(1): 15-39; Aziz et al., 1999. "Variables that affect assays for plasma cytokines and soluble activation markers," Clin Diagn Lab Immunol. 6(l):89-95; Moldoveanu et al, 2001. "The cytokine response to physical activity and training,'" Sports Med. 31(2): 115-44; Tarrant, 2010. "Blood Cytokines as Biomarkers of in vivo Toxicity in Preclinical Safety Assessment: Considerations for Their Use," Toxicol Sci. 117(1):4-16). Proteins and metabolic biomarkers are heterogeneous and have stability issues (Deane et al., 2010. "The number of elevated cytokines and chemokines in preclinical seropositive rheumatoid arthritis predicts time to diagnosis in an age-dependent manner," Arthritis Rheum. 62(11):3161-72.; Aziz et al, 1999. "Variables that affect assays for plasma cytokines and soluble activation markers," Clin Diagn Lab Immunol. 6(1):89— 95; Madsen et al, 2011. "Diagnostic Properties of Metabolic Perturbations in Rheumatoid Arthritis," Arthritis Research & Therapy. 13(1)). Gene expression diagnostics suffer from high variability on an individual level, have less of a dynamic range, and sample stability is also an issue (Bauer et al., 2009. "Gene-expression profiling in rheumatic disease: tools and therapeutic potential," Nat Rev Rheumatol 5:257-265). Collectively, these new approaches lack sensitivity and specificity, and have not yet been clinically validated. (Rifai et al, 2006. "Protein biomarker discovery and validation: the long and uncertain path to clinical utility," Nat Biotechnol 24:971-83).
[0010] Joint damage and synovial inflammation in autoimmune rheumatic diseases are influenced by genetic and environmental factors (Firestein, 2009. "Etiology and pathogenesis of rheumatoid arthritis, " In Kelley Textbook of Rheumatology. Firestein et al. (eds). 8th edition, Elsevier, Philadelphia, pp. 1035-86). Research on autoimmune diseases such as RA and systemic lupus erythematosus (SLE) has started to focus on epigenetic influences as major contributors to the phenotypes in these diseases (Portela et al., 2010. "Epigenetic modifications and human disease, " Nature Biotechnology 28(10): 1057-1068.; Feinberg et al, 2007. "Phenotypic plasticity and the epigenetics of human disease, " Nature 447:433-40; Lu a et al., 2006. "Epigenetics, disease, and therapeutic interventions, " Ageing Research Reviews 5:449-467; Brooks et al., 2010. "Epigenetics and autoimmunity. Journal of Autoimmunity; 34:J207-J219; Huber et al., 2007. "Epigenetics in Inflammatory Rheumatic Diseases, " Arthritis & Rheumatism 56;3523-353; Richardson, 2003. "DNA methylation and autoimmune disease, " Clin Immunol. 109:72-9; Richardson, 2007. "Primer: epigenetics of autoimmunity, " Nature Clin Practice Rheum 3(9):521-527). Adult somatic cells have a stable phenotype maintained by epigenetic mechanisms (non-DNA encoding changes) such as DNA methylation of cytosine within cytosine-guanine (CpG) dinucleotide sequence contexts. CpG sequences are often clustered together, which are called CpG islands (Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526.); Beck et al, 2008. "The methylome: approaches for global DNA methylation profiling, " Trends in Genetics 24:231-237). Methylation of promoters within CpG islands increase or decrease gene expression (hypomethylation and hypermethylation patterns, respectively) (Portela et al., 2010. "Epigenetic modifications and human disease, " Nature Biotechnology 28(10): 1057-1068; Feinberg et al., 2007. "Phenotypic plasticity and the epigenetics of human disease, " Nature 447:433-40). Environmental factors and lifestyle factors can modify the epigenome and in some cases lead to gene dysregulation and disease (Lu a et al., 2006. "Epigenetics, disease, and therapeutic interventions, " Ageing Research Reviews 5:449-467; Mann et al., 2004. "Selective loss of imprinting in the placenta following preimplantation development in culture, " Development, 131 :3727-3735; Heijmans et al, 2009. "The epigenome: Archive of the prenatal environment, " Epigenetics 4:526-531; Grolleau- Julius et al, 2010. "The role of epigenetics in aging and autoimmunity, " Clin Rev Allergy Immunol 39(l):42-50. In a pathogenic state, the epigenetic changes in a cell become stable or permanent, leading to chronic aberrant or over-expression of genes that mediate the pathogenesis of certain diseases such as RA (Ospelt et al., 2011. "Inflammatory memories: Is epigenetics the missing link to persistent stromal cell activation in rheumatoid arthritis?" Autoimmunity Reviews 10:519-524). Abnormalities in DNA methylation patterns have been described in many diseases; most notably cancer, where increased or decreased methylation of CpG loci can alter oncogene or signaling gene expression (Sharma et al, 2010. "Epigenetics in cancer, " Carcinogenesis 31 :27-36). Autoimmunity has also been associated with abnormal methylation in RA synovium, and possibly RA synoviocytes (Jungel et al. 2010. "What can we learn from epigenetics in the year 2009? Curr Opin Rheumatol. 22:284-92; Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526). The mechanisms responsible, the downstream consequences, and the regulation of methylation in inflammatory arthritis are not well defined. However, aberrant epigenetic modifications, especially DNA methylation, may play an important role in the pathogenesis of RA, suggesting that multiplexed methylation biomarkers could be developed as a valuable diagnostic tool (Laird, 2003. "The power and the promise of DNA methylation markers, " Nature Rev. Cancer 3:253-266). The DNA methylation signatures within cells are considered to be a novel and important source of biomarkers to better diagnose RA and other autoimmune diseases (Brooks et al., 2010. "Epigenetics and autoimmunity. Journal of Autoimmunity; 34:J207-J219; Huber et al., 2007. "Epigenetics in Inflammatory Rheumatic Diseases, " Arthritis & Rheumatism 56;3523-353; Richardson, 2003. "DNA methylation and autoimmune disease, " Clin Immunol. 109:72-9; Richardson, 2007. "Primer: epigenetics of autoimmunity, " Nature Clin Practice Rheum 3(9):521-527; Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526). DNA methylation signatures are a more chemically and biologically stable source of molecular diagnostic information compared to RNA and many proteins. They reflect past environmental influences leading to persistent changes in cellular transcription and function with consequences for disease risk, diagnosis, prognosis, and potential response to therapy. The prevalence of DNA methylation biomarkers is higher than most genetic markers of disease, can be associated with multiple loci within a cell potentially affecting several genes or other regulatory molecules (Laird, 2003. "The power and the promise of DNA methylation markers, " Nature Rev. Cancer 3:253-266), and can be detected with very high sensitivity and specificity, including blood-based tests, making methylation biomarkers for RA attractive for a clinical diagnostic laboratory (Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526).
[0011] Epigenetic mechanisms (DNA Methylation) play a fundamental role in the etiology of autoimmune diseases by modulating the methylation state and transcriptional activity of critical genes that affect immune maturation and function that lead to the development of autoimmunity. The identification of the key differentially methylated loci (DML) in RA PBMCs and cell subsets serve as novel biomarkers for RA diagnostics compared to other autoimmune and arthritic diseases. [0012] DML have been identified and studied in human samples (Shoemaker et al, 2011. "Mediators and dynamics ofDNA methylation, " Wiley Interdiscip Rev Syst Biol Med. 3(3):281-98; Lister et al, 2009. "Human DNA methylomes at base resolution show widespread epigenomic differences, " Nature 462(7271):315-22; Deng et al., 2009. "Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming, " Nat Biotechnol. 27(4):353-60; Stark et al, 2011. "The BioGRID Interaction Database: 2011 update, " Nucleic Acids Res. 39:D698-704; Szklarczyk et al., 2011. "The STRING database in 2011 : functional interaction networks of proteins, globally integrated and scored, " Nucleic Acids Res. 39:D561-8). A diagnostic model using DML has been developed for RA that outperforms current standard serological tests (Nishimura et al, 2007. "Meta-analysis: Diagnostic Accuracy of Anti-Cyclic Citrullinated Peptide Antibody and Rheumatoid Factor for Rheumatoid Arthritis, " Ann Intern Med. 146:797-808; Aggarwal et al, 2009. "Anti-citrullinated peptide antibody assays and their role in the diagnosis of rheumatoid arthritis, " Arthritis Rheum. 61(11): 1472-1483) with a minimum of 80% sensitivity and 90% specificity.
[0013] However, there is currently no clinically reliable, cost-effective test to correctly diagnose or predict outcome in a patient diagnosed with RA.
SUMMARY OF THE INVENTION
[0014] Disclosed herein are methods, reagents, and kits helpful for the diagnosis of rheumatoid arthritis. In some embodiments, the methods, reagents and kits comprise one or more panels of DML that may be used to distinguish rheumatoid arthritis (RA) from osteoarthritis (OA), systemic lupus erythematosus (SLE), other autoimmune diseases, other rheumatic diseases, or normal healthy control (HC) patients.
[0015] Panels of DML may comprise three or more DML, and may comprise one or more DML selected from the following Tables. In each table the following data are provided: the position of the DML; identity of any associated gene; the sample source from which a DML was identified; and the condition corresponding to the sample with which an RA sample was compared to identify the DML is indicated. The sample sources are PBMCs, T-cells, B-cells and Monocytes. DML were identified by comparing RA sample methylation patters with those of SLE samples, OA samples, or healthy control (HC) samples, individually or in combination, and a larger "not RA" category that includes samples taken from individuals having a number of autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
[0016] Tables 1A, IB, 2A, 2B, 3A and 3B disclose DMLs corresponding to methylation sites at which the inventors have discovered a diagnostically relevant association between methylation status and RA status.
[0017] Table 1A and IB. DML reported in Tables 1A and IB identify loci corresponding to sites for which a previously-reported association between methylation status and RA exists, but which were independently identified and reported herein. Importantly, the list of sites for which a previously-reported association between methylation status and RA exists is substantially greater than the list of DML in Table 1. That is, Tables 1A and IB represent a specific subset of DML which, although previously reported as methylation sites related to RA, have been affirmed herein to have a diagnostic value not uniformly present in RA-associated sites reported in the literature.
[0018] Tables 2 A and 2B. DML reported in Tables 2 A and 2B identify loci for which no previous association between methylation status at the listed sites and RA was reported, and for which no previous association between the associated loci and RA was reported. That is, Tables 2A and 2B report novel DML that identify novel loci in the context of RA.
[0019] Tables 3A and 3B. DML reported in Tables 3A and 3B identify loci for which no previous association between methylation status at the listed sites and RA was reported, but for which a previous association between the associated loci and RA has been reported.
[0020] Panels comprising DML selected at random from Tables 1A-3B have been generated and are reported herein to demonstrate performance characteristics substantially above the performance characteristics of randomly selected panels of methylation sites that are not known to be differentially methylated in the context of RA. Accordingly, a randomly selected panel of DML from any of Tables 1A, IB, 2A, 2B, 3A and 3B will substantially outperform a random panel of DML not known to be implicated in RA diagnosis in an assay for the presence of an RA methylation signature in an individual.
[0021] Table 4. DML reported in Table 4 represent a subset of the DML reported in Tables 1A, IB, 2A, 2B, 3A, 3B, above that most robustly discriminate RA from other conditions ("not RA"). DML listed in Table 4 have been cross-validated across data sets. Table 4 DML are observed in some embodiments to contribute to panels having performance characteristics substantially above the performance characteristics of randomly selected panels of loci selected from one or more of Tables 1A, IB, 2A, 2B, 3A and 3B, which in turn have performance characteristics substantially above the performance characteristics of randomly selected panels of loci not associated with RA diagnosis.
[0022] Tables 1A, 2 A, and 3 A were generated from DML identified from analysis of PBMC samples from 39 patients (13 RA, 11 SLE, 10 OA, and 5 HC patients), and T-cell, B-cell, and Monocyte DML were generated from 23 patients (7 RA, 5 SLE, 6 OA, and 5 HC). These samples came from a single source in the US.
[0023] Tables IB, 2B, and 3B, were generated from DML identified from analysis of PBMC samples from 937 patients (431 RA, 32 SLE, 13 OA, 371 HC, 48 autoimmune and rheumatic diseases, and 42 other). These samples came from 15 sources worldwide.
[0024] Methods, reagents, kits, and product combinations disclosed herein concern the use of DML panels in sample assessment for a disease status such as RA disease status. In some embodiments, panels may comprise from one to hundreds of DML, such as the DML listed herein, and may further comprise other DML and other non-DML indicia of disease status, such as single nucleotide polymorphisms, other alleles, transcript accumulation levels, protein accumulation levels or activities, antibody levels, clinical data or other data relevant to the assessment of an individual or a sample from an individual regarding RA status. In some embodiments the assessment involves steps performed on a computer to analyze large arrays of data, such as data related to DML methylation levels for one or more than one sample.
[0025] In some embodiments, a method of characterizing a potential autoimmune disease in a subject is disclosed. In some embodiments a method comprises ascertaining the methylation status of a panel comprising at least 3 differentially- methylated loci (DML) in DNA of peripheral blood mononuclear cells (PBMCs) from a mammalian subject. The DML may be differentially methylated in individuals with the autoimmune disease. In some embodiments a method comprises electronically comparing in a computer values reflective of said methylation status of said panel of DMLs with stored information reflective of methylation status of DMLs in at least one standard population, generating a report based on the comparison relative to the potential autoimmune disease; and providing the report to a caregiver or to a subject; wherein the at least 3 DML are selected from the DML listed. In some aspects of these embodiments the autoimmune disease is RA. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from PBMCs of said subject. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from circulating cells of a subject comprising PBMC cells. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of said subject comprising PBMC DNA.
[0026] In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of a subject. In some aspects of these embodiments the ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from T-cells of a subject. In some aspects of these embodiments ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from B-cells of said subject. In some aspects of these embodiments ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from monocytes of said subject. In some aspects of these embodiments an ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from whole blood of said subject.
[0027] In some aspects of these embodiments a laboratory analysis comprises chemical treatment of DNA extracted from said sample that differentially affects methylated and unmethylated bases. In some aspects of these embodiments the treatment comprises bisulfite treatment.
[0028] In some aspects of these embodiments the fragments comprise 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb on either side of DML.
[0029] In some aspects of these embodiments the laboratory analysis further comprises contacting said amplified DNA with a reagent that distinguishes between bisulfite-treated methylated and bisulfite -treated unmethylated DNA. In some aspects of these embodiments the reagent is an oligonucleotide probe.
[0030] In some aspects of these embodiments the reagent is a protein that differentially binds DNA according to its methylation status. [0031] In some aspects of these embodiments the panel comprises at least 1, at least 2, at least 3, at least 4, at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24 25, 26, 27, 28, 29, 30, 31, 32 33, 34, 35, 36 37, 38, 39, 40 41, 42, 43, 44,
45, 46, 47, 48 49, 50, 51, 52, 53, 54, 55, 56 57, 58, 59, 60 61, 62, 63, 64 65, 66, 67, 68, 69, 70, 71, 72 73, 74, 75, 76, 77, 78, 79, 80 81, 82, 83, 84 85, 86, 87, 88 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,
116, 117, 118, 1 1 128, 129, 134, 135, 136, 13 146, 147, 152, 153, 154, 155 164, 165, 170, 171, 172, 173 182, 183, 188, 189, 190, 191 200, 201, 206, 207, 208, 20 218, 219, 224, 225, 226, 22 236, 237, 242, 243, 244, 245 254, 255, 260, 261, 262, 263 272, 273, 278, 279, 280, 281 290, 291, 296, 297, 298, 29 308, 309, 314, 315, 316, 31 326, 327, 332, 333, 334, 335 344, 345, 350, 351, 352, 353 362, 363, 368, 369, 370, 371 380, 381, 386, 387, 388, 38 398, 399, 403, 404, 405, 40 415, 416, 421, 422, 423, 42 433, 434, 439, 440, 441, 44 451, 452, 457, 458, 459, 46 469, 470, 475, 476, 477, 47
Figure imgf000014_0002
487, 488,
Figure imgf000014_0001
493, 494, 495, 496, 497, 498, 499, 500, or more than 500 DML.
[0032] In some aspects of these embodiments a standard population comprises individuals not having said autoimmune disease, or having said autoimmune disease.
[0033] In some aspects of these embodiments the standard populations comprise individuals with RA, OA, SLE, HC, or a collection of rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
[0034] In some aspects of these embodiments the ascertaining step further comprises ascertaining values reflective of one or more additional non-DML characteristics of the subject, and wherein said electronically comparing step further comprises comparing those non-DML values with non-DML values from one or more standard populations in a computer.
[0035] In some aspects of these embodiments the non-DML values are selected from the group consisting of: SNP or gene variation status, levels of autoantibodies such as anti-dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
[0036] In some embodiments method for detecting methylation events is disclosed.
[0037] In some aspects of these embodiments the methylation events are detected at loci set forth in Tables 1A, IB, 2A, 2B, 3A, 3B or 4 in this disclosure. In some aspects of these embodiments the method comprises subjecting a sample from a human individual comprising DNA to treatment that differentially affects methylated bases of said human sample, and ascertaining the extent of methylation of a panel of loci, wherein a plurality of said loci are listed in one or more of Tables 1A, IB, 2A, 2B, 3A, 3B and 4 .
[0038] In some aspects of these embodiments the sample comprises circulating DNA, DNA from circulating blood cells, or comprises DNA from PBMCs or from whole blood. In some aspects of these embodiments the sample comprises B-cell DNA, T-cell DNA, or Monocyte DNA, or DNA selected from the list of DNA sources consisting of T-cell DNA, B-cell DNA and monocyte DNA.
[0039] In some aspects of these embodiments the method further comprises comparing the methylation status of the loci of the panel with methylation status indicative of RA, OA, HC, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or and HC individuals. In some aspects of these embodiments the treatment comprises contacting said locus with bisulfite. In some aspects of these embodiments the panel comprises at least 5, 10, 20, 50, 200, 250 or more than 250 loci. [0040] In some aspects of these embodiments the method further comprises determining the status of one or more of the traits from the individual selected from the list comprising: SNP or gene variation status, levels of auto-antibodies such as anti- dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels, inflammatory molecules and miRNA levels.
[0041] In some embodiments a method is disclosed of diagnosis of a disorder in a mammalian subject comprising the steps of: isolating PBMCs from a patient; determining an accumulation level of transcripts from at least two genes identified from said PBMCs; and diagnosing whether the patient has a disorder based on said determination. In some embodiments the panel comprises at least two genes associated with DML of Tables 1A, IB, 2A, 2B, 3A, and 3B, and optionally also listed in Table 4.
[0042] In some aspects of these embodiments the gene is within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in a table above. In some aspects of these embodiments a PBMC comprises at least on cell selected from the list of cells consisting of T-cells, B-cells and monocytes.
[0043] In some aspects of these embodiments accumulation levels of a panel of transcripts are determined, such as a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 1 15, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, or more than 500 transcripts. In some aspects of these embodiments the method involves oligonucleotides to detect transcript accumulation levels.
[0044] In some aspects of these embodiments the oligonucleotides anneal within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Table 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
[0045] In some aspects of these embodiments the method involves comparing the accumulation levels to those of corresponding transcripts in a cell of an individual or population not suffering from RA, OA, SLE, HC individuals, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals.
[0046] In some embodiments a method is disclosed of diagnosis of a disorder in a mammalian subject comprising the steps of: isolating at least one circulating cell from a patient; determining a protein accumulation level or activity level of proteins from genes identified from said at least one cell; and diagnosing whether the patient has a disorder based on said determination; wherein said genes are genes associated with DML in one or more of Tables 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4; and wherein said disorder is RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis. In some aspects of these embodiments at least one circulating cells is a PBMC. In some aspects of these embodiments at least one circulating cells is a B-cell, T-cell or Monocyte. [0047] In some aspects of these embodiments the circulating cells comprise PBMCs. In some aspects of these embodiments the said gene is within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Table 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
[0048] In some aspects of these embodiments the accumulation levels or activity levels of a panel of proteins are determined, such as a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
Figure imgf000018_0001
498 499, 500, or more than 500 proteins. In some aspects of these embodiments the method involves comparing the accumulation levels or activities to those of corresponding transcripts in a cell of an individual or population not suffering from RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or from an individual or population suffering from RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis. In some aspects of these embodiments the detection comprises differential antibody binding.
[0049] In some embodiments a method is disclosed of evaluation of differential methylation in a subject comprising: (a) determining the extent of methylation at a plurality of DNA loci selected from the loci in the tables above in a sample comprising PBMC DNA taken from the subject; (b) evaluating values reflective of the extent of methylation at said loci; and (c) providing a report based on the evaluation of step (b).
[0050] In some aspects of these embodiments the evaluating step comprises processing values reflective of methylation at said loci in a computer and comparing said processed values to values known to be reflective of an autoimmune disorder status.
[0051] In some aspects of these embodiments the report further discusses a treatment regimen for said autoimmune disorder based on said evaluating step.
[0052] In some aspects of these embodiments the loci comprise a panel of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, or more than 500 loci.
[0053] In some embodiments a set of PCR primers capable of amplifying loci of human chromosomal DNA in a PCR reaction are disclosed. In some aspects of these embodiments the loci are selected from the DML identified in the tables above.
[0054] In some aspects of these embodiments the loci comprise DNA within 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 500 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb or more than 10 kb from a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B below, and optionally also listed in Table 4.
[0055] In some embodiments a kit for the diagnosis of a disorder selected from the group of disorders consisting of RA, OA, SLE, or other rheumatic diseases and other autoimmune diseases in a mammalian subject comprising a plurality of DNA reagents is disclosed. The reagents may be capable of distinguishing between methylated and unmethylated DNA from loci listed in the Tables above upon subjecting said DNA to a treatment that differentially affects methylated bases.
[0056] In some aspects of these embodiments the reagents comprise oligonucleotides. In some aspects of these embodiments the treatment is a chemical modification. In some aspects of these embodiments the treatment comprises bisulfite mapping. In some aspects of these embodiments the kit comprises a plurality of different reagents, each capable of distinguishing between methylated and unmethylated DNA at a respective locus listed in the Tables above. [0057] In some embodiments an isolated DNA molecule having a sequence spanning a DML of a Table above is disclosed. In some embodiments DNA at said DML has been chemically modified as a result of the presence of methylation at said DML, resulting in a detectable moiety reflective of methylation at said DML.
[0058] In some aspects of these embodiments the DNA molecule has a sequence which anticipates the sequence of the vicinity of a DML of a Table above upon chemical modification to identify methylation status. In some aspects, the modified form is an expected product of a reaction whereby an isolated DNA molecule mentioned above having a methylation signature characteristic of a disorder selected from the list of disorders consisting of RA, OA, SLE, or other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis in DNA isolated from blood is subjected to treatment that differentially affects methylated bases.
[0059] In some aspects of these embodiments the DNA isolated from blood is isolated from at least one PBMC cell. In some aspects of these embodiments the PBMC is a T-cell, a B-cell or a monocyte.
[0060] In some aspects of these embodiments the treatment comprises contacting said isolated DNA molecule with bisulfite. In some aspects of these embodiments the molecule comprises at least 14 bases.
[0061] Some embodiments comprise a panel of different DNA molecules mentioned above.
[0062] In some aspects of these embodiments treatment of the molecules comprises contact with bisulfite. In some aspects of these embodiments the panel comprises of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, or more than 500 molecules.
[0063] In some embodiments a method is disclosed of treating a patient with symptoms of RA comprising: ascertaining the methylation status of loci of the patient's DNA, wherein the loci are selected from the loci listed in the Tables above; ascertaining that the loci are differentially methylated consistent with RA; selecting an autoimmune disorder treatment from among available treatment options; and treating the patient for said autoimmune disorder. In some aspects of these embodiments the panel comprises 1 , 2, 3, 4, 5, 10, 20, 50, 200, 250 or more than 250 loci. In some aspects of these embodiments the treatment alters the methylation status of loci in said panel. In some aspects of these embodiments the said treatment affects the activity of gene products of loci listed in said panel or the genes regulated by methylation of the loci in said panel.
[0064] In some embodiments a method is disclosed of developing an assay for the detection of a methylation profile comprising the steps of: selecting a plurality of DML from the DML listed in the Tables above; analyzing with a computer the extent of methylation at said loci; and ascertaining a methylation pattern at said loci that correlates with a positive diagnosis indicative of a status of an autoimmune disorder selected from the list comprising RA, OA, SLE, or other rheumatic diseases or other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
BRIEF DESCRIPTION OF THE DRAWINGS
[0065] Figures 1A-D: Diagnostic Error Rate versus Number of DML included. A sliding window moved along a list of 51 CpGs and the diagnostic accuracy of the CpGs captured in each window was measured using leave-one-out cross validation. The size of the window corresponded to the diagnostic panel size, which was 1, 2, 3, 5, 10 or 25 CpGs. Leave-one-out cross validation involved randomly selecting one sample from each phenotype (i.e., RA, OA, SLE, or HC) and placing it into a test set. The diagnostic model was then trained on the remaining data. Once trained, the model predicted the phenotypes of the test set samples. This process was repeated 100 times for each window. A computer algorithm was used as the diagnostic model. The averaged diagnostic accuracies for each window size were graphed and an error bar represents a single standard deviation of diagnostic error.
[0066] Figure 1 A. Diagnostic Error Rate versus number of DML Included for B-cell DML.
[0067] Figure IB. Diagnostic Error Rate versus number of DML Included for T-cell DML.
[0068] Figure 1C. Diagnostic Error Rate versus number of DML Included for Monocyte DML.
[0069] Figure ID. Diagnostic Error Rate versus number of DML Included for PBMC DML.
[0070] Figures 2A-B. Larger DML panels have lower error rates. Typical 10- member and 25 -member DML panels from the analysis above were selected for presentation. The two 25-membered DML panels shown have error rates, specificities and sensitivities substantially improved over those of typical 10-member panels.
[0071] Figure 2A presents error rates, sensitivity and specificity for a selection of 10-member DML panels.
[0072] Figure 2B presents error rates, sensitivity and specificity for a selection of 25-member DML panels.
[0073] Figure 3 presents True Positive Rates as a function of False Positive Rates for a Randomly Selected DML panel, a ranked DML panel selected from Tables 2A and 2B ("Enriched Panel"), and a ranked DML panel selected from Table 4 ("Optimized Panel"). The Randomly Selected DML panel shows an approximately equal True Positive and False Positive rate, while both the Enriched Panel, and, even more so, the Optimized Panel, are skewed towards identification of True Positives.
DETAILED DESCRIPTION
[0074] The methods, DML panels, associated gene panels and other material disclosed herein provide a novel means for the diagnosis of an autoimmune disorder such as RA. In the following detailed description, illustrative embodiments are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the spirit or scope of the subject matter presented here. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the Figures, can be arranged, substituted, combined, and designed in a wide variety of different configurations, all of which are explicitly contemplated and make part of this disclosure.
[0075] A minimally-invasive blood-based RA diagnostic is desired for RA diagnostic tests to rule in RA definitively and to rule out other conditions which have arthritic symptoms (e.g., OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.). A study of RA/OA/SLE/HC patients conducted using peripheral blood mononuclear cells (PBMCs) and enriched PBMC subsets performed to assess the potential of a blood-based RA diagnostic test identified new RA associated DML, demonstrating an RA methylation signature in blood unique from that identified in FLS (Nakano et al., 2012. "DNA methylome signature in rheumatoid arthritis, " Ann Rheum Dis. doi: 10.1136/annrheumdis-2012-201526). Bioinformatics and computational algorithms have been used to determine the strongest methylation signature set that most accurately identifies RA phenotypes from either any circulating nucleic acid or nucleic acid reservoir including those isolated from the blood of a human subject, such as PBMC samples or from more homogeneous PBMC subsets.
[0076] Embodiments of the present disclosure involve panels of DML. Said DML were obtained by determining methylation patterns of Whole blood, PBMCs, T- cells, B-cells and Monocytes derived from individuals suffering from RA, OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis or from HC individuals suffering from none of the above ailments or disorders, and comparing these methylation patterns to identify DML relevant to distinguishing each disease class.
[0077] The additional statistical power from PBMC subsets has allowed for the identification of significantly differentially methylated CpGs and allowed a more confident assessment of the RA methylation signature in PBMCs and PBMC subsets such as T-cells, B-cells and Monocytes.
[0078] To identify the strongest DMLs for multiplex panel development and to align the blood-based RA methylation signature to RA pathogenesis, the methylation signatures of whole blood, isolated PBMCs, T-cells, B-cells, and monocytes from RA, OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC patient PBMC samples were investigated.
Determining Methylation Patterns
[0079] It is one aspect of many embodiments of the present invention that methylation patterns, particularly 5-methylcytosine methylation patterns, of the nucleic acids of certain cells or cell populations, or other DNA reservoirs may be determined. A number of methods for the determination of cytosine methylation status are known to one of skill in the art. For example, bisulfite mapping may be used. Through this process, extracted DNA is treated with a bisulfite as part of a process that differentially converts cytosine unmethylated at the C5 position to uracil, while leaving 5 -methyl cytosine unaffected. Other methods for the determination of methylation status at one or more cytosine positions are also known in the art, and embodiments disclosed herein are not limited to any particular method of determining methylation status at a particular locus to the exclusion of any other method.
[0080] In some embodiments an array such as an ILLUMINA HumanMethylation 450 BeadChip may be used to determine a methylation status (Sandoval, et al., (2011) Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 6:6, 692-702). In some embodiments, the sequencing method may comprise one or more technologies such as pyrosequencing, e.g., 'the '454' method (Margulies et al., (2005) Genome sequencing in microfabricated high- density picolitre reactors. Nature 437:376-380; Ronaghi, et al. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem. 242:84-89), 'Solexa' or Illumina-type sequencing (Fedurco et al, (2006), BTA, a novel reagent for DNA attachment of glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acid Research 34, e22; Turcatti et al. (2008), A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acid Research 36, e25), SOLiD sequencing technology (Shendure, J. et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732; McKernan, K. et al, (2006) Reagents, methods, and libraries for bead-based sequencing. US patent application 20080003571), Heliscope Technology (Harris, T.D. et al. (2008) Single-molecule DNA sequencing of a viral genome. Science 320, 106-109), Ion Torrent Technology (Rothberg et al, (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-352), SMRT Sequencing Technology (Pacific Biosciences; http://www.pacificbiosciences.com/ products/smrt-technology/), or GridlON nanopore- based sequencing (Oxford Nanopore Technologies; http://www.nanoporetech.com/technology/the-gridion-systern/the-gridion-system). In some embodiments any number of so-called 'next generation' DNA sequencing methods may be used, as described in Shendure and Ji, 'Next-generation DNA sequencing" , Nature Biotechnology 26(10): 1135-1145 (2008) or in other art available to one of skill in the art. Other methods for the determination of DNA sequence are also known in the art, and embodiments disclosed herein are not limited to any particular method of determining base identity at a particular locus to the exclusion of any other method.
[0081] In some embodiments, methods for assaying the methylation status, particularly the 5 -methyl cytosine methylation status, at one or more loci may include randomly shearing or fragmenting genomic DNA, cutting with a methylation-dependent or methylation sensitive restriction endonuclease, of which many are known to one of skill in the art, and analyzing the resultant DNA fragments. In some embodiments analysis may involve amplification of nucleic acids. In some embodiments this amplification can be performed using gene or locus specific primers, or using primers specific to, for example, adapters that may be added to the ends of fragmented DNA. In some embodiments, the DNA may be amplified using a quantitative PCR protocol, such as one that allows for real time quantification of amplification products. See, e.g., U.S. Patent No. 7,186,512; U.S. Patent Application Ser. Nos. 10/971,986; 11/071,013; and 10/971,339; U.S. Pat. Nos. 6,180,349; 6,033,854; and 5,972,602, Gibson et al, "A novel method for real time quantitative RT-PCR, " Genome Research 6:995-1001 (1996); DeGraves, et al., "High-sensitivity quantitative PCR platform," Biotechniques 34(1): 106- 10, 112-5 (2003); and Deiman B., et al., "Characteristics and applications of nucleic acid sequence-based amplification (NASBA)," Mol. Biotechnol. 20(2):163-79 (2002). In some embodiments, methods for detecting DNA methylation may involve genomic sequencing before and after treatment that differentially affects methylated bases. See, e.g., Frommer et al., (1992) "A genomic sequencing protocol that yields a positive display of 5- methylcytosine residues in individual DNA strands, " Proc. Natl. Acad. Sci. USA 89: 1827-1831. Additional methylation detection methods include methods described in, for example, the following references: Toyota et al, "Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification,'" Cancer Res. 59:2307-12 (1999), U.S. Patent Publication 2005/0069879; Rein, et al. "Identifying 5-methylcytosine and related modifications in DNA genomes," Nucleic Acids Res. 26 (10): 2255-64 (1998); Olek, et al. "The pre-implantation ontogeny of the H19 methylation imprint " Nat. Genet. 17(3): 275-6 (1997); and PCT Publication No. WO 00/70090.; Herman et al., "Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands," (1996) Proc. Natl. Acad. Sci. USA 93:9821-9826; U.S. Pat. No. 5,786,146; Gonzalgo & Jones, "Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE)," Nucleic Acids Res. 25:2529-2531 (1997).
[0082] There are a number of ways known in the art in which a methylation assay may be run to obtain data for use in some embodiments. One set of methods are predicated upon methylation-specific changes in hybridization efficiency that result from bisulfite treatment. For example, a PCR primer that specifically anneals to a differentially methylated site may be used in a PCR amplification reaction wherein the amplification efficiency is dependent upon either the methylation status or the identity of the base following bisulfite treatment. By comparing the amplification efficiency of treated versus untreated DNA templates, or by comparing amplification directed by a treated template as compared to a treated, unmethylated control template sequence, one may be able to determine the methylation status of the differentially methylated locus in the primer annealing region. Amplification efficiency may be assayed by the generation of a signal, such as light, in proportion to the concentration of double-stranded DNA during the course of a PCR reaction. Alternately, a signal may be generated by the binding of an oligonucleotide probe, such as a labeled probe, to a region spanning a differentially methylated site of interest. [0083] Alternate methods of assaying for the outcome of bisulfite treatment on a sample may be used. For example, chemical differences between methylated and unmethylated DNA that manifest themselves after bisulfite treatment may be indicative of substrate sequence after bisulfite treatment and, by inference, methylation status before treatment. One such difference, the melting temperature of a double-stranded DNA molecule, may be assayed using, for example, high-resolution melt analysis using techniques known in the art (White HE, et ah, 2007. "Methylation sensitive high resolution melt curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes, " Clin Chem. 2007 Nov; 53(11): 1960-2; Dahl C. and Guldberg P. 2007. "High-resolution melting for accurate assessment of DNA methylation, " Clin Chem. 2007 Nov; 53(11) 1877-1878 ).
[0084] Methods which do not rely upon bisulfite treatment may also be used, such as chromatographic, biological, or spectrographic means. DNA to be assayed may, for example, be contacted with proteins that preferentially bind methylated or unmethylated sequences (e.g., methyl binding domain [MBD] binding proteins such as MECP2, MBD1, MBD2, MBD3, and MBD4, other methylation-distinguishing proteins, or antibodies such as MeDIP). See, e.g., Nair et al, (2011) "Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture or genome-wide DNA methylation analysis reveal CpG sequence coverage bias," Epigenetics 6(l):34-44. Measurement of signals, such as light, that correspond to quantities of isolated methylated or unmethylated sequences may be used to assay methylation status of the assayed DNA sequence.
[0085] DNA sequences may be sequenced directly, either after bisulfite treatment or after methylation-based separation as discussed above. Any of the sequencing methods known in the art may be used, including those mentioned above. Embodiments are not limited by the sequencing method used, and sequencing innovations may be incorporated into various embodiments as the sequencing innovations become available to those of skill in the art.
[0086] Sequencing methods which assay for methylation directly on input sequences may also be used. For example, measurable transcription rate changes may be used to determine methylation status at specific bases (e.g., single molecule real time (SMRT) sequencing), or spectrographic or electric field measurements may be used to discriminate between methylated and unmethylated bases during single molecule sequencing such as nanopore sequencing. [0087] Sequencing methods may target individual methylation sites or loci to assay. Targeted regions may be amplified or preserved in processes that degrade sequences not of interest. Alternately, methylation sites of interest may be sequenced as part of whole-genome sequencing efforts whereby all or substantially all sequence information in a DNA sample is determined.
[0088] DNA to be analyzed may be obtained from a number of sources. In some embodiments, DNA may be obtained from any circulating nucleic acid or nucleic acid reservoir including those isolated from the blood of a human subject. In some embodiments the sample from which DNA is to be assayed is whole blood. In some embodiments the cell population from which DNA is to be assayed is a whole blood cell population. In some embodiments the cell population from which DNA is to be assayed is peripheral blood mononuclear cells (PBMCs). In some embodiments the cell population is selected from a group comprising T-cells, B-cells and monocytes. In some embodiments the cell population from which DNA is to be assayed is a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) or a subset of monocytes (such as Ml and M2 monocytes and dendritic cells) [see Littman and Rudensky (2010) Thl 7 and regulating T- cells in mediating and restraining inflammation. Cell 140:845-858; Lo and Tsokos (2011) T- cells in Systemic Lupus Erythematosus. The Rheumatologists; Allman and Pillai (2008) Peripheral B- cell subsets. Curr. Opin. Immunol. 20(2): 149-157. Gordon and Taylor (2005) Monocyte and macrophage heterogeneity. Nat. Rev. Immunol. 5:953-964; MacDonald et al.(2002) Characterization of human blood dendritic cell subsets. Blood 100(13):4512-4520]. Cells from any of these groups may be obtained using any of a number of methods known to those of skill in the art (see, e.g., Mallone et al, (2011) Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T- cell responses: position statement of the T-Cell Workshop Committee of the Immunology of Diabetes Society. Clin. Exp. Immunol. 163(l):33-49). Embodiments disclosed herein are not limited to any particular method of cell or DNA isolation method to the exclusion of any other.
[0089] DNA may be extracted from cells using any of a number of methods known in the art. The DNA extraction method will preferably substantially preserve the methylation pattern of the extracted DNA and yield DNA of a purity and integrity suitable for downstream analysis, but is not otherwise limited. If peripheral blood mononuclear cells are used as a DNA source, the extraction method should be appropriate to these cells. Alternately, free circulating DNA from, for example, the blood, urine, other body fluid, or other tissue of a patient may be used as a sample source.
[0090] In some embodiments, methylation patterns determined for one or more of the above cell populations may be compared to methylation patterns determined from similar cell types in one or more individuals with a known autoimmune disorder status, or from one or more different cell populations taken from the same or different individuals compared to the individual to be diagnosed.
[0091] In some embodiments an increase or decrease in the methylation state of loci from a cell or population of cells of an individual to be diagnosed may be indicative of that individual's autoimmune disorder status. In some embodiments, the methylation status of loci from a cell or population of cells of an individual to be diagnosed may be determined and then normalized to the methylation status of a control locus to control for error in detection methods that may otherwise impact a diagnosis as to the presence or absence of an autoimmune disorder. Appropriate control loci or control techniques are known to one of skill in the art.
[0092] In some embodiments, the methylation patterns may be deduced by determining the methylation status, for example the presence of 5-methyl cytosine, of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 1000, 2000, 3000, 4000, or more than 4000 methylation sites. Isolation of Cell Populations
[0093] A number of cell isolation protocols are contemplated in the present disclosure, and the subject matter does not require that any single cell isolation protocol be used to the exclusion of others. The methylation status at DML disclosed herein may be assayed in cells isolated by these or other cell isolation protocols.
[0094] In a preferred embodiment, cell populations may be isolated as follows. Approximately 10 ml of blood is obtained from a patient. PBMCs are purified from whole blood using standard Ficoll gradient centrifugation (Ruitenberg JJ, Mulder CB, Maino VC, Landay AL, Ghanekar SA. "VACUTAINER CPT and Ficoll density gradient separation perform equivalently in maintaining the quality and function of PBMC from HIV seropositive blood samples." BMC Immunol. 2006; 7: 11). Some embodiments additionally include a purification by Percoll gradient (Gutierrez C, Bernabe RR, Vega J, Kreisler M. "Purification of human T and B- cells by a discontinuous density gradient of percoll." J Immunol Methods. 1979; 29(l):57-63). In some embodiments the PBMCs are further enriched for T-Cells, B-cells, and monocytes by magnetic beads with biotinylated monoclonal antibodies towards human cell surface markers (anti-huCD4, huCD19 and huCD68 or other appropriate CD-markers or other cytokine receptors) as described (Vallee I, Guillaumin JM, Thibault G, Gruel Y, Lebranchu Y, Bardos P, Watier H. "Human T lymphocyte proliferative response to resting porcine endothelial cells results from an HLA-restricted, IL-10-sensitive, indirect presentation pathway but also depends on endothelial-specific costimulatory factors." J Immunol. 1998 Aug 15;161(4): 1652-8; Lea T, Vartdal F, Nustad K, Funderud S, Berge
A, Ellingsen T, Schmid R, Stenstad P, Ugelstad J. "Monosized, magnetic polymer particles: their use in separation of cells and subcellular components, and in the study of lymphocyte function in vitro." J Mol Recognit. 1988 Feb;l(l):9-18; Funderud S, Erikstein
B, Asheim HC, Nustad K, Stokke T, Blomhoff HK, Holte H, Smeland EB. "Functional properties of CD19+ B lymphocytes positively selected from buffy coats by immunomagnetic separation." Eur J Immunol. 1990 Jan;20(l):201-6).
[0095] Other embodiments of cell isolation protocols consistent with the present disclosure are described in the following references: Neurauter AA, Bonyhadi M, Lien E, Nokleby L, Ruud E, Camacho S, Aarvak T. "Cell isolation and expansion using Dynabeads" Adv Biochem Eng Biotechnol. 2007;106:41-73; Bildirici L, Rickwood D. "An investigation into the suitability of silica beads for cell separations based on density perturbation." J Immunol Methods. 2001 Jun l;252(l-2):57-62; S. Farzana Hussain, David Yang, Dima Suki, Kenneth Aldape, Elizabeth Grimm and Amy B. Heimberger. "The role of human glioma-infiltrating microglia/macrophages in mediating antitumor immune responses." Neuro. Oncol. (July 2006) 8 (3): 261-279.
[0096] Some samples require no cell isolation prior to downstream sample processing such as DNA extraction. For example, some whole blood samples are used to extract total nucleic acids from all cell sources and from extracellular sources, such as free circulating nucleic acids as well as cellular components of whole blood.
Use of Loci in Connection With Autoimmune Disorders such as RA
[0097] Some embodiments disclosed herein relate to the diagnosis, typing, or prognosis of an autoimmune disorder such as RA in an individual based in part on the methylation status at a set of loci, or a "panel," from a restricted population of cells from that individual. Disclosed herein are Tables of loci provided for the purpose of enabling the diagnosis of RA in an individual. The Tables list Differentially Methylated Loci (hereinafter "DMLs") corresponding to methylation sites at which the inventors have discovered a correlation between extent of status in an isolated cell population such as PBMCs, T Cells, B Cells, Monocytes, or cells from whole blood, and RA status. The cell population of origin from which each DML was identified is indicated in each table as appropriate.
[0098] Given the number of methylation sites reported herein, these data represent a substantial contribution to the understanding of RA above and beyond the utility of these methylation sites as constituents in diagnostic panels in the context of RA diagnosis.
[0099] Loci are sorted into tables as discussed in the summary of the invention, above.
[0100] Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 disclose Differentially Methylated Loci (hereinafter "DML") corresponding to methylation sites at which the inventors have discovered an association between methylation status and disorder status. In some embodiments, a set of loci where methylation status is relevant to an RA, diagnosis relative to OA, SLE, or other rheumatic and autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, or relative to a HC, is selected from among the loci listed in Tables 1A, IB, 2A, 2B, 3A, and 3B, and optionally also listed in Table 4. In some embodiments this set of loci may be additionally supplemented by at least one locus selected from an additional source.
[0101] Throughout the disclosure, reference is occasionally made to Tables
IA, IB, 2A, 2B, 3A, 3B, and/or 4. Table 4 consists of methylation sites which also appear in at least one of Tables 1A, IB, 2A, 2B, 3A, or 3B. Accordingly, reference to "a DML of Tables 1A, IB, 2A, 2B, 3A, 3B, or 4" or "Tables 1A, IB, 2A, 2B, 3A, 3B and 4" is not to be read to indicate that a DML of Table 4 is not also included in one of the preceding Tables 1A, IB, 2A, 2B, 3A, or 3B. Table 4 consists of a subset of DML from tables 1A, IB, 2A, 2B, 3A, or 3B.
[0102] In some embodiments a methylation site or sites listed in Tables 1A,
IB, 2A, 2B, 3A, 3B, and 4 may be used as guides to direct a researcher, medical professional or other interested party to determine the methylation status of loci marked by listed methylation sites. In some embodiments these loci may comprise 20 bp, 40bp, 60bp, 80bp, lOObp, 500bp, lkb, 1.5 kb, 2kb, 2.5kb, 5kb, lOkb, or more than lOkb on either side of methylation sites listed in Table 1A, IB, 2A, 2B, 3A, or 3B, and optionally listed in Table 4.
[0103] We have shown significant association between the differential methylation of loci in Tables 1A, IB, 2A, 2B, 3A, and 3B, and optionally Table 4, and an autoimmune disorder such as RA. The associations and correlations include positive correlations and negative correlations - in other words, at some loci, methylation is associated with a disorder, and at other loci, a lack of methylation is associated with a disorder. At some loci, the extent of methylation is associated or indicative of a disorder. In some embodiments a condition such as RA may be indicated by an extent of methylation of 0%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%.
[0104] Changes at these loci, and patterns of changes at these loci, can help to differentiate between true occurrence of a disorder and many other conditions that have overlapping symptomology. [0105] Methylation status is a matter of degree, wherein some bases at a particular locus will be methylated in one cell and unmethylated in another cell. Thus, a determination of methylation status not only includes ascertaining whether an individual locus on an individual chromosome is methylated, but also can include determining the extent of methylation at that locus across a population of cells. Although methylation status at a single locus has value in diagnosis and prognosis of an autoimmune disorder, combinations of loci have enhanced diagnostic and prognostic value. Thus, various embodiments include assays in which loci in Tables 1A, IB, 2A, 2B, 3A, 3B, and 4 are analyzed, together with one or more additional loci.
[0106] Using multiple loci for a diagnosis or prognosis can significantly enhance both sensitivity and specificity and better characterize a complex disease such as an autoimmune disorder. Figure 1 presents an example wherein combining information from multiple DML produces better performing models than do uncombined data sets. In this figure, DML panels of increasing size show a decrease in diagnostic error. Whereas individual DML show error up to 50% or more, a panel of 25 such DML shows an error below 5% representing a substantial increase in the accuracy and therefore the utility of the test.
[0107] Figure 1 illustrates that the incremental increase in DML panel size leads to an incremental decrease in the error rate. With the increase in panel size, the error rate decreases until the optimal DML panel size is reached.
[0108] Autoimmune diseases such as RA cover many clinical subtypes (e.g., disease stages, severity, organs involved in the pathology) and it is expected that a single locus may not be able to discriminate across these subtypes with acceptable sensitivity and specificity. The multiplex design of the assay is due to the complex nature of the disease and the heterogeneity of disease within the patients.
[0109] Determining and evaluating the methylation status of panels of loci rather than single loci have a number of advantages. For example, an assay that uses a panel detects not only the single loci that may have strong prognostic or diagnostic value in comparing disorder presenting or pre-disorder presenting samples to non-disorder presenting samples, but it also detects the subtle deviations in methylation status at diagnostic loci that may not be individually statistically significant enough to warrant a diagnosis or to justify selection or administration of a course of treatment, but can cumulatively lead to a clear diagnosis of a disorder or a risk of developing a disorder. [0110] Methylation status of a panel of loci from a selected cell type in an individual to be diagnosed may be compared to the methylation status of the same loci of a control individual, control tissue or a composite value derived from analysis of a control population of prior samples. Diagnosis may be based upon the extent of difference in methylation status at individual loci selected from within a panel, or may be based on deviations from the control methylation pattern in the aggregate. Thus, it is possible that a single locus, which shows a great difference in methylation status between a test sample and a control, may be sufficient to diagnose an autoimmune disorder or a risk of an autoimmune disorder. However, in most cases, a single locus will not provide adequate specificity and/or sensitivity. By using a panel of DML rather than an individual locus and evaluating panel results in the aggregate, better sensitivity and specificity can usually be attained. Such a diagnosis may involve noting that a test sample presents a number of loci, which differ in methylation status only subtly, from a control, but where these differences collectively support a diagnosis of a disorder such as RA. Statistical evaluation of the aggregate results of a panel assay may be performed using a complex algorithm and performed on a computer. This may include use of a weighting algorithm in which certain loci are weighted differently than others, or any other algorithm derived from analysis of patient data that gives the desired specificity and sensitivity. By assaying a panel of loci and by evaluating the resulting methylation patterns in the aggregate, one may detect disorder-specific patterns despite the fact that no individual locus demonstrates a methylation status that, evaluated in isolation, would have a desired level of sensitivity and specificity sufficient to warrant a disorder or pre-disorder diagnosis.
[0111] A number of algorithms for combining results from multiple loci to reach a diagnosis may be used. For example, classification models may be used to assign probabilities of phenotypes to samples. Each of these models is considered to be an algorithm and each is known in the art. This list is not limiting; other algorithms may be used to combine the results of multiple loci to reduce noise or improve specificity or sensitivity. The model's input is a list of methylation values at a panel of methylation sites, transcript accumulation levels, or protein accumulation levels or activity levels. In some embodiments, the output is a list of phenotype-specific probabilities. The phenotype with the highest probability is assigned to the sample.
[0112] Regardless of the particular algorithm used, for purposes of this disclosure, such algorithms are considered to compare values reflective of the methylation status of DMLs from a subject, individual, or patient (preferably vertebrate, more preferably mammalian, and more preferably human). Thus, the term "compare" and its variants are used in a broad sense in the context of this disclosure. In "ascertaining" the methylation status of DMLs in the computerized methods, it is not necessary that the same person or organization perform the computerized analysis and analyze a patient sample for DML status. Instead, the term "ascertaining" and its variants simply means getting the data, perhaps from another who performed the methylation analysis.
Selecting DML for Inclusion in a Panel
[0113] A variety of criteria may be used to determine which DML to include in a given panel. A panel may comprise, for example, loci with methylation statuses that are individually strong indicators of an autoimmune disorder or a risk of an autoimmune disorder, for example due to a consistently large difference in methylation status between an individual having an autoimmune disorder and an unaffected individual. Such a panel may be useful when a statistically very strong signal is needed (i.e., a statistical signal that may be generated from loci the methylation status of which differs greatly, such as from near zero to near 1 , in samples from affected or pre-affected cells compared to unaffected controls). A strong signal may be needed, for example, when relatively little starting material is available or when there is reason to believe that a sample may have degraded to some extent.
[0114] In many cases, a panel may advantageously include multiple loci that are not strong indicators of an autoimmune disorder on an individual basis, but which in combination produce a robust indication of (or correlation with) an autoimmune disorder and improve the clinical diagnostic utility.
[0115] In some embodiments, a panel is selected based on population studies that in the aggregate can provide a desired level of sensitivity and specificity over the broad population, so that a single assay can be commercialized that is appropriate for all patients. In some embodiments, assays can be tailored for a particular population based on gender, age, ethnicity, or any other result-effective variable. Thus, there may be a panel of assays from which one may select the assay most appropriate for any particular patient. In some embodiments, a computer can be used to select an appropriate assay based on relevant patient data.
[0116] Methylation sites may also be selected for inclusion or exclusion based on criteria other than those above. For example, loci may be selected based in part on the degree of allelic variation at the site or in the immediate region of an identified methylation site. The presence of multiple alleles at or near a methylation site may complicate data acquisition or analysis by affecting the primers necessary for amplification, the probe sequence necessary to assay a site, or the sequence to be derived from a site, for example. Alternately, a methylation site at or near a locus wherein alleles of said locus correspond to differential diagnoses may be included in some panels because the assay technique, such as sequencing, may easily be able to obtain and incorporate any allelic information obtained into the data used to generate a final determination.
[0117] Methylation sites may be selected for inclusion based on their utility within a specific population or ethnic group rather than their utility among patients at large. Thus panels may be selected to maximize the diagnostic efficacy as to a specific patient demographic, such as women (for whom methylation sites located on the Y- Chromosome are unlikely to be informative), or specific genetically similar ethnic groups (which may present allelic frequencies at one or more given loci that differ from the frequencies of humanity as a whole, and which may affect the utility of one or more methylation sites as panel constituents). See, e.g., John Butler (2006) "Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing," J. Forensic Sci. 51(2): 253-265.
[0118] One or more control loci may be included in a panel. These loci are not known to demonstrate a change in methylation status in autoimmune disorder or pre- autoimmune disorder samples compared to non-disorder samples. The assay of the methylation status of one or more control loci may be useful as a measure of the reliability of the results obtained from a given sample analysis. External control loci that are not present in the human genome (e.g., synthetic oligos) may be included as controls. The methylation values of these control loci may change relative to autoimmune disorder or pre-autoimmune disorder patients' samples but since they are not from the human genome, they will not be mistaken as patient data.
[0119] In some embodiments, the methylation patterns may be deduced by determining the methylation status, for example the presence of 5 -methyl cytosine, of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 125, 150, 175, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500, 3000, 3500, 4000, or more than 4000 loci from 1A, IB, 2A, 2B, 3A, 3B, and 4. Additionally, in some embodiments, the methylation patterns may be deduced by determining the methylation status, for example the presence of 5 -methyl cytosine, of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci from other sources in addition to the methylation patterns from the one or more loci of Tables
IA, IB, 2A, 2B, 3A, 3B, and 4, above.
[0120] In some embodiments, the selection of at least two DML of Tables 1A,
IB, 2A, 2B, 3A, 3B, and 4 may comprise a panel. In some embodiments the panel may further comprise at least one locus elsewhere. In some embodiments a panel may comprise at least two loci of Tables 1A, IB, 2A, 2B, 3 A, 3B, and 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or more than 23 loci elsewhere. In some embodiments a panel may comprise at least three loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least four loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least five loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least six loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seven loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least eight loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least nine loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least ten loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least eleven loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least twelve loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least thirteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least fourteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least fifteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least sixteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seventeen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least eighteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least nineteen loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least twenty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least twenty-five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least thirty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least thirty- five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least forty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least forty-five loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least fifty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least sixty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seventy loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least eighty loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least ninety loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least one hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least two hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least three hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least four hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least six hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least seven hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least eight hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least nine hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least one thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least one thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least two thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least two thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least three thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least three thousand five hundred loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least four thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere. In some embodiments a panel may comprise at least more than four thousand loci of Tables 1A, IB, 2A, 2B, 3A, 3B or 4 and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 loci elsewhere.
[0121] Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with SLE samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with OA samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with HC samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with SLE, OA and HC samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of RA samples with other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis samples.
[0122] Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with SLE samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with OA samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with HC samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with SLE, OA and HC samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of RA samples with other rheumatic diseases and other autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis samples.
[0123] Panels may comprise at least one locus identified in a comparison of methylation patterns of PBMC samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of T-cell samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of B-cell samples. Panels may comprise at least one locus identified in a comparison of methylation patterns of monocyte samples.
[0124] Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of PBMC samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of T-cell samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of B-cell samples. Panels may specifically exclude at least one locus identified in a comparison of methylation patterns of monocyte samples.
Oligonucleotides
[0125] In some embodiments an oligonucleotide primer or probe is disclosed. In some embodiments probes or primers are designed having sequences that match those of loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or a locus listed elsewhere. In some embodiments probes or primers are designed having sequences that span loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4. In some embodiments the probes or primers are designed to base pair with nucleotide sequences that are predicted to result from the treatment of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere with a reagent that alters nucleotide base identity in a manner that is methylation-sensitive. In some embodiments this treatment is bisulfite treatment as part of a process that selectively transforms cytosine but not 5 -methyl cytosine to uracil, thus changing the base pairing properties of the molecule treated. In some embodiments, a population of oligonucleotide probes is synthesized such that the population comprises one or more of the possible probes corresponding to each possible methylation pattern for a given locus given the known methylation patterns of the loci selected from Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere. In some embodiments these probes may distinguish between DNA that was methylated at a given base or bases prior to a chemical treatment which differentially affects methylated DNA as compared to unmethylated DNA from DNA that was not methylated at a given base or bases prior to chemical treatment which differentially affects methylated DNA as compared to unmethylated DNA.
[0126] In some embodiments the oligonucleotides are designed to anneal to templates comprising the methylation loci selected from the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4. In some embodiments the oligonucleotides are designed to anneal to cDNA molecules derived from the mRNA or other RNA product associated with loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or elsewhere.
[0127] In some embodiments the oligonucleotide may comprise a panel of 2, 3, 4, 5, or more, 10 or more, 20 or more, 50 or more, 200 or more, 250 or more than 250 oligo probes. In some embodiments said panel may comprise oligos spanning or related to loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4,. In some embodiments the panel may further comprise an oligo spanning or related to a locus listed elsewhere.
[0128] In some embodiments the primers are designed to base pair with nucleotide sequences that are predicted to result from the treatment of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 or elsewhere with a reagent that alters nucleotide base identity in a manner that is methylation-sensitive. In some embodiments this treatment is bisulfite treatment that selectively transforms cytosine but not 5-methyl cytosine to uracil, thus changing the base pairing properties of the molecule. In some embodiments the oligonucleotide primers selectively anneal to specific DNA sequences corresponding to specific methylation patterns of loci of Tables 1A, IB, 2 A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere, or to a specific embodiment of one of the complete set of possible methylation patterns of loci of Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere.
[0129] In some embodiments primer pairs are designed to amplify loci comprising differentially methylated sites. In some embodiments primer pairs are designed to amplify segments of transcripts or cDNA molecules derived from transcripts the synthesis of which is directed from loci associated with differentially methylated sites, such as transcripts from the genes listed in Tables 2, 3, or 1.
[0130] In some embodiments primer pairs are synthesized in combination with one or more oligonucleotide probes. In some embodiments these probes are labeled such that binding to a target sequence results in a detectable configuration change in a probe or detectably affects another probe. In some embodiments these probes are specific to DNA that results from bisulfite-treated methylated DNA or to bisulfite treated unmethylated DNA or to untreated DNA.
[0131] In some embodiments an oligonucleotide is 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or more than 35 bases long.
[0132] In some embodiments primer pair sets may be assembled wherein primer pair sets are capable of amplifying loci identified in Tables 1A, IB, 2 A, 2B, 3 A, 3B or 4 under standard PCR conditions known to one of skill in the art. Under the appropriate conditions, primer pairs may be able to direct the amplification of loci spanning differentially methylated sites, or additionally spanning 20 bp, 40bp, 60bp, 80bp, lOObp, 500bp, lkb, 1.5kb, 2kb, 2.5kb, 5kb, lOkb, or more than lOkb on either side of methylation sites listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4or elsewhere.
Determining Transcript accumulation patterns
[0133] In some embodiments, transcript accumulation levels for a gene or genes corresponding to one or more loci of one or more of Tables 1A, IB, 2 A, 2B, 3 A, or 3B, and optionally also listed in Table 4, may be determined. Additionally, transcript levels for at least one additional locus may be determined. Methylation sites from Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4were associated with gene promoters if they were located between 2.5 kb upstream and 500 bp downstream of a gene's transcription start site. Generally, an increase in methylation status at a methylation site indicates a decrease in the accumulation level of transcripts from loci corresponding to or near the methylation site.
[0134] In some embodiments, transcript accumulation levels of each member of a panel discussed above may be assayed. Embodiments disclosed herein are not limited to any particular method of assaying transcript accumulation levels. [0135] Transcripts to be used in performing an assay may be selected from transcripts that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within lOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 or from transcripts derived from genes that are located within 200bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 300bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 400bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 500bp of the loci listed in Tables 1 A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 750bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within lOOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 1500bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 2000bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 2500bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within 5000bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from transcripts derived from genes that are located within lOOOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
[0136] In some embodiments, transcript accumulation levels are assayed in one or more cell populations, for example a circulating cell population. In some embodiments transcript accumulation levels are assayed in cell populations comprising whole blood. In some embodiments transcript accumulation levels are assayed in cell populations comprising peripheral blood mononuclear cells. In some embodiments the cell population is selected from a group comprising T-cells, B-cells and monocytes. In some embodiments the cell population from which DNA is to be assayed is a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells). Cells from any of these groups may be obtained using any of a number of methods known to those of skill in the art. Embodiments disclosed herein are not limited to any particular method of cell or transcript isolation to the exclusion of any other.
[0137] In some embodiments, transcript accumulation patterns determined for one or more of the above cell populations may be compared to transcript accumulation or methylation patterns determined from similar cell types in one or more individuals with a known autoimmune disorder status or other disease state, or from one or more different cell populations taken from the same or different individuals compared to the individual to be diagnosed.
[0138] In some embodiments an increase or decrease in the transcript accumulation levels of genes corresponding to loci from a cell or population of cells of an individual to be diagnosed may be indicative of that individual's autoimmune disorder status. In some embodiments, the transcript accumulation levels of genes corresponding to loci from a cell or population of cells of an individual to be diagnosed may be determined and then normalized to the transcript accumulation levels or methylation status of control transcripts or loci to control for error in detection methods that may otherwise impact a diagnosis as to the presence or absence or progression or regression of an autoimmune disorder. Appropriate control loci, transcripts or techniques are known to one of skill in the art.
[0139] Transcript accumulation levels may be assayed using quantitative PCR, ribonucleic acid blot hybridization assays, microarray assays, DNase protection assays, or quantitative nucleic acid sequencing methods, for example. Embodiments disclosed herein are not limited to any particular method of transcript isolation or accumulation level assay to the exclusion of any other. R A may be purified from an isolated cell or cells from, for example, a patient to be diagnosed, using methods known in the art. The cell source may be a circulating cell, such as at least one whole blood cell or at least one peripheral blood mononuclear cell, or may specifically be at least one T- cell, B-cell or monocyte. Transcripts may be isolated from any white blood cell type, or from circulating exosomes. In some embodiments, free circulating RNA transcripts may be used.
[0140] Accumulation levels of 2, 3, 4, 5 or more, 10 or more, 20 or more, 50 or more than 50 genes may be determined. [0141] Transcript accumulation levels may be used much like methylation status determinations. In each case, the set of values determined for a test sample is compared to the values from controls, and deviation from control values, either absolute or relative, may be used to assess the presence or risk or progression of an autoimmune disorder in an individual, and may be further used to suggest a course of treatment.
Proteins taught by Tables 1A. IB, 2A. 2B, 3A. 3B, and 4
[0142] In some embodiments the activity or accumulation level of proteins encoded by genes at loci identified or associated with Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 is monitored. In some embodiments the activity or accumulation levels of proteins encoded by genes at loci identified or associated with loci identified elsewhere is monitored. In some embodiments, the activity or accumulation level or both are measured in a protein population derived from peripheral blood mononuclear cells. In some embodiments proteins are isolated from circulating white blood cells, exosomes or from free circulating proteins. Generally, an increase in methylation status at a methylation site indicates a decrease in the accumulation level and/or total activity of proteins encoded by loci corresponding to or near methylation sites. In some embodiments the protein population is selected from a group comprising proteins corresponding to T-cells, B-cells and monocytes. In some embodiments the protein population is selected from a group comprising proteins corresponding to a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells). In some embodiments, measurements from a protein population corresponding to cells from an individual suffering from an autoimmune disorder or an individual whose DNA extracted from whole blood, whole blood cells, peripheral blood mononuclear cells, or T- cells, B-cells or monocytes, or subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), subset of B-cells (such as Bl, B2) and/or subset of monocytes (such as Ml and M2 monocytes or dendritic cells) present a methylation profile indicative of an autoimmune disorder according to the methods disclosed herein.
[0143] In some embodiments, activity or accumulation levels of protein populations comprising proteins encoded by genes associated with loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 corresponding to a non- autoimmune disorder individual are compared to similar levels from similar protein populations corresponding to an individual having an autoimmune disorder or an individual presenting a methylation profile corresponding to an autoimmune disorder or an individual for which the presence of an autoimmune disorder or early signs of an autoimmune disorder are to be diagnosed. In some embodiments the above protein populations comprise purified proteins selected from the list of proteins encoded by genes at the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
[0144] Proteins to be used in an assay may be selected from proteins encoded by genes that span one or more of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within lOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 200bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 300bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 400bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 500bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 750bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within lOOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 1500bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 2000bp of the loci listed in Tables 1A, IB, 2 A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 2500bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within 5000bp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or from proteins encoded by genes that are located within lOOOObp of the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
[0145] Proteins may be assayed by accumulation level, using protein-specific antibodies, mass-spectrometric methods, nonspecific staining techniques, purification techniques, or a combination of the above. Proteins may also be quantified by measuring their activity levels in a sample extract by, for example, measuring the rate at which they metabolize or otherwise modify a substrate. Method of measuring protein accumulation levels and activity are known to those of skill in the art.
[0146] In some embodiments a panel of proteins is assayed. Accumulation levels of 2, 3, 4, 5 or more, 10 or more, 20 or more, 50 or more than 50 proteins may be determined. In some embodiments the panel comprises proteins encoded by genes associated with the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4. In some embodiments the panel may additionally comprise at least one protein from the proteins encoded by genes at loci identified elsewhere.
[0147] In some embodiments, the activity or accumulation level or both of proteins selected from the list of proteins taught in Tables 1 A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 is measured. In some embodiments these proteins are taken from a population of an individual's circulating cells, such as an individual's whole blood cells, peripheral blood mononuclear cells, or T-cells, B-cells or monocytes or a subset of T-cells (such as Thl, Th2, Thl7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells). In some embodiments this measurement is compared to a reference measurement made from a similar cellular protein source (i.e., circulating cell such as whole blood cells, peripheral blood mononuclear cells, or T-cells, B-cells or monocytes, or a subset of T- cells (such as Thl, Th2, Thl 7, T-regs, NK cells), a subset of B-cells (such as Bl, B2) and/or a subset of monocytes (such as Ml and M2 monocytes or dendritic cells) from a healthy individual. In some embodiments the relative levels of these measurements are used to ascertain the presence of an autoimmune disorder in said individual.
[0148] Protein activity or accumulation levels may be used much like methylation status determinations. In each case, the set of values determined for a test sample is compared to the values from controls, and deviation from control values, either absolute or relative, may be used to assess the presence or risk or progression of an autoimmune disorder in an individual, and may be further used to suggest a course of treatment.
[0149] Any of the foregoing assays in which methylation status of one or more markers is evaluated can be supplemented by additional data, because the methylation state of DML may be informative when integrated with other non- methylation data such as transcription profiles and genomic profiles. Thus, for example, other types of biomarkers may be used in combination with any of the forgoing assays. For example, SNPs or other allelic data relating to, for example, PTPN2; ITGAM- ITGAX; IRF5; IRF8; the FcRy genes; CTLA-4; STAT-4; BANK; IRAKI; FCRL3; Clq; C2; C4; C5aR; Complement Factor H and Factor H-Related Genes, MECP2; IKZF3; TMEM39a BLK; KIAA1542; PXK; or the MHC alleles HLA DR2, DR3, DR5, or HLA- DQ may be used. Similarly, protein levels, markers including but not limited to blood or serum chemical, biochemical, or protein markers, antibodies or auto-antibodies associated with RA or other autoimmune disease, may be used. A non-limiting list of examples comprises the antibodies ACPAs and Anti-CCP, Rheumatoid Factor, anti-dsDNA; anti- nuclear antibodies; anti-phospholipids; anti-cardiolipin; anti-P2glycoprotein; anti-Ro anti- La; anti-snRNP (Ul-RNP); anti-ribonuclear protein; anti-histone; anti-nucleosome; anti- N-methyl-D-aspartate (NR2); anti-Clq; cell surface molecules such as CD27; CD 154; CD95; levels of cytokine and chemokine such as a-interferon; IL-1, IL-6, IL-17, IL-23; TNFSF13B/BAFF;CXCL10;CCL2;CCL19; enzymes such as neutrophil gelatinase- associated lipocalin (NGAL); serum proteins and lipoproteins such as acute phase proteins such as C-reactive protein (CRP) or serum amyloid A protein (SAA); or proinflammatory HDL (piHDL); or complement levels such as Total Complement levels; C3,C4 levels; or Cell bound C4d, C3d. Similarly, other markers such as microRNA (miRNA) can be used in combination with the methylation information to further enhance the diagnosis of an autoimmune disorder. See, for example, van der Helm-van Mil et al. (2008) "Genome-Wide Single-Nucleotide Polymorphism Studies in Rheumatology: Hype or Hope!" Arthritis & Rheumatism 58(9):2591-2597, describing miRNA-148a as an autoimmune marker.
[0150] Any of the foregoing assays in which methylation status of markers is evaluated can be supplemented by additional data. Thus, for example, other types of biomarkers, such as Human Leukocyte Antigens (e.g. HLA-DR4 and HLA-DRB1; Wagner U, Kaltenhauser S, Sauer H et al. "HLA markers and prediction of clinical course and outcome in rheumatoid arthritis. " Arthritis Rheum 1997; 40:341-51), CD (cluster of differentiation) cell surface markers on leukocytes (Mo YQ, Dai L, Zheng DH, Zhu LJ, Wei XN, Pessler F, Shen J, Zhang BY. "Synovial infiltration with CD79a-positive B- cells, but not other B- cell lineage markers, correlates with joint destruction in rheumatoid arthritis." J Rheumatol. 2011 Nov;38(l l):2301-8), SNPs (such as PTPN22, TNF-a, TRAFl, IL2RA/CD25 and STAT4; Harrison P, Southam L, Chapman K, Locklin R, Sabokbar A, Wordsworth B, Pointon J. "Evidence of cis-acting regulatory variation in PTPN22 in patients with rheumatoid arthritis." Scand J Rheumatol. 2012;41(4):249-52, Krintel SB, Palermo G, Johansen JS, Germer S, Essioux L, Benayed R, Badi L, Ostergaard M, Hetland ML. "Investigation of single nucleotide polymorphisms and biological pathways associated with response to TNFa inhibitors in patients with rheumatoid arthritis." Pharmacogenet Genomics. 2012 Aug;22(8):577-89, Stahl EA, Wegmann D, Trynka G, Gutierrez- Achury J, Do R, Voight BF, Kraft P, Chen R, Kallberg HJ, Kurreeman FA; Diabetes Genetics Replication and Meta-analysis Consortium; Myocardial Infarction Genetics Consortium, Kathiresan S, Wijmenga C, Gregersen PK, Alfredsson L, Siminovitch KA, Worthington J, de Bakker PI, Raychaudhuri S, Plenge RM. "Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis." Nat Genet. 2012 Mar 25;44(5):483-9, Suzuki A, Kochi Y, Okada Y, Yamamoto K. "Insight from genome-wide association studies in rheumatoid arthritis and multiple sclerosis." FEBS Lett. 2011 Dec l;585(23):3627-32, Hinks A, Eyre S, Ke X, Barton A, Martin P, Flynn E, Packham J; Childhood Arthritis Prospective Study (CAPS); UKRAG Consortium; BSPAR Study Group, Worthington J, Thomson W. "Overlap of disease susceptibility loci for rheumatoid arthritis and juvenile idiopathic arthritis." Ann Rheum Dis. 2010 Jun;69(6): 1049-53) gene expression panels of inflammatory mediators, proteins biomarker levels (Curtis JR, van der Helm-van Mil AH, Knevel R, Huizinga TW, Haney DJ, Shen Y, Ramanujan S, Cavet G, Centola M, Hesterberg LK, Chernoff D, Ford K, Shadick NA, Hamburger M, Fleischmann R, Keystone E, Weinblatt ME. "Validation of a novel multi-biomarker test to assess rheumatoid arthritis disease activity." Arthritis Care Res (Hoboken). 2012 Jun 26. Bakker MF, Cavet G, Jacobs JW, Bijlsma JW, Haney DJ, Shen Y, Hesterberg LK, Smith DR, Centola M, van Roon JA, Lafeber FP, Welsing PM. "Performance of a multi-biomarker score measuring rheumatoid arthritis disease activity in the CAMERA tight control study." Ann Rheum Dis. 2012 May 17.), markers including but not limited to blood or serum chemical, biochemical, or protein panels of markers (such as C-reactive protein [CRP], Serum Amyloid A Protein [SAA], or Haptoglobin ), antibodies or auto-antibodies including Rheumatoid Factors [RF] and Anti-Citrullinated Protein Antibodies [ACPA]; Lee DM, Schur PH. "Clinical utility of the anti-CCP assay in patients with rheumatic diseases." Ann Rheum Dis 2003;62:870-4, Nishimura K, Sugiyama D, Kogata Y, Tsuji G, Nakazawa T, Kawano S, Saigo K, Morinobu A, Koshiba M, Kuntz KM, Kamae I, Kumagai S: "Meta-analysis: diagnostic accuracy of anti-cyclic citrullinated peptide antibody and rheumatoid factor for rheumatoid arthritis." Ann Intern Med 2007, 146:797-808, De Rycke L, Peene I, Hoffman IE, et al. "Rheumatoid factor and anticitrullinated protein antibodies in rheumatoid arthritis: diagnostic value, associations with radiological progression rate, and extra-articular manifestations." Ann Rheum Dis. 2004;63: 1587-1593, Greiner A, Plischke H, Kellner H, et al. "Association of anti-cyclic citrullinated peptide antibodies, anti-citrullin antibodies, and IgM and IgA rheumatoid factors with serological parameters of disease activity in rheumatoid arthritis." Ann NY Acad Sci. 2005;1050:295-303) or other auto-antibodies associated with RA or autoimmune disease (such as Anti-nuclear antibodies [ANA] or Anti-double stranded DNA), cytokines, chemokines, or growth factors (e.g., Tumor necrosis factor-a [TNF-a], Interleukin-1 [IL-1], Interleukine-6 [L-6] or Interleukin-17 {IL-17]) as mediators of inflammation, (David S. Gibson, Madeleine E. Rooney, Sorcha Finnegan, Ji Qiu, David C. Thompson, Joshua LaBaer, Stephen R. Pennington and Mark W. Duncan. "Biomarkers in rheumatology, now and in the future." Rheumatology 51 :423-433 (2012), Deane KD, O'Donnell CI, Hueber W, Majka DS, Lazar AA, Derber LA, Gilliland WR, Edison JD, Norris JM, Robinson WH, Holers VM, "The number of elevated cytokines and chemokines in preclinical seropositive rheumatoid arthritis predicts time to diagnosis in an age-dependent manner." Arthritis Rheum. 2010 Nov;62(l 1):3161-72, Kokkonen H, Soderstrom I, Rocklov J, Hallmans G, Lejon K, Rantapaa Dahlqvist S. "Up-regulation of cytokines and chemokines predates the onset of rheumatoid arthritis." Arthritis Rheum. 2010 Feb;62(2):383-91, Hitchon CA, Alex P, Erdile LB, Frank MB, Dozmorov I, Tang Y, Wong K, Centola M, El-Gabalawy HS. "A distinct multicytokine profile is associated with anti-cyclical citrullinated peptide antibodies in patients with early untreated inflammatory arthritis." J Rheumatol. 2004 Dec;31(12):2336-46) metabolic biomarkers (Rasmus K Madsen; Torbjorn Lundstedt; Jon Gabrielsson; Carl-Johan Sennbro; Gerd- Marie Alenius; Thomas Moritz; Solbritt Rantapaa-Dahlqvist; Johan Trygg. "Diagnostic Properties of Metabolic Perturbations in Rheumatoid Arthritis." Arthritis Research & Therapy. 2011;13(1)), microRNAs (Filkova M, Jungel A, Gay RE, Gay S. "MicroRNAs in rheumatoid arthritis: potential role in diagnosis and therapy." BioDrugs. 2012 Jun 1 ;26(3): 131-41.) or other markers can be used in combination with the methylation information to further enhance the diagnosis of RA or the classification of patients and their prognosis.
Evaluating panel assay results
[0151] Evaluation of results obtained using methods described herein may involve computer-based calculations and tools. For example, a methylation profile for a DNA region or portion thereof, or multiple regions or portions thereof selected from regions corresponding to the loci listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 and optionally additionally including regions corresponding to loci identified elsewhere can, for example, be given a value reflective of methylation status that may be compared by a computer to a threshold value or standard values, including values embedded in an algorithm, as described herein, or each methylation site may be evaluated individually. Ratios or degrees of methylation of certain loci within an individual patient sample may be compared. Values reflective of methylation status need not be methylation values themselves, but can include values generated by processing methylation status of an individual DML or a panel of DMLs together, with or without weighting.
[0152] Similarly, an activity profile or an accumulation profile or both for a set or proteins taught by Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4 can, for example, be given a value reflective of activity or an accumulation that may be compared by a computer to a threshold value or standard values, as described herein, or each value may be evaluated individually.
[0153] Evaluation of the results of a panel assay may be accomplished using a computer-based algorithm. Such an algorithm may evaluate the methylation status of the loci evaluated in comparison to known or measured values generated from standard populations to generate a signal indicative of the presence or absence or progression of an autoimmune disorder. As above, ratios or degrees of methylation of certain loci within an individual patient sample may be compared. Standard populations can include individuals without a target disease (e.g., without RA, OA, SLE, or other rheumatic and autoimmune disease, such as autoimmune and rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis), as well as individuals with one such disease and not another. It is preferred that a differential diagnosis be performed, ruling out particular disease states or the absence of particular disease states, as the case may be. Thus, a dataset can be generated comparing RA to any of the diseases or the HC condition as reported herein. .
[0154] An algorithm may assess the absolute or relative difference in methylation status between loci, and may weigh all loci equally or may give greater or lesser significance to certain loci based on, for example, prior knowledge of the significance of these loci in diagnosis, or redundancy of certain loci in comparison to other loci assayed. [0155] Evaluation of the results obtained by assaying to obtain a panel of data from a sample taken from an individual may involve evaluating individual or combined values reflective of the extent of methylation at said loci or perturbations in gene product accumulation or activity. This evaluation may involve calculating the difference between values for samples in terms of absolute or normalized values obtained, or may involve calculating the ratio of values obtained in comparison to reference or control values, for example.
[0156] The results of such an evaluation may be collected into a report that may contain values for the assay results, information regarding autoimmune disorder status of the individual, progression or regression of disease, or all of the aforementioned. The report may, for example, contain a metric indicating the number of methylation sites showing a methylation status indicative of an autoimmune disorder, or the aggregate deviation from an autoimmune disorder-free methylation pattern or from an autoimmune disorder pattern. The report may contain a statistical probability, or a simple yes/no assessment of the presence of an autoimmune disorder methylation pattern.
[0157] Reports may be generated providing information mentioned above resulting from an assay of transcript accumulation level panels, protein accumulation level panels, or protein activity panels as well.
[0158] A panel used to generate a report such as those described above may involve loci selected from Tables 1A, IB, 2A, 2B, 3A, 3B or 4. A panel involving an assay of methylation status may be comprised of loci from more than one table. A panel involving transcript or protein accumulation levels or protein activity levels may be comprised exclusively of levels taught in Table 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4, or may also comprise levels associated with loci identified elsewhere. The panel assessed may comprise at least 5, at least 10, at least 20, at least 50 or more than 50 loci or loci associated levels. Generally, an increase in methylation at a methylation site within the promoter region of a gene indicates a decrease in transcript accumulation level, protein accumulation level and, subsequently, total protein activity of a gene product corresponding to or adjacent to a methylation site. For loci outside of promoter regions (e.g., within introns or farther removed from a gene of interest), the effect of methylation may be less predictable. A change in methylation status may, for example, affect RNA processing such as splicing, may affect chromatin structure, or regulate the production of microRNAs, either increasing or decreasing transcription all of which can be measured using standard biochemical techniques. [0159] The methylation levels, transcript accumulation levels, protein accumulation levels or protein activity levels may serve as the input for a classification model, which may generate a list of phenotype-specific probabilities. In some embodiments, the highest probability phenotype will be assigned to the sample. In some embodiments, a classification model will be trained on samples with known phenotypes. Using these training samples, some models may automatically weigh the loci's methylation levels to maximize its ability to correctly predict these training samples. For example, if one locus is more informative than the others, its methylation value will have a stronger influence in the assignment of phenotype probabilities. Loci can be considered independently or combinatorially by the classification model. Other methods of evaluation are contemplated, and embodiments are not limited to a specific method of analysis.
[0160] The tools are advantageously provided in the form of computer programs that are executable, for example, by a general purpose computer system (referred to herein as a "host computer"). The host computer may be of conventional design. The host computer may be made in any number of dimensions and styles (e.g., desktop PC, laptop, Tablet PC, handheld computer, server, workstation, mainframe) and may be configured with many different hardware components. Standard components, such as disk drives, CD and/or DVD drives, monitors, and keyboards, for example, may be included in some configurations. Where the host computer is connected to a network, the connections may be effected via any suitable transport media (e.g., wired, optical, and/or wireless media) and any suitable communication protocol (e.g., TCP/IP). The host computer may include suitable networking hardware (e.g., modem, Ethernet card, WiFi card). Data accessible by the computer can include local RAM, local nonvolatile memory (e.g., optical storage or Flash memory), network-accessible storage, internet storage, and the like. Predetermined or standard population values can be stored in any such location that is accessible by the computer. The host computer may implement any of a variety of operating systems, including UNIX, Linux, Microsoft Windows, MacOS, or any other commercially available operating system. Embodiments disclosed herein are not limited to any particular hardware or software.
[0161] Aspects of the present invention may be implemented using any of a variety of computer code languages, including PERL, Python, R, MATLAB, C, C++, Java, JavaScript, VBScript, Bash or any other scripting or programming language that can be executed on the host computer or that can be compiled to execute on the host computer. Code may also be written or distributed in low level languages such as assembler languages or machine languages. Embodiments disclosed herein are not limited to any particular computer language.
[0162] The host computer system advantageously provides an interface through which the user directs operation of the tools. Those skilled in the art will appreciate that commands can be adapted to a number of operating systems as appropriate. In other embodiments, a graphical user interface may be provided, which allows the user to control operations using a pointing device. Thus, embodiments of the present invention are not limited to any particular user interface.
[0163] Programs or scripts for incorporating various features of the present invention may be encoded on various computer readable media for storage and/or transmission. Storage or transmission media such as magnetic disk or tape, optical storage media such as compact disk (CD) or digital versatile disk (DVD), flash memory, and carrier signals adapted for transmission via wired, optical, and/or wireless networks conforming to a variety of protocols, including the Internet are contemplated. Embodiments disclosed herein are not limited to any particular storage or transmission medium.
Methylation status analysis protocol
[0164] In some embodiments an analysis platform is used to analyze bisulfite converted sequences. Exemplary analysis platforms include: (1) Illumina BeadChips and (2) next generation sequencing (NGS), although other platforms are contemplated and no platform should be perceived as limiting. The first step in either platform is the bisulfite conversion of sample DNA. This forms an artificial oligonucleotide (i.e., not found in nature) where every unmethylated cytosine is transformed into a uracil. For Illumina BeadChips, there are two probe types. For type I probes, the bisulfite converted sample sequences hybridize to BeadChip- oligonucleotides in a methylation state specific matter. If a sample sequence is hybridized to a BeadChip-bound oligonucleotide, an artificially marked nucleotide is added to the BeadChip-bound oligonucleotide. For type II probes, bisulfite converted sequences hybridize to BeadChip-attached oligonucleotides, independent of methylation status. An artificially marked nucleotide is then selectively added. The identity of the added nucleotide is dependent on the methylation status of the sample sequence. The methylation states of the sample sequences for both type I and type II probes result read by red and green light intensities, generated by a BeadChip scanner. The ratio of these captured intensities estimates the degree of methylation for each CpG.
[0165] Regarding NGS, targeted CpGs in the bisulfite converted sample sequence are selectively PCR amplified for NGS processing. Determining which CpGs are amplified is not obvious (described below). Due to the artificial nature of the generated sequences, special experimental conditions are required to amplify our targeted regions. For example, one must use a DNA polymerase that properly reads uracil nucleotides, and one must be mindful that bisulfite converted DNA is single stranded and thus more unstable relative to natural DNA. In some NGS configurations, one will need to make further adjustments to account for the lower GC content of bisulfite converted sequences. For example, one may add control DNA on the Illumina NGS platform so that there is sufficient representation of all 4 detected nucleotides, as required by some Illumina bioinformatics software. The NGS platform produces sequence read-outs of targeted regions. One may transform these sequences via in silico demethylation so that one can accurately map them back to an unmethylated bisulfite converted genome. Once mapped to the genome, one may identify the nucleotides present at methylation sites on the sequence. Due to bisulfite conversion, unmethylated cytosines are artificially transformed into another base (i.e., uracil), and as a result, unmethylated cytosines are read as a different base than methylated cytosines. Counting the number of methylated bases and unmethylated bases per potential methylation site, one may generate the degree of methylation for each targeted CpG by dividing the number of methylated bases by the sum of methylated and unmethylated bases. The output from both BeadChip and NGS platforms may be formatted, for example into an n x m matrix, where n represents the number of interrogated CpGs and m represents the number of samples. For example, a BeadChip matrix may consist of 480,000 CpGs across 48 samples, representing a total of 23 million data points. Each data point may represent a degree of methylation (e.g., methylation frequency).
Sample assessment protocol
[0166] To assess whether a sample is labeled as RA or non-RA, a classification model is trained on a static data set that contains methylation frequency profiles for samples of known phenotypes. A methylation profile consists of an arbitrary number of methylation frequency values. We use a statistical algorithm to determine which CpG sites to analyze out of the approximately 27,000,000 present in the human genome. Similar methods may be used on other genomic sequence. The method is not limited to the human genome in its application. This statistical algorithm transforms methylation frequencies so that their statistical importance can be measured. An example entails transforming these methylation frequencies into phenotype-specific methylation frequency distributions and assessing the similarity of these distributions.
[0167] Prior to analysis by a classification model, methylation frequency profiles may be transformed. An example is subtracting each methylation frequency in a methylation profile by the profile's methylation frequency average and dividing by the standard deviation. When the training data is inputted into a classification model, the classification model determines which methylation signature across all input CpGs best identifies each phenotype.
[0168] The classification model may perform additional transformations. For example, a methylation profile containing 25 CpG methylation frequency values may be transformed via a kernel function into a unitless profile containing 30 values. While training, the classification model analyzes the CpGs in the methylation profile simultaneously and may use CpGs independently or in various combinations to classify phenotypes.
[0169] In some embodiments, the assignment of phenotypes is arbitrary. Samples may be partitioned into two phenotype groups (e.g., disease and no-disease). A multi-disease data set may be partitioned such that each disease is assigned a distinct phenotype or subtypes of a disease is represented as individual phenotypes (e.g., disease subtype I, disease subtype II, and disease subtype III, and no disease).
[0170] Once trained, a test methylation profile is inputted into the classification model and it is compared against the patterns learned from the training data set. The model outputs a classification value per phenotype included in the training set. For some models, these classification values can directly represent classification probabilities. For other models, the output values are not probabilistic and may be further transformed to represent probabilistic values (via linear regression, for example).
[0171] The output values, which may or may not be probabilistic, are then compared against thresholds determined based on the training data to classify the sample. These classification threshold values are not obvious. For example, the training data set may be used in combination with cross validation algorithms to assess an optimal cutoff value that best identifies a phenotype of interest relative to all other phenotypes. The resultant classification may be further transformed so that it is more interpretable to the data recipient. For Example, classification information can show sensitivity and specificity numbers, or recite a probability that the patient has RA.
Kits to assay for methylation status
[0172] In some embodiments a kit is disclosed comprising reagents disclosed herein. Said reagents may comprise oligonucleotide probes or primers, a gene chip, an antibody, a panel list or any other reagents disclosed herein provided that the kit comprises reagents specific for loci disclosed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4. In some embodiments this kit provides reagents that facilitate the determination of the methylation status of loci selected from the list of loci in Tables 1A, IB, 2A, 2B, 3A, 3B or 4, or of a panel of loci that may further comprise at least one locus identified elsewhere.
[0173] In some embodiments a kit may comprise reagents for the determination of the methylation state of loci selected from Tables 1A, IB, 2A, 2B, 3A, 3B or 4. In some embodiments the kit also includes oligonucleotide primers each comprising a sequence hybridizing to at least a portion of a locus selected from the group consisting of the loci listed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4. In some embodiments the kit can include one or more of methylation-sensitive restriction endonucleases, amplification reagents such as PCR reagents, probes and/or primers.
Definitions
[0174] As used herein, a "DNA reservoir" is any source of DNA that may be informative in diagnosis, such as DNA from an individual or individuals, DNA from a cell population taken from an individual or individuals, or extracellular DNA found within an individual, such as free circulating DNA.
[0175] As used herein, a "Differentially Methylated Locus" or "DML" is a methylation site of Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
[0176] As used herein, a "locus" is a specific place on a chromosome where a base (nucleic acid residue) or a consecutive set of bases is located. A locus may be a methylation site, or it may be a consecutive set of bases comprising a methylation site and adjacent sequence. It may comprise, for example a methylation site as well as 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 100 bp, 200 bp, 300 bp, 400 bp, 500 bp, 750 bp, 1 kb, 1.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb, or more than 10 kb on either side of the methylation site. [0177] As used herein, "methylation" refers to the addition of a methyl (CH3) moiety, for example onto a cytosine base at positions C5 or N4, onto an adenine at the N6 position, or onto any other molecular structure capable of forming a covalent bond with CH3. In some embodiments, "methylation" refers to cytosine methylation at positions C5 to produce 5-methyl cytosine. Additionally, the terms "unmethylated DNA" or "methylated DNA" can also be used informally to refer to a segment of DNA having at least one base capable of being methylated and wherein said at least one base is unmethylated or methylated, respectively.
[0178] As used herein, a "methylation pattern" refers to the set of methylation states of two or more bases in a genome. The profile can include the methylation state of every base in a cell, tissue or individual, or can comprise any subset thereof comprising more than one base.
[0179] As used herein, a "methylation state" or "methylation status" refers to the presence, absence or extent of methylation at a particular base or set of bases, or nucleotides within a portion of DNA, or other molecule capable of being methylated. Determination of the methylation status of a particular DNA sequence (e.g., a locus, a DNA biomarker or DNA region as described herein) can involve determination of the methylation state of every cytosine C5 position in the sequence or can involve determination of the methylation state of a subset of the cytosine C5 positions (such as the methylation state of cytosines in one or more specific restriction enzyme recognition sequences) within the sequence, or can involve determining regional methylation density within the sequence without providing precise information of where in the sequence the methylation occurs, or can refer to the determination of the methylation status at other positions along a given molecule.
[0180] As used herein, a "methylation site" is a specific base that is known to be differentially methylated in one cell, population of cells or individuals as compared to another cell, population of cells or individuals (i.e., cells of individuals suffering from an autoimmune disorder or rheumatic disorder such as RA, in comparison to cells of individuals suffering from OA or SLE, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC indiviauals, or pre-autoimmune or autoimmune- like symptoms in comparison to cells of autoimmune disorder- free or rheumatic disorder- free individuals). A methylation site need not be methylated under all conditions - for example, a methylation site may be completely unmethylated in some individuals or cell populations
[0181] As used herein, a "p-value" represents the probability of finding a test statistic that is at least as extreme as the one reported.
[0182] As used herein, a "q-value" represents the false discovery rate (FDR) to account for multiple hypothesis testing.
[0183] As used herein, a "panel" is a set of loci, genes or proteins whose methylation states, transcript accumulation levels, or activities or accumulation levels, respectively. A panel may be used to diagnose a condition, such as an autoimmune disorder, determine a cell type, determine a cell fate or otherwise evaluate a cell, cell population or individual from which a cell, cell population, DNA sample, transcript sample or protein sample is derived.
[0184] As used herein, a "primer" is a probe which is used to provide a 3ΌΗ moiety to which a nucleotide triphosphate may be added in a DNA synthesis reaction such as, for example, a polymerase chain reaction.
[0185] As used herein, a "probe" is an oligonucleotide which specifically binds a given DNA sequence. Probes may be modified so that binding to a substrate differentially affects an assayable output.
[0186] As used herein, a "protein accumulation level" is the aggregate amount of that protein which is present in a sample from a cell or cell population. It represents the net effects of translation and degradation on a given protein population, and is often colloquially referred to as 'expression level' of a protein.
[0187] As used herein, a "protein accumulation profile" is the measure of accumulation levels for a panel of proteins.
[0188] As used herein, a "protein activity" is a measure of the rate at which a reaction in which the protein participates occurs in a sample from a cell or cell population comprising a given protein. It represents the net effects of translation, degradation, post- translational modification and substrate availability for a given protein population, and is often colloquially referred to as 'expression level' of a protein.
[0189] As used herein, a "protein activity profile" is the measure of protein activities for a panel of proteins.
[0190] As used herein, an isolated DNA molecule having a sequence "spanning" a differentially methylated site has a sequence which base pairs with the sequence immediately on either side of the differentially methylated site. [0191] As used herein, a "standard population" is any population of DML data used as a basis for comparison of a given result. A standard population can comprise DML data from a set of individuals with known disease status, or from a set of cells having a known or expected DML pattern. A standard population may be compared to sample DML data, such as a result obtained from a patient sample.
[0192] As used herein, a "transcript accumulation level" of a related gene is the aggregate amount of R A derived from that gene which is present in a sample from a cell or cell population. It represents the net effects of transcription and transcript degradation on a given transcript population, and is often colloquially referred to as 'expression level' of a transcript.
[0193] As used herein, a "transcript accumulation pattern" is the set of transcript accumulation levels for each member of a gene panel.
EXAMPLES
Example 1 - Cell and DNA Extraction
[0194] DNA from peripheral blood mononuclear cells or other cells found in blood are extracted using techniques known to those of skill in the art. The protocols of Mallone (Mallone, R. et al., (2010) Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T- cell responses: position statement of the T-cell Workshop Committee of the Immunology of Diabetes Society, Clin. Exp. Immunol. 163:33-49) and Al-Moundhri (Al-Moundhri, et al., (2010) The prognostic significance of whole blood global and specific DNA methylation levels in gastric adenocarcinoma. PloS one 5:el5585) are among the protocols known in the art.
[0195] Circulating cell-free DNA is extracted with methods from Li, M et al. (Li, M. et al., (2009) "Sensitive digital quantification of DNA methylation in clinical samples," Nat Biotechnol (27)9: 858-863). Up to 18 ml of blood is collected into standard blood collection tubes containing EDTA. The tubes are immediately chilled to 8 °C and processed within 30 min of collection. The blood cells are pelleted for 15 min at 200g in a Leucosep tube (Greiner) filled with 15 ml of Ficoll-Paque solution. After centrifugation, the supernatant (that is, plasma) is transferred into 1.5 ml tubes, immediately frozen, and stored at -80 °C. The plasma samples are then thawed at 25 °C for 5 min, and any remaining debris is pelleted at 16,000g for 5 min. The supernatant is transferred to a new tube. Total genomic DNA is then purified from aliquots of 2 ml plasma supernatant using the QIAamp MinElute Virus Vacuum Kit (Qiagen) as recommended by the manufacturer. The DNA is finally eluted in elution buffer (Qiagen), and stored at -20 °C.
Example 2 - Cell Sorting
[0196] Peripheral blood mononuclear cells are extracted using techniques known to those of skill in the art. The protocol of Mallone (Mallone, R. et al., (2010) Isolation and preservation of peripheral blood mononuclear cells for analysis of islet antigen-reactive T- cell responses: position statement of the T-cell Workshop Committee of the Immunology of Diabetes Society, Clin. Exp. Immunol. 163:33-49) is among the protocols known in the art.
[0197] For example, total PBMCs obtained from RA, OA, SLE, other autoimmune disease, or other rheumatic disease conditions such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and normal patient blood samples are prepared by Ficoll gradient. (Langevin et al., 2012. "Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: An epigenome-wide association study, " Epigenetics. 7(3):291-9). The isolated cell subsets are further enriched for T-Cells, B-cells, and Monocytes by magnetic beads pre -bound with biotinylated monoclonal antibodies towards human cell surface markers (including nonlimiting examples such as anti-huCD4, huCD19 and huCD68) as described. (Vallee et al, 1998. "Human T lymphocyte proliferative response to resting porcine endothelial cells results from an HLA-restricted, IL- 10- sensitive, indirect presentation pathway but also depends on endothelial-specific costimulatory factors, " J Immunol. 161(4): 1652-8.; Lea et al., 1988. "Monosized, magnetic polymer particles: their use in separation of cells and subcellular components, and in the study of lymphocyte function in vitro, " J Mol Recognit. 1(1):9-18; Funderud et al, 1990. "Functional properties of CD19+ B lymphocytes positively selected from buffy coats by immunomagnetic separation, " Eur J Immunol. 20(l):201-6).
Example 3 - Bisulfite Treatment of DNA
[0198] Extracted DNA is treated largely following the protocol of Frommer et al., (1992) A genomic sequencing protocol that yields a positive display of 5- methylcytosine residues in individual DNA strands. Proc. Nat. Acad. Sci. USA 89. 2 μg of human DNA and 8 μg of carrier plasmid DNA are sheared through a fine needle, alkali denatured, neutralized, and precipitated. DNA is then incubated in a total volume of 1.2mL with freshly prepared 3.1M Sodium bisulfite / 0.5mM hydroquinone, pH 5.0 for 16 hours at 50°C under mineral oil. The solution is dialyzed at 4°C in an excess volume of 5mM Sodium acetate / 0.5mM hydroquinone, pH 5.2, and then at 4°C in an excess volume of 5mM Sodium acetate, pH 5.2, and finally in an excess of deionized water. The solution is dried under a vacuum and the solid residue is resuspended in 100 μΐ, of lOOmM Tris/HCl, 01. mM EDTA, pH 7.5 buffer. NaOH is added to a final concentration of 0.3mM and the reaction is allowed to stand at room temperature for 10 minutes. Ammonium acetate is then added to a final concentration of 3M. The DNA is then precipitated, washed and resuspended in lOOuL of lOmM Tris/HCl, 0.1 mM EDTA pH 7.5 buffer, and used immediately or stored at -20°C. Commercial kits for bisulfite conversion are also readily available and can be used in place of the foregoing procedure.
Example 4 - Sequencing of Specific Loci of Interest
[0199] l-5uL of bisulfite-treated DNA is amplified for 25-30 cycles using specific primers under standard cycling conditions. Amplified fragments are purified. Optionally, fragments are cloned into a vector of interest, which is transformed into a host organism wherein the vector is replicated, and then purified from the host for sequencing.
[0200] Sequencing is performed using dideoxy chain-termination methods and position extension products are visualized using electrophoretic methods appropriate to the label for each dideoxy nucleotide (other sequencing techniques, such as pyrosequencing, single strand sequencing, or NGS can also be used.)
Example 5 - Methylation Determination using an Infinium® HumanMethylation450 BeadChip
[0201] 4 uL of Bisulfite-treated DNA are treated using Illumina's Infinium ® HumanMethylation450 BeadChip protocol. The whole genome sequence is amplified in a single step, followed by an enzymatic fragmentation step. Samples are then precipitated and resuspended. Resuspended samples are hybridized on a HumanMethylation450 BeadChip at 48°C for 16 hours. The hybridized chips are washed, and a single-nucleotide extension is performed using the hybridized bisulfite treated DNA as a template. The ddCTP and ddGTP ("dideoxy"-) nucleotides to be incorporated are labeled with biotin, while the ddATP and ddTTP are labeled with 2,4-dinitrophenol. Following the extension reaction, the hybridized chip is subjected to repeated rounds of antibody staining to apply fluorophores.
[0202] The hybridized chips are placed in an Illumina HiScan SQ scanner, a two-color laser (532 nm/660 nm) fluorescent scanner with a 0.375 μηι spatial resolution, which is capable of exciting the fluorophores generated during the staining step of the protocol. Image intensities are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software, scored as 0 (unmethylated) to 1 (fully methylated).
Example 6 - Sites Identified
[0203] Methylation patterns were determined in whole blood, purified PBMC and subsets comprising T-cells, B-cells and Monocytes obtained from individuals suffering from RA, OA, SLE, or a collection of other rheumatic or autoimmune diseases such as Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis, and HC individuals suffering from none of the above disorders. Among the DML identified in T-cells, a partial list includes DML associated CD 160, a cell surface glycoprotein expression of which is tightly associated with peripheral blood NK cells and CD8 T lymphocytes with cytolytic effector activity; CXCL17, a chemokine ligand (CXC motif) ligand 17-CXCL17 that attracts dendritic cells and monocytes; DUSP22, Dual specificity protein phosphatase 22, which regulates focal adhesion kinase (FAK) and controls cell motility and adhesion; IL17RB, a receptor on lymphocytes that binds to interleukin- 17B and E regulators of autoimmune diseases; IL6R, Receptor for Interleukin-6, a mediator of inflammation in RA which is antagonistic to regulatory T- cells that shut down autoimmunity; ITGAM, Integrin alpha M receptor which binds C3; Mirl46b, which regulates inflammatory cytokines and immune cells; ADAMTS14, a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin; and ALOX15, which produces mediators of inflammation listed in Tables 1-6, below, a partial list of genes of interest identified through this work includes the following: HLA- DMA, a protein that plays a critical role in peptide loading of MHC class II molecules; HLA-DRA, am MHC II gene that binds peptides derived from antigens that access the endocytic route of antigen presenting cells and presents them on the cell surface for recognition by CD4 T-cells; HMGB1, a DNA binding protein that can drive the pathogensis of inflammatory and autoimmune diseases; CCR10, a receptor for chemokines SCYA27 and SCYA28 that stimulates chemotaxis in a pre-B-cell line; IL17RC, the cognate receptor for human IL-17F (hIL-17F) that also binds human IL-17A, both of which are proimflammatory cytokines; IL27, which plays an important function in regulating the activity of B and T-cells; IL27RA, the receptor for IL27; ICAM4, a ligand for the leukocyte adhesion protein LFA-1 (integrin alpha-L/beta-2) and for alpha- 4/beta-l and alpha-V integrins; CD59, a potent inhibitor of the complement membrane attack complex (MAC) action; CD22, a B-cell B-cell interaction mediator; IL6, a cytokine that functions in inflammation and B-cell maturation; CD40LG, a member of the TNF family that mediates B-cell proliferation and antigen specific T-cell response, whose high expression is correlated with increased and prolonged inflammatory activity; and CD81, a cell surface protein known to be upregulated in rheumatoid arthritis synviocytes. This list is demonstrative of the efficacy of the assay and the relevance of the DML identified as a whole. It is in no way limiting on the entirety of the DML listed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
[0204] Among the DML identified in B-cells, a partial list includes DML associated with CD40LG, CD40 ligand-expressed on activated B-cells; CD84, which functions in adhesion interactions between T lymphocytes and accessory cells and enhances cytokine synthesis; Chemokine (C-X-C motif) ligand 6, which attacks neutrophils; Interleukin-21 receptor, which is important for the proliferation and differentiation of T-cells, B-cells, and natural killer (NK) cells; Interleukin-6 receptor, which plays a role in B-cell activation and immunoglobulin synthesis; Interleukin-27, which plays an important function in regulating the activity of B- and T-lymphocytes and which is found in RA synovium; and Interleukin-7, which causes expansion of T and B- cells, is associated with increased levels of proinflammatory mediators, and drives B-cell development; BCL2L14, which regulates B-cell proliferation, survival and apoptosis; and IL13RA2, which regulates B-cell maturation. This list is demonstrative of the efficacy of the assay and the relevance of the DML identified as a whole. It is in no way limiting on the entirety of the DML listed in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
[0205] Among the DML identified in Monocytes, a partial list includes DML associated with CD226, which mediates cellular adhesion to other cells bearing its ligands, CD112 and CD155 confers the risk of RA in certain populations; CD59, Protectin, a complement regulatory protein which inhibits the complement membrane attack complex, and decrease of which is associated with increase inflammation and tissue damage; CXCR-4, an alpha-chemokine receptor specific for stromal-derived- factor-1 (SDF-1 also called CXCL12), a molecule endowed with potent chemotactic activity for lymphocytes, and which is important for angiogenesis in RA synovium; Interleukin-1 beta (IL-Ιβ) also known as catabolin, is a cytokine that is an important mediator of the inflammatory response, and is involved in a variety of cellular activities, including cell proliferation, differentiation, and apoptosis, and which induces Cyclooxygenase 2; Interleukin 1 receptor-like 1, a member of the Toll-like receptor superfamily that plays a role in inflammatory and cardiovascular diseases; Matrix metalloproteinase 21, which is important in connective tissue remodeling and pathobiology of various benign inflammatory skin disorders; Matrix metalloproteinase 21, which is important in connective tissue remodeling and pathobiology of various benign inflammatory skin disorders; platelet-derived growth factor B (PDGF), which interacts with and IL-1 in both a synergistic and antagonistic manner to regulate synovial fibroblast-like cells, and induces synoviocyte proliferation and production of collagenase and prostaglandins; and RUNX2, which is associated with connective tissue disorders; Caspase-10; which plays a central role in the execution-phase of cell apoptosis; and CD99-like 2(CD99), a glycoprotein found on the surfaces of leukocytes and concentrated at the borders of endothelial cells, that plays a major role in the migration of leukocytes across endothelial cells into sites of inflammation. This list is demonstrative of the efficacy of the assay and the relevance of the DML identified as a whole. It is in no way limiting on the entirety of the DML listed in Tables 1A, IB, 2A, 2B, 3A, or 3B, and optionally also listed in Table 4.
Example 7 - Assay Development and Protocol
[0206] Using data generated from a genome -wide approach, significantly DML are identified via a multiple hypothesis corrected statistical test. Data are generated for all phenotypes that the diagnostic model identifies. The loci are ranked based on their differential methylation significance. The samples are randomly segregated into two equally sized sets, a training set and a test set. A classification model is then trained using the top 5- 50 ranked DML and the training data. The classification model is used to assign phenotypes to the samples in the test set. This data segregation and phenotype assignment is repeated (usually 50 - 100 times) and the specificity and sensitivity metrics are calculated for each DML set size. The optimal locus size is chosen based on this data. For each locus in the diagnostic panel, multiple sets of candidate primers are designed to efficiently amplify the 50-200 bp bisulfite converted region covering the locus. The best performing primer pair is used in the final diagnostic. Taqman probes are used during this amplification process to determine methylation values. Alternately, the amplified regions are sequenced to determine methylation values. The DML panels are used to screen patient samples based on their disease state and response or lack of response to treatment to develop diagnostic, predictive or therapeutic selection tests, disease monitoring tests, and prognostic tests.
Example 8 - Data Analysis
[0207] Differentially methylated loci (DML) identified by methylation- specific, arbitrarily primed PCR and methylated CpG island amplification were scored and prioritized using the following scoring variables: (a) appearance using multiple discovery methods; (b) appearance in multiple pools of like samples; (c) located within a CpG island; (d) located within the promoter region of a gene; (e) located near or within predicted or known genes; (f) known to be associated with disease; (g) class of gene (transcription factor, growth factor, apoptosis gene, oncogene, cytokine gene; and (h) repetitive element. Under this scoring scheme, a sequence received a point for each of the above criteria and received a score of -8 for having repetitive sequence content >50%. Therefore, the highest score possible was 7; the lowest was -8. Scores were automatically calculated for each sequence using genomic annotations from current databases, such as Ensembl or the UCSC genome browser.
[0208] In conclusion, DNA methylation patterns in key genes may serve as a biomarker for inflammation and RA in some embodiments of the methods and compositions disclosed herein.
Example 9 - Confirmation of Efficacy of Disclosed DML in RA Diagnosis
[0209] Ranked DMLs were selected from Tables 1A and IB, Tables 2A and 2B, Tables 3A and 3B, and Table 4, below to constitute panels of 50 loci. Control panels were selected comprising methylation sites known in related literature to be methylated independent of RA status. That is, control panels consisted of methylation sites that were randomly selected without consideration of RA status.
[0210] A first set of samples from individuals each having a known RA status were assayed for their relative methylation status at the loci in panels from the Tables disclosed herein and from the random methylation sites unrelated to RA. Using these results as a 'training set', a second set of samples from individuals each having a known RA status were assayed for their relative methylation status at each locus in the ranked panels and the control panels.
[0211] Sensitivity, or 'True Positive' and Specificity, or 'True Negative' metrics were generated by 1,000 rounds of leave -one-out cross validation using DML from the indicated table. Randomly selected DML were selected from a genome-wide set of 452,768 methylation sites.
[0212] The ranked DML panels and the control panels were evaluated for their ability to accurately identify RA status in the sample data set. Panels were assessed as to their Sensitivity, which is their utility to identify True Positive RA samples, that is, to correctly identify RA positive samples relative to the total number of analyzed RA positive patient samples. Panels were also evaluated as to their Specificity, which is their utility to identify True Negative RA samples, that is, to correctly call RA negative samples relative to the total number of analyzed RA negative samples. Importantly, both high sensitivity and high specificity values are required for a panel to have good performance. An effective panel must be able to classify RA negative patients as RA negative and RA positive patients as RA positive. Panels were also evaluated as to their overall Accuracy, which is a metric that includes measurement of both True Positive and True Negative call rates.
[0213] The randomly selected DML panels demonstrated a True Positive Rate of 19.4% a True Negative Rate of about 90.0%, and an accuracy of 54.3%. Ranked Table 1 DML, selected from Tables 1A and IB, demonstrated a True Positive Rate of 37.7%, a True Negative Rate of about 90.1%, and an accuracy of 63.5%. Ranked Table 2 DML, selected from Tables 2A and 2B, demonstrated a True Positive Rate of 48.8%, a True Negative Rate of about 90.3%, and an accuracy of 69.8%. Ranked Table 3 DML, selected from Tables 3 A and 3B, demonstrated a True Positive Rate of 85.9%, a True Negative Rate of about 90.1%, and an accuracy of 88.0%.
[0214] These results clearly indicate that ranked DML from any of Tables 1A, IB, 2A, 2B, 3 A and 3B substantially outperforms a control background panel in identifying RA status in a given patient sample.
Example 10 - Exemplary Panel Performance
[0215] DMLs were selected from Tables 1A, IB, 2A, 2B, 3A, and 3B for inclusion in diagnostic panels based upon their capacity to predict RA status, and included in Table 4. Table 4 DML were ranked for further analysis. Ranked Table 4 DML, demonstrated a True Positive Rate of 85.1%, a True Negative Rate of about 90.5%, and an accuracy of 87.6%.
[0216] The results clearly indicate that an exemplary ranked panel of DML selected from Tables 1 A through 3B substantially outperforms a randomly selected DML panel in all parameters of RA diagnostic identification.
[0217] While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention.
[0218] The term "comprising" as used herein is synonymous with "including," "containing," or "characterized by," and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps.
[0219] All numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification are to be understood as being modified in all instances by the term "about." Accordingly, unless indicated to the contrary, the numerical parameters set forth herein are approximations that may vary depending upon the desired properties sought to be obtained. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of any claims in any application claiming priority to the present application, each numerical parameter should be construed in light of the number of significant digits and ordinary rounding approaches.
[0220] The above description discloses several methods and materials of the present invention. This invention is susceptible to modifications in the methods and materials, as well as alterations in the fabrication methods and equipment. Such modifications will become apparent to those skilled in the art from a consideration of this disclosure or practice of the invention disclosed herein. Consequently, it is not intended that this invention be limited to the specific embodiments disclosed herein, but that it cover all modifications and alternatives coming within the true scope and spirit of the invention.
[0221] All references cited herein, including but not limited to published and unpublished applications, patents, and literature references, are incorporated herein by reference in their entirety and are hereby made a part of this specification. To the extent publications and patents or patent applications incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material.
[0222] For Tables 1A, IB, 2A, 2B, 3A, 3B and 4. DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (UCSC hgl9 genome build). The DML coordinate is labeled according to its position on the + strand for simplicity but the DML refers to the CpG on the + and/or - strand.
Table 1A
Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
11 : 1316142, TOLLIP||Intron 2: 14750, PBMC:HC; 13: 113700994, MCF2L|| Intron 4:44967|Intron 4:77460, Tcell:OA; 16: 1503662, CLCN7||Intron 13:Intron 14:21423, Mono:OA; 16:83273795, CDH13||Intron 4:Intron 5:Intron 6:613397, TcelhOA; 17:46651920, HOXB4||3' Proximal Enhancer: 3823, BcelhHC; 19: 17514600, BST2||Exon 4: 1784, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 19: 17516329, BST2||Proximal Promoter:55, PBMC:SLE; 2: 191875807, STATl ||Intron 2:3169, PBMC:SLE,Tcell:SLE; 2: 191876673, STATl ||Intron 2:2303, Bcell:SLE,PBMC:SLE,Tcell:SLE; 2: 191883483, STATl ||Distal Promoter:-4507, TcelhSLE; 3: 193857540, HES1 ||3' Proximal Enhancer:3610, PBMCSLE; 4: 144303008, GABl ||Intron 1 :45026, PBMC:HC; 4:55534703, KIT|| Intron 1 : 10609, TcelhOA; 5: 1255458, TERT||Exon 13:Exon 14:39704, PBMC:SLE; 8:74237401, RDH10||Exon 6:30565, TcelhOA; 8:80550161, STMN2||Intron 2:27113, PBMC:SLE
Table IB
Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:72362292, PRFl ||Proximal Promoter:239, PBMC:HC; 10:72362730, PRFl ||Proximal Promoter:-199, PBMC:HC; 10:72362809, PRFl ||Proximal Promoter: -278, PBMC:HC; 10:90749920, FAS||Proximal Promoter: -367, PBMC:notRA; 10:90749966, FAS||Proximal Promoter:-321, PBMC:notRA; 11 : 104916018, CASPl ||Intron 1 :56140, PBMC:notRA; 11 : 113928473, ZBTB16||Distal Promoter:-2814|Proximal Promoter:-1957, PBMC:OA_SLE_HC; 11: 128554586, FLI1 ||5' Proximal Enhancer:-9226|5' Proximal Enhancer:-9224, PBMC:HC; 11 :2163174, IGF2||Distal Promoter:-2970|Proximal Promoter:-833|Intron 2:7659, PBMC:notRA; 12: 104853274, CHSTl l ||Intron 1 :2583, PBMC:notRA; 12: 104855500, CHSTl l ||Intron 1 :4809, Tcell:OA_SLE_HC,Tcell:SLE; 12: 130819008, PIWILl || Distal Promoter: -3424, Tcell:OA; 12: 130821607, PIWILl ||Proximal Promoter:-825, Tcell:HC; 12:47159659, SLC38A4||Exon 16:Exon 17:60121, BcelhHC; 12:50355995, AQP5||Exon 1 :717, PBMC:notRA; 12:6553145, CD27||Proximal Promoter:-905, Bcell:OA_SLE_HC; 12:6570167, CD27||3' Proximal Enhancer: 16117, PBMC:HC; 12:93960818, SOCS2||Distal Promoter: -2779, BcelhHC; 13: 113634978, MCF2L|| Intron 1 : 11444, PBMC:OA_SLE_HC; 13: 113664019, MCF2L||Intron l :7992|Intron 1 :40485, PBMC:notRA; 13: 113700027, MCF2L||Intron 4:44000|Intron 4:76493, PBMC:OA; 15:25200253, SNRPN||Proximal Promoter: 119|Intron 3:98556|Intron 3:Intron 4: 131460, PBMC:notRA; 15:39871923, THBSl ||Proximal Promoter:-1356, PBMC:notRA; 15:67354460, SMAD3||Distal Promoter:-3734, PBMC:OA,PBMC:SLE; 15:67396487, SMAD3||Intron 1 :38293, PBMC:OA_SLE_HC; 15:99256251, IGFlR||Intron 2:63491, PBMC:notRA; 15:99317340, IGF lR||Intron 2: 124580, PBMC:HC; 15:99332004, IGF lR||Intron 2: 139244, PBMC:HC; 16: 1486462, CLCN7||3' Proximal Enhancer: 38623, PBMCSLE; 16: 1487018, CLCN7||3' Proximal Enhancer:38067, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 16: 1495122, CLCN7||Exon 24:Exon 25:29963, Mono:SLE; 16: 1507866, CLCN7||Intron 6:Intron 7: 17219, PBMC:notRA; 16: 1524174, CLCN7||Intron 1 :911, Bcell:OA_SLE_HC; 16:2007559, RPS2||3' Proximal Enhancer:7268, PBMC:OA_SLE_HC; 16:2012373, RPS2||Intron 6:2454, PBMC:OA_SLE_HC; 16:3292971, MEFV||Exon 10:Exon 9: 13656, PBMC:HC; 16:58548995, SETD6||Proximal Promoter:-387, PBMC:OA_SLE_HC; 16:68772430, CDHl ||Intron 2: 1236, Wholeblood:notRA; 16:82071433, HSD17B2||Intron 1 :2576, PBMC:OA_SLE_HC,PBMC:SLE; 16:82129088, HSD17B2||Intron 4:60231,
PBMC:OA_SLE_HC,PBMC:SLE; 16:83273795, CDH13||Intron 4:Intron 5:Intron 6:613397, Tcell:OA_SLE_HC; 17: 17110353, FLCN||3' Proximal Enhancer:30149, Mono:OA; 17:40489584, STAT3||Exon 8:50821 |Exon 8:50929, PBMC:HC; 17:40489785, STAT3||Exon 7:50620|Exon 7:50728, PBMC:HC,PBMC:OA_SLE_HC; 17:46656690, HOXB4||Proximal Promoter: -947, PBMCSLE; 17:46679135, HOXB7||3' Proximal Enhancer:9248, Mono:OA_SLE_HC; 17:46693336, HOXB7||Distal Promoter: -4953, PBMC:OA; 17:48545805, CHAD || Proximal Promoter:422, PBMC:HC; 19: 17505860, BST2||3' Proximal Enhancer: 10524, PBMC:SLE; 19: 17514600, BST2||Exon 4: 1784, Mono:OA_SLE_HC,PBMC:HC; 19: 17516329, BST2||Proximal Promoter:55, PBMC:OA; 19:2774520, SGTA||Intron 1 :8834, BcelhHC; 19:45417793, APOE||3' Proximal Enhancer:8755, Wholeblood:notRA; 1 :27990967, IFI6||3' Proximal Enhancer:7757, Mono:SLE; 1 :3583333, TP73||Intron 1 : 14205, Mono:HC; 1 :6514663, TNFRSF25||3' Proximal Enhancer: 11592, Wholeblood:notRA; 1 :6515580, TNFRSF25||3' Proximal Enhancer: 10675, Wholeblood:notRA; 1 :6526182, TNFRSF25||Proximal Promoter:73, PBMC:OA_SLE_HC; 1 :6526398, TNFRSF25||Proximal Promoter:-143,
Bcell:OA_SLE_HC,Mono:HC,Mono:OA_SLE_HC,PBMC:HC; 1 :65428216, JAKl ||Intron 1 :3971, PBMC:notRA; 20:31349939, DNMT3B||Proximal Promoter: -251, PBMCSLE; 20:36041285, SRC||3' Proximal Enhancer:66729|3' Proximal Enhancer:68198, PBMC:SLE; 21 :46349496, ITGB2||5' Proximal Enhancer:-8531 |Proximal Promoter:-743, PBMC:notRA; 22:24236284, MIF||Proximal Promoter:-280, PBMC:notRA; 22:37545423, IL2RB||Intron 1 :539, PBMC:HC; 2: 102606829, IL1R2||5' Proximal Enhancer:-8629|Proximal Promoter: -1476, Mono:HC; 2: 102608192, IL1R2||5' Proximal Enhancer:- 7266|Proximal Promoter:- 113, PBMC:HC; 2: 113593785, ILlB||Exon 2:571, PBMC:HC; 2: 119602546, ENl ||Intron 1 :3213, BcelhOA; 2: 162934111, DPP4||Distal Promoter:-3059, PBMC:notRA; 2: 177029608, HOXD3||Intron 1 :804, PBMC:OA; 2: 177046513, HOXD3||3' Proximal Enhancer: 17709, PBMC:OA_SLE_HC; 2: 191875807, STATl ||Intron 2:3169, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2: 191876673, STATl ||Intron 2:2303, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2: 191883483, STATl ||Distal Promoter: -4507, Bcell:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 2:25391830, POMC|| Proximal Promoter:-271, Mono:OA; 2:86703710, KDM3A||Intron 12:35127|Intron 12:35440, PBMC:notRA; 3: 10190289, VHL||Intron l :Intron 2:6971, Bcel OA; 3: 12442682, PPARG||Intron 4:49682|Intron 5: 112247|Intron 4:Intron 5: 113334, Bcel OA; 3: 134710864, EPHBl ||Intron 3: 196766, PBMC:OA_SLE_HC; 3: 181428280, SOX2||Proximal Promoter:-1431, Mono:HC; 3:30673459, TGFBR2||Intron l :Intron 2:25466, PBMC:notRA; 3:39543515, MOBP||Intron 2:34446, PBMC:notRA; 3:50373735, ZMYND10||3' Proximal Enhancer:9421, Bcel HC; 3:50376000, ZMYND10||3' Proximal Enhancer:7156, PBMC:notRA; 4: 15843463, CD38||Intron 7:63533, PBMC:notRA; 5: 1268949, TERT||Intron 8:26213, PBMC:HC; 6: 160380572, IGF2R||5' Proximal Enhancer: -9558, PBMC:HC; 6:33151512, RXRB||3' Proximal Enhancer: 16920, PBMC:OA_SLE_HC; 6:33161394, RXRBpxon 10:7038, Bcel SLE; 7: 116367599, MET||Intron 2:55141, Mono:HC; 7: 130131403, MEST||Proximal Promoter: -495 IProximal Promoter:234|Intron l :5216|Intron 1 :5388, BcelhOA; 8: 134094173, TG||Intron 41 :214969, PBMC:SLE; 8: 141568712, EIF2C2||Intron 6:76934, PBMC:notRA; 8: 141599185, EIF2C2||Intron 1 :46461, PBMC:HC; 8: 141599208, EIF2C2|| Intron 1 :46438, PBMC:HC; 8:41169433, SFRPl ||Proximal Promoter:-2443, PBMC:HC; 8:80522577, STMN2||Proximal Promoter: -471, Mono:HC; 8:80550161, STMN2||Intron 2:27113, PBMC:OA_SLE_HC; 9: 116861404, KIF12||Proximal Promoter:-67, Mono:OA; X:48644859, GATAl ||Proximal Promoter:-122, Bcell:OA_SLE_HC
Table 2 A Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:102988389, FLJ41350||Proximal Promoter:-961,LBXl||Proximal Promoter:328, PBMC:OA; 10:116073949, AFAPlL2||Intron 6:90566, PBMC:OA; 10:118608138, EN04||Proximal Promoter:-884, Tcell:OA; 10:121798120, Mono:OA; 10:124138853, PLEKHA1||5' Proximal Enhancer:-6731|Intron 1:4760, PBMC:SLE; 10: 125425690, GPR26|| Proximal Promoter:- 180, Mono:OA; 10: 126599966, Mono:OA; 10:14620934, FAM107B||Intron 2: 195962, PBMC:HC; 10:16032954, TcelhOA; 10:21799314, C10orfl40||3' Proximal Enhancer: 15297, Tcell:OA; 10:23572214, Tcell:OA; 10:29700804, LOC3876471 |Intron 1:2304, Bcell:HC; 10:34344580, PBMC:SLE; 10:43277745, BMSl||Proximal Promoter:-208, Mono:OA; 10:49348564, Bcell:HC,PBMC:HC; 10:58346379, Mono:HC; 10:69609793, PBMC:HC; 10:75227339, PPP3CB||Exon 9:28443, Tcell:OA; 10:79561476, DLG5||Intron 27:124872, PBMC:HC; 10:88730407, AGAPl l||Proximal Promoter: -90,C10orfl l6||Exon 3:2220,SNCG||3' Proximal Enhancer: 12120, Mono:OA; 10:90642003, STAMBPL 11 |Intron 1: 1978, PBMC:SLE; 10:91173811, IFIT5||Proximal Promoter:-513, PBMC:SLE,Tcell:SLE; 10:91175366, IFIT5||Intron 1:1042, PBMC:SLE; 10:99696260, CRTACl||Intron 2:94325, Tcel OA; 11:100558484, ARHGAP42||Proximal Promoter:78, Mono:OA; 11: 100999399, PGRpxon l:1145|Proximal Promoter:395, Tcel OA; 11: 1030347, MUC6||Intron 7:6359, TcelhOA; 11: 111848326, DIXDCl||Intron 5:40400|Proximal Promoter:294, Tcel OA; 11:113185802, TTC12||Intron 1:552, TcelhOA; 11:119993780, TRIM29||Intron 4:15083, Tcel OA; 11: 12524208, PARVA||Intron 5:125183, Bcel HC; 11:130398900, BcelhHC; 11:1460312, BRSK2||Intron 3:49184, Tcel OA; 11:14927456, PBMC:SLE; 11: 14927489, PBMCSLE; 11:1983308, MRPL23||3' Proximal Enhancer: 14807, Tcel OA; 11:312560, IFITMl ||Proximal Promoter:- 1430,IFITM2||3' Proximal Enhancer:4454,IFITM3||3' Proximal Enhancer: 8354, Bcell:SLE,Mono:SLE; 11:313267, IFITMl ||Proximal Promoter:-723,IFITM2||3' Proximal Enhancer:5161,IFITM3||3' Proximal Enhancer:7647, Bcell:SLE,PBMC:SLE,Tcell:SLE; 11:313354, IFITMl ||Proximal Promoter:- 636,IFITM2||3' Proximal Enhancer:5248,IFITM3||3' Proximal Enhancer:7560, Bcell:SLE,Mono:SLE; 11:313478, IFITMl ||Proximal Promoter:-512,IFITM2||3' Proximal Enhancer:5372,IFITM3||3' Proximal Enhancer:7436, Mono:SLE,PBMC:SLE; 11:313527, IFITMl ||Proximal Promoter: -463,IFITM2||3' Proximal Enhancer:5421,IFITM3||3' Proximal Enhancer:7387, Bcell:SLE,Mono:SLE,Tcell:SLE; 11:313624, IFITMl I |Proximal Promoter:-366,IFITM2||3' Proximal Enhancer:5518,IFITM3||3' Proximal Enhancer:7290, Bcell:SLE,Mono:SLE,PBMC:SLE; 11:315102, IFITMl||Exon 2: 1112,IFITM2||3' Proximal Enhancer:6996,IFITM3||3' Proximal Enhancer:5812, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 11:315118, IFITMl||Exon 2:1128,IFITM2||3' Proximal Enhancer:7012,IFITM3||3' Proximal Enhancer:5796, BcelhSLE; 11:315262, IFITMl||Exon 2:1272,IFITM2||3' Proximal Enhancer:7156,IFITM3||3' Proximal Enhancer:5652, Bcell:SLE,Mono:SLE,PBMC:SLE; 11:315751, IFITM1||3' Proximal Enhancer:1761,IFITM2||3' Proximal Enhancer:7645,IFITM3||3' Proximal Enhancer: 5163, PBMC:SLE; 11:315908, IFITM1||3' Proximal Enhancer:1918,IFITM2||3' Proximal Enhancer:7802,IFITM3||3' Proximal Enhancer:5006, Mono:SLE,PBMC:SLE; 11:316339, IFITM1||3' Proximal Enhancer:2349,IFITM2||3' Proximal Enhancer:8233,IFITM3||3' Proximal Enhancer: 4575, PBMC:SLE; 11:319555, IFITM1||3' Proximal Enhancer:5565,IFITM3||3' Proximal Enhancer: 1359, Bcell:SLE,Mono:SLE,PBMC:SLE; 11:319667, IFITM1||3' Proximal Enhancer:5677,IFITM3||3' Proximal Enhancer: 1247, Mono:SLE,PBMC:SLE; 11:319718, IFITM1||3' Proximal Enhancer:5728,IFITM3||Exon 2:1196, Bcell:SLE,Mono:SLE,PBMC:SLE; 11:35638398, FJXl||Proximal Promoter:- 1336, Tcel OA; 11:46366643, DGKZ||Intron l: 12189|Proximal Promoter:- 173 |Proximal Promoter: -2312, Tcel SLE; 11:46366840, DGKZ||Intron l: 12386|Proximal Promoter:-2115|Proximal Promoter:24, Tcel SLE; 11:46368045, DGKZ||Intron l:1229|Intron 1: 13591 |Proximal Promoter: -910, Tcel SLE; 11:47873225, NUP160||Distal Promoter:-3168, Bcel OA; 11:55736968, OR10AGl||Proximal Promoter: - 1029,OR7E5P||3' Proximal Enhancer: 16913, PBMC:OA; 11:5645703, TRIM34||5' Proximal Enhancer: - 7781|Intron 1: 4530| Proximal Promoter:-503,TRIM6-TRIM34||Intron 7:27839, Bcell:SLE,PBMC:SLE; 11:5716255, TRIM22||Intron 1:5439,TRIM5||5' Proximal Enhancer: -9916, Mono:SLE; 11:57519364, BTBD18||Proximal Promoter:-l l l,Cl lorG l||3' Proximal Enhancer:10643,CTNNDl||5' Proximal Enhancer: -9869,TMX2-CTNNDl||Intron 2:39370, Bcel HC; 11:57958248, OR9Q2|| Proximal Promoter:343, TcelhOA; 11:61283865, LRRC10B||3' Proximal Enhancer:7594,MIR4488||3' Proximal Enhancer:7798,SYT7||Exon 10:Exon 9:64479, Mono:OA; 11:62382998, B3GAT3||Exon 5:6649,EML3||Distal Promoter:-2761,GANAB||3' Proximal Enhancer:31106,ROMl||3' Proximal Enhancer:2786, Tcell:OA; 11:63330918, HRASLS2||Proximal Promoter:-63, BcelhHC; 11:65780880, BANFIP' Proximal Enhancer:11331,CATSPERl||3' Proximal Enhancer: 13108,CST6||Exon 3:1419, BcelhSLE; 11:66104993, B3GNT1||3' Proximal Enhancer: 10168,BRMSl||Exon 10:7589,RINl||Proximal Promoter: -993, PBMC:HC; 11:67207574, COR01B||Intron 8:3409|Intron 9:3718,PTPRCAP||Proximal Promoter: -2421,RPS6KB2||3' Proximal Enhancer: 11640, PBMC:SLE; 11:67384040, DOC2GP||Proximal Promoter:-905,NDUFV1||3' Proximal Enhancer:9718, Tcel HC; 11:67761514, UNC93Bl||Intron 9:10079, PBMC:SLE; 11:68607622, CPTlA||Intron 1:1777, Tcel SLE; 11:70961765, Mono:OA; 11:71147213, DHCR7||Intron 8:12264, TcelhOA; 11:75062225, Tcel SLE; 11:79130675, PBMC:OA; 11:8046101, PBMC:OA; 11:89443662, TRIM77P||Proximal Promoter:196, Mono:OA; 12:105956397, PBMC:OA; 12:107380263, CRY1||3' Proximal Enhancer:107335,MTERFD3||Intron 1:666, TcelhSLE; 12:110840579, ANAPC7||Intron 1:956, Mono:HC; 12:113344923, OASl||Proximal Promoter: 185,RPH3A||3' Proximal Enhancer: 115375, TcelhSLE; 12:113375896, OAS3||Proximal Promoter:-352, PBMC:SLE; 12:117415439, FBXW8||Intron 5:66679, BcelhHC; 12:121088408, CABPl||Intron 1: 99871 Proximal Promoter:38, Mono:OA,PBMC:OA; 12:122019117, KDM2B|| Proximal Promoter:-197|Proximal Promoter:-753, PBMC:SLE; 12:122250518, LOC338799||5' Proximal Enhancer: -9128,SETDlB||Intron 5:7881, Tcel SLE; 12:12509705, LOH12CRl||Proximal Promoter:-314,LOH12CR2||Proximal Promoter:296,MANSCl||5' Proximal Enhancer:-6536, Mono:OA; 12:131502934, GPR133||Intron 13:64483, PBMC:OA; 12:132687376, GALNT9||Intron 3:3197|Intron 7:218529, PBMC:OA; 12:132855381, GALNT9|| Intron 2:50524,LOC100130238||Exon 4:3405, TcelhOA; 12:132935480, Mono:SLE; 12:133349383, GOLGA3||Exon 24:55905, Mono:HC; 12:13349273, EMPl||Proximal Promoter:-328, TcelhOA; 12:14135228, GRIN2B||Proximal Promoter: -2206, Tcel OA; 12:1612770, ERC1||3' Proximal Enhancer:512367,LOC100292680||Exon 2:3114, Tcel HC; 12:1964603, BcelhHC; 12:28651427, CCDC91||Intron 11:241295, BcelhHC; 12:29936845, TMTCl||Intron 1: 8471 Proximal Promoter: -102, PBMC:OA; 12:31079694, TSPANll||Proximal Promoter: -143, TcelhOA; 12:34374453, Bcel OA; 12:38447636, Mono:HC; 12:49504981, LMBR1L|| Proximal Promoter:-301, Bcel OA; 12:51441443, LETMD 11 |Proximal Promoter:-638|Proximal Promoter: -656, BcelhHC; 12:52715661, KRT83||Proximal Promoter:-479, Tcel OA; 12:62685785, USP15||Intron 1:31665, Tcel SLE; 12:6277045, PBMC:SLE; 12:66125776, PBMC:OA; 12:6933451, CD4||3' Proximal Enhancer:34814,GPR162||Exon 2:Intron 2:2489,LEPREL2||Distal Promoter:-4120, TcelhOA; 12:6949472, CDCA3||3' Proximal Enhancer:10984,GNB3||Proximal Promoter:98,LEPREL2||3' Proximal Enhancer: 11901, TcelhOA; 12:77417738, E2F7||Exon 13:41622, Mono:OA; 12:78635247, PBMC:OA; 12:90057674, ATP2B1||5' Proximal Enhancer: -7830, PBMC:SLE; 12:92501570, PBMC:SLE; 13:111819481, ARHGEF7|| Intron l:13421|Intron l:Intron 2:Intron 3:51858, Tcel HC; 13:111973089, C13orfl6|| Proximal Promoter:75, Mono:HC; 13:112507773, Bcel HC; 13:112722719, SOXlpxon 1:807, TcelhOA; 13:113803273, F10||Exon 8:26161,PROZ||5' Proximal Enhancer:-9694, Bcel OA; 13:114810096, RASA3||Intron 3:87999, PBMC:HC; 13:114837654, RASA3||Intron 2:60441, Mono:OA; 13:114908876, PBMC:HC; 13:24477610, C1QTNF9B||5' Proximal Enhancer: -6485, Tcel OA; 13:24824078, TcelhSLE; 13:25085301, PARP4||Intron 1:1647, Mono:HC; 13:28562900, PRHOXNB||Proximal Promoter:-126, PBMC:SLE; 13:28965632, FLT1||3' Proximal Enhancer: Intron 12:103633, PBMC:OA; 13:42615991, DGKH||5' Proximal Enhancer:-6851|Intron 1:1820, Bcel OA; 13:43355739, C13orG0||Proximal Promoter:54, Mono:SLE; 13:52006267, INTS6||Intron 3:Intron 4:21008, Mono:OA; 13:53421688, PCDH8||Exon 1:1087, PBMC:OA; 13:60842133, BcelhOA; 13:65532878, TcelhOA; 13:67801125, PCDH9||Exon 2:3343, PBMC:SLE,Tcell:SLE; 13:97640663, OXGRl||Intron 3:5941, PBMC:OA; 14:101827449, Mono:HC; 14:103541561, Mono:OA; 14:105107459, PBMC:OA; 14:106186239, TcelhOA; 14:23844876, CMTM5||Proximal Promoter:-l 140,IL25||Exon 2:2807|Exon 3:2859,MYH6||3' Proximal Enhancer:32610, TcelhOA; 14:24045274, AP1G2||5' Proximal Enhancer:-7995,JPH4||Exon 3:Exon 4:2735, PBMC:OA; 14:37445440, PBMC:HC; 14:53324934, FERMT2||3' Proximal EnhancenExon 15:Exon 16:92881, Tcel OA; 14:59873480, PBMC:HC; 14:64932678, AKAP5||Proximal Promoter:462,MTHFDl||3' Proximal Enhancer:77920, TcelhHC; 14:70077191, KIAA0247||Proximal Promoter:-1118, PBMC:SLE,Tcell:SLE; 14:76819370, BcelhOA; 14:92720273, Mono:OA; 14:94254726, PRIMA l||Proximal Promoter:40, Bcel OA; 14:94577101, IFI27||Proximal Promoter:23,IFI27Ll||3' Proximal Enhancer:29463, PBMC:SLE,Tcell:SLE; 14:96345612, LOC100507043||Intron 1:2504, Tcel OA; 14:96890445, AK7||Intron 5:31998, Mono:OA; 14:99613193, Mono:OA; 15:101697236, BcelhHC; 15:22550643, REREP3||Intron 1:4079, PBMC:HC; 15:25438860, SNORD115-10||3' Proximal Enhancer:2298|3' Proximal Enhancer:6178|3' Proximal Enhancer:8083,SNORD115-ll||3' Proximal Enhancer:4300,SNORDl 15-12||3' Proximal Enhancer:2298|3' Proximal Enhancer:8083,SNORD115-13||Proximal Promoter:393,SNORDl 15- 14||Proximal Promoter:-1207,SNORD115-16||5' Proximal Enhancer:-5734,SNORDl 15-17||5' Proximal Enhancer:-7609|5' Proximal Enhancer:-9513,SNORDl 15-18||5' Proximal Enhancer:-7609|5' Proximal Enhancer:-9513,SNORD115-19||5' Proximal Enhancer: -7609|5' Proximal Enhancer:-9513,SNORDl 15- 29||3' Proximal Enhancer:4300,SNORDl 15-36||3' Proximal Enhancer:4300,SNORDl 15-43||3' Proximal Enhancer:4300,SNORD115-5||3' Proximal Enhancer:2295|3' Proximal Enhancer:8080,SNORDl 15-8||3' Proximal Enhancer:9408,SNORDl 15-9||3' Proximal Enhancer:2298|3' Proximal Enhancer:8083, Tcell:OA; 15:26044289, ATP10A||Intron 1 :64060, PBMC:HC; 15:45028161, TRIM69|| Proximal Promoter:-398, Bcell:SLE; 15:45427734, DUOXl ||Exon 6:Exon 7:5543,DUOXAl ||5' Proximal Enhancer:-5677, PBMC:OA; 15:55513621, RAB27A||Intron 5:48971 |Intron 6:48863 |Intron 6:49486|Intron 6:68392, PBMC:SLE; 15:66858008, LCTL|| Proximal Promoter: -173, Tcell:OA; 15:69452320, GLCE||Proximal Promoter: -652, Mono:OA; 15:69744390, KIF23||3' Proximal Enhancer: 37764,RPLPl ||Proximal Promoter: - 768, TcelhSLE; 15:70393940, Tcel HC; 15:79575485, ANKRD34C||Proximal Promoter:340, Tcel HC; 15:83241867, CPEBl ||Intron 2:7486 l |Proximal Promoter: -1294, Bcel HC; 15:85774499, PBMC:OA; 15:89181732, AEN||3' Proximal Enhancer: 17206,ISG20||Proximal Promoter:-306, Tcel SLE; 15:89951184, LOC254559||3' Proximal Enhancer:29912, Tcel OA; 15:89959854, Tcel OA; 15:90291141, MESP1 ||3' Proximal Enhancer:3399,WDR93||3' Proximal Enhancer:57114, Mono:OA; 15:90578555, ZNF710||Intron 1 :33804, Mono:OA; 15:96952237, PBMC:OA; 16: 11764847, S N||Intron 1 :2559,TXNDC11 ||3' Proximal Enhancer:71801, BcelhHC; 16: 1309210, TPSD1 ||3' Proximal Enhancer:2938, Mono:OA; 16: 1331495, Mono:HC; 16: 1609529, IFT140||Intron 18:52580,TMEM204||3' Proximal Enhancer:25299, TcelhHC; 16: 1610898, IFT140||Intron 18:51211,TMEM204||3' Proximal Enhancer:26668, PBMC:SLE; 16: 1611966, IFT140||Intron 18:50143,TMEM204||3' Proximal Enhancer:27736, Tcel SLE; 16: 1611973, IFT140||Intron 18:50136,TMEM204||3' Proximal Enhancer:27743, Tcel SLE; 16:20338808, GP2||Proximal Promoter:27,UMOD||3' Proximal Enhancer:25229, Tcel OA; 16:28959310, CD19||3' Proximal Enhancer: 1605 l,NFATC2IP||Distal Promoter:-3007, Mono:HC; 16:2904862, PRSS22||Intron 4:3309, PBMC:OA; 16:30758831, C16orl 3||3' Proximal Enhancer: 14734,PHKG2||Proximal Promoter:-788, PBMC:OA; 16:55793200, CESlPl ||Proximal Promoter:-1310,CES1P2||3' Proximal Enhancer:34364, PBMC:OA; 16:57022486, CETP||3' Proximal Enhancer:26652, PBMC:SLE,Tcell:SLE; 16:57023022, CETP||3' Proximal Enhancer:27188, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 16:57023191, CETP||3' Proximal Enhancer: 27357, Bcell:SLE,Mono:SLE; 16:6425686, RBFOXl ||Intron 2:356555, PBMC:OA; 16:68034227, DPEP2|| Proximal Promoter:-863, PBMC:SLE; 16:69360307, COG8||3' Proximal Enhancer: 13219,PDF||3' Proximal Enhancer:4191,VPS4A||3' Proximal Enhancer: 15021, Mono:HC; 16:6953997, RBFOXl ||Intron l : 130188|Intron 3:884866, BcelhHC; 16:71843647, PBMC:SLE; 16:758683, FBXL16||Distal Promoter: -2858,METRN||5' Proximal Enhancer: -6489, Mono:OA; 16:82048758, SDR42El ||Distal Promoter:-3665, Bcel HC; 16:86519105, LOC400550||3' Proximal Enhancer: Intron 1 :23361, Bcel HC; 16:87323420, Mono:SLE; 16:87736889, JPH3||3' Proximal Enhancer: 100391,KLHDC4||3' Proximal Enhancer:62709, BcelhSLE; 16:88547533, ZFPMl ||Intron 1 :27520, BcelhHC; 16:89033785, CBFA2T3|| Intron 1 :9719, Tcel SLE; 16:89034292, CBFA2T3||Intron 1 :9212, PBMC:SLE; 17: 12567873, MYOCD||Proximal Promoter:- 1333, TcelhOA; 17: 14206871, HS3ST3Bl ||Intron l :2366,MGC12916||Proximal Promoter:-185, PBMC:HC; 17: 16397992, FAM211A| Distal Promoter:-2512, Mono:OA; 17:27045164, PROCAl ||5' Proximal Enhancer: - 6292,RAB34||Proximal Promoter:-256|Proximal Promoter: 122|Proximal Promoter: 87,RPL23A||Proximal Promoter:-1835,SNORD42A||5' Proximal Enhancer: -5282, SNORD42B||Proximal Promoter: - 2403,SNORD4A||Distal Promoter: -4435,SNORD4B||5' Proximal Enhancer: -5534,TLCD1 ||3' Proximal Enhancer: 8066| 3' Proximal Enhancer:8785, Mono:OA; 17:29811956, RABl lFIP4||Intron 3:93315, Tcel OA; 17:33306307, LIG3|| Proximal Promoter:- 1209, Tcel OA; 17:34839287, ZNHIT3|| Distal Promoter:-3185, Mono:OA; 17:37321890, ARL5C||Intron 1 :524,CACNB1 ||3' Proximal Enhancer:32066, Tcel OA; 17:37379606, STAC2||Intron 1:2434, PBMC:OA; 17:39279735, KRTAP4-11 ||5' Proximal Enhancer:-5129,KRTAP4-12||Exon 1 :684, BcelhSLE; 17:39791734, KRT42P||Intron 2:4717, Mono:OA; 17:42426506, FAM171A2||3' Proximal Enhancer: 14729,GRN||Intron 1 :4016, Tcel OA; 17:45608823, NPEPPS||Proximal Promoter:380, Bcel OA; 17:46669485, HOXB5||Exon 2: 1618,HOXB6||3' Proximal Enhancer: 12849,LOC404266||Distal Promoter:-3834|Intron l : 1644|Intron l : 1663|Proximal Promoter: - 168|Proximal Promoter:-196, BcelhOA; 17:47092156, IGF2BPl ||Intron 2: 17383, Mono:HC; 17:47438093, ZNF652||Intron l : 1383|Intron 1 : 1742, Tcel SLE; 17:4812443, C17orfl07||3' Proximal Enhancer:9496,CHRNE||5' Proximal Enhancer:-6074, Tcel SLE; 17:48981371, Tcel SLE; 17:49761771, CA10||Intron 4:474361 |Intron 5:475390|Intron 5:475606, TcelhHC; 17:55822272, Mono:HC; 17:58216651, Tcel OA; 17:60500856, EFCAB3||3' Proximal Enhancer: 42943 Proximal
Enhancer:53278,METTL2A||Proximal Promoter: -389, TcelhSLE; 17:64300729, PRKCA||Intron 1 : 1804, Tcel HC; 17:6658898, XAF l ||Proximal Promoter: -257, Bcel SLE; 17:6659070, XAFl ||Proximal Promoter:-85, Bcel SLE; 17:6659164, XAFl ||Proximal Promoter^, PBMC:SLE,Tcell:SLE; 17:6926194, BCL6B||Proximal Promoter:-174,C17orf49||3' Proximal Enhancer:8139,MIR195||5' Proximal Enhancer: - 5174,MIR497||Distal Promoter:-4853,MIR497HG||Distal Promoter:-3221,RNASEK||3' Proximal Enhancer: 10459,RNASEK-C17ORF49||3' Proximal Enhancer: 10459, Tcel OA; 17:72359190, BTBD17||Proximal Promoter:-1232,GPR142||Distal Promoter:-4454,KIF19||3' Proximal Enhancer:36840, PBMC:OA; 17:72744131, MIR3615||Proximal Promoter:-620,RAB37||3' Proximal Enhancer: 10776|3' Proximal Enhancer: 11173,SLC9A3Rl ||Proximal Promoter:-631, TcelhOA; 17:74266574, FAM100B||Exon 3:5289,QRICH2||3' Proximal Enhancer:37187, PBMC:SLE; 17:74878420, MGAT5B||Intron 2:9692|Intron 3: 13623, PBMC:SLE; 17:74945219, MGAT5B||Exon 16:76491 |Exon 17:80422, Tcel OA; 17:75445905, SEPT9||Proximal Promoter:-707, PBMC:SLE; 17:75473610, SEPT9||Intron l :2286|Intron 1 :26998, PBMC:SLE; 17:76335184, Bcell:OA,PBMC:OA; 17:76967695, LGALS3BP||Exon 6:8366, BcelhSLE; 17:76975944, LGALS3BP||Proximal Promoter: l 17, TcelhSLE; 17:76976010, LGAL S3 BP || Proximal Promoter:51, TcelhSLE; 17:76976057, LGAL S3 BP || Proximal Promoter^, Mono:SLE; 17:76976091, LGALS3BP||Proximal Promoter:-30, Mono:SLE,PBMC:SLE; 17:76976245, LGAL S3 BP || Proximal Promoter:- 184, Bcel SLE; 17:76976267, LGALS3BP||Proximal Promoter:-206, Bcell:SLE,Mono:SLE; 17:76976352, LGALS3BP||Proximal Promoter:-291, Bcel SLE; 17:76976357, LGAL S3 BP || Proximal Promoter: -296, BcelhSLE; 17:77023266, C1QTNF1 ||5' Proximal Enhancer:-7205|Intron l :3016,LOC100507410||Proximal Promoter:471, PBMC:OA; 17:77478927, RBFOX3|| Proximal Promoter: - 364, Bcel OA; 17:78233937, RNF213||Proximal Promoter:-722|Proximal Promoter:-729,SLC26Al 1 ||3' Proximal Enhancer:39738, Bcel SLE; 17:78720226, RPTOR||Intron 5:201602, TcelhSLE; 17:78764256, RPTOR||Intron 6:245632, PBMC:HC; 17:79269884, LINC00482||3' Proximal Enhancer: 13164,SLC38A10||Proximal Promoter:-788, Mono:OA; 18: 11751566, GNAL||Intron l :62431 |Proximal Promoter:5, TcelhOA; 18:28621985, DSC3||Intron 1 :796, PBMC:OA; 18:28681689, DSC2||Intron 1 :699, PBMC:OA; 18:29170928, TTR||Proximal Promoter:-801, BcelhOA; 18:4454189, Tcel OA; 18:53450352, Tcel OA; 18:55816433, NEDD4L||Intron l : 101976|Intron l : 104824|Proximal Promoter:-131, PBMC:OA; 18:5892245, TMEM200C||Proximal Promoter:-142, BcelhOA; 18:72916311, TSHZ1 ||5' Proximal Enhancer: -6419,ZADH2||Intron 1 :4970, BcelhSLE; 18:74208345, ZNF516||Proximal Promoter:-1199, PBMC:OA; 18:77682412, PQLCl ||Intron 3:Intron 4:29241, TcelhOA; 19: 10197856, ANGPTL6||3' Proximal Enhancer: 15569,C19orf66||Intron 2: 1051, Bcel SLE; 19: 10206568, ANGPTL6||Intron 2:6857,C19orf66||3' Proximal Enhancer:9763, Mono:HC; 19: 10206746, ANGPTL6||Exon 2:6679,C19orf66||3' Proximal Enhancer: 9941, PBMC:HC; 19: 1080034, HMHAl ||Exon 13: 12861,POLR2E||3' Proximal Enhancer: 15357, PBMC:SLE; 19: 14142205, IL27RA|| Proximal Promoter: - 56,RLN3||3' Proximal Enhancer:3189, PBMC:SLE,Tcell:SLE; 19: 15311666, NOTCH3||Proximal Promoter: 126, PBMC:OA; 19: 16126318, LOCI 26536||Proximal Promoter:-125, Bcel OA; 19: 18229454, MAST3||Intron 2:20852, Bcel OA; 19: 1828388, LOC100288123||3' Proximal Enhancer:6301, PBMC:OA; 19: 18545062, ELL||3' Proximal Enhancer:87875,ISYNAl ||3' Proximal Enhancer:3057|3' Proximal Enhancer:3859|3' Proximal Enhancer:3910|3' Proximal Enhancer:4049,SSBP4||Exon 17:Exon 18: 14917, Mono:SLE; 19: 1885442, FAM108Al ||Proximal Promoter:76, BcelhOA; 19: 19256748, MEF2B||Exon 9:24350,MEF2BNB-MEF2B||Exon 10:Exon 12:Exon 13:46652,TMEM161A||5' Proximal Enhancer:-7481, Bcel OA; 19:291306, PPAP2C||Proximal Promoter:-137|Proximal Promoter: 129, PBMC:OA; 19:291315, PPAP2C||Proximal Promoter:-146|Proximal Promoter: 120, PBMC:OA; 19:30866365, ZNF536||Intron 1 :3038, Tcel OA; 19:30869034, ZNF536||Intron 1 :5707, Tcel OA; 19:35630279, FXYDl ||Intron l :548|Proximal Promoter:-l 12,FXYD7||Distal Promoter: -3874,LGI4||Distal Promoter: -4101, PBMC:HC; 19:35630334, FXYDl ||Intron l :603|Proximal Promoter:-57,FXYD7||Distal Promoter:-3819,LGI4||Distal Promoter:-4156, PBMC:HC; 19:37825307, HKRl ||Proximal Promoter: -272, BcelhSLE; 19:37825309, HKRl ||Proximal Promoter: -270, BcelhSLE; 19:37825320, HKRl ||Proximal Promoter: -259, Bcel SLE; 19:37825388, HKRl ||Proximal Promoter: -191, Bcell:SLE,Mono:SLE; 19:37825406, HKRl ||Proximal Promoter:-173, Mono:SLE,Tcell:SLE; 19:37826008, HKRl ||Proximal Promoter:429, Bcell:SLE,Mono:SLE; 19:44200812, PBMC:SLE; 19:46319153, RSPH6A||Proximal Promoter: - 548,SYMPK||Exon 26:47395, PBMC:OA; 19:48101437, PBMC:OA; 19:48547989, CABP5||Proximal Promoter: -678,PLA2G4C||3' Proximal Enhancer:66120, BcelhOA; 19:4950888, PBMC:HC; 19:49891494, CCDC155||Proximal Promoter:20, Mono:HC; 19:49894178, CCDC155||Exon 2:2704, BcelhHC; 19:50059946, NOSIP||Exon 8:23857, TcelhOA; 19:50706577, MYH14||Proximal Promoter: -307, PBMC:OA; 19:51513296, KLK10||3' Proximal Enhancer: 10135|3' Proximal Enhancer:9658|3' Proximal Enhancer:9986,KLK8||5' Proximal Enhancer:-8338,KLK9||Proximal Promoter:-406, TcelhOA; 19:51588819, KLK14||Proximal Promoter:-1317, PBMC:OA; 19:52391078, ZNF577||Proximal Promoter: l l l|Proximal Promoter: 151,ZNF649||3' Proximal Enhancer: 17227, TcelhOA; 19:53192577, ZNF83||Intron 1 : 1309, Mono:SLE; 19:54177678, MIR1323||3' Proximal Enhancer:2457,MIR498||Proximal Promoter:228,MIR512-l ||3' Proximal Enhancer:5262|3' Proximal Enhancer:7746,MIR512-2||3' Proximal Enhancer:5268|3' Proximal Enhancer:7752,MIR515-l ||Distal Promoter: -4578,MIR515-2||Distal Promoter: - 4578,MIR519E||5' Proximal Enhancer:-5515,MIR520E||Proximal Promoter:-1286,MIR520F||5' Proximal Enhancer:-7734, Mono:OA; 19:5587239, SAFB2||Exon 21 :35699, PBMC:SLE; 19:5691899, HSD11B1L||3' Proximal Enhancer: 10825|3' Proximal Enhancer: 10848|3' Proximal Enhancer: 10853|3' Proximal Enhancer: 10865,LONPl ||Exon 18:28277,RPL36||3' Proximal Enhancer: 1554| 3' Proximal Enhancer: 1628, Bcel HC; 19:56989102, LOC100128252||Proximal Promoter: -1401 Proximal Promoter:- 390,ZNF667||Proximal Promoter:-332, PBMC:OA; 19:57349709, MIMTl ||Distal Promoter: -2560, BcelhSLE; 19:57352465, MIMTl ||Proximal Promoter:196, Bcel OA; 19:58220657, ZNF154||Proximal Promoter:-78, Tcel SLE; 19:58399865, ZNF814||Intron 1:577, Bcell:SLE,Mono:SLE,PBMC:SLE; 19:607586, HCN2||Intron 3:17694,POLRMT||3' Proximal Enhancer: 25982, Mono:OA; 19:6274208, MLLTl||Intron 1:5751, PBMC:HC; 19:8118857, CCL25||Intron 2:1212, Mono:HC; 1:101174567, TcelhSLE; 1:1102417, MIR200A||Proximal Promoter:-825,MIR200B||Proximal Promoter: - 66,MIR429||Proximal Promoter:-1967,TTLL10||5' Proximal Enhancer:-6868, Mono:OA; 1:110307811, EPS8L3||Proximal Promoter:- 1167, Tcel OA; 1:111817803, RP11-165H20.1||5' Proximal Enhancer:-5342, Mono:OA; 1:144539026, PBMC:SLE; 1:145017064, PDE4DIP||Intron 2:59122, TcelhOA; 1:150245988, APHlA||Distal Promoter:-4379,Clorf51||5' Proximal Enhancer: -9240,Clorf54||Intron 1:806,CA14||3' Proximal Enhancer: 15771, Mono:HC; 1:154986512, DCST2||3' Proximal Enhancer:19745,ZBTB7B||Exon 3:Intron 2:Intron 4:11407|Intron 3:11311, PBMC:SLE; 1:155910523, ARHGEF2||3' Proximal Enhancer: 3744313' Proximal Enhancer:37813,RXFP4||Proximal Promoter:-956, Mono:OA; 1:158259268, CDlC||Proximal Promoter:-294, Mono:HC; 1:159795518, Clorf204||3' Proximal Enhancer:29619,FCRL6||3' Proximal Enhancer:23346,SLAMF8||Proximal Promoter:-960, TcelhOA; 1:159891638, IGSF9||3' Proximal Enhancer:23748,TAGLN2||Intron 1:3646, TcelhSLE; 1:161184305, APOA2||3' Proximal Enhancer:9113,FCERlG||Proximal Promoter:-781,NDUFS2||3' Proximal Enhancer: 12369|3' Proximal Enhancer: 15201, PBMC:HC; 1:165326269, LMXlA||Proximal Promoter:- 317|Proximal Promoter: -791, Bcel OA; 1:17022524, ESPNP||Intron 10:24128, PBMC:OA; 1:173640200, BcelhSLE; 1:178062811, LOC100302401||Proximal Promoter:317,RASAL2||Proximal Promoter: -52, PBMC:OA; 1:178368509, RASAL2|| Intron 2:57904|Intron 4:305646, PBMC:OA; 1:17866039, ARHGEF 10L| I Proximal Promoter:-290, PBMC:OA; 1:182642214, RGS8||Proximal Promoter:-147, BcelhHC; 1:185303447, LOC100288079||Exon 2:724, Mono:HC; 1:20511095, PLA2G2C||5' Proximal Enhancer:-9408,UBXN10||Proximal Promoter: -1482, BcelhHC; 1:205254523, PBMC:SLE; 1:207490952, CD55||Distal Promoter: -3864, PBMC:HC; 1:212671907, Bcel HC; 1:2164542, SKI||Intron 1:4409, PBMC:SLE,Tcell:SLE; 1:2165579, SKI||Intron 1:5446, TcelhHC; 1:21670736, TcelhSLE; 1:216897293, ESRRG||Intron l:81416|Intron l:Intron 2:215724|Intron l:Intron 3:215722|Intron 2:Intron 3:365694|Intron 3:353019|Intron 3:365903|Intron 3:413804|Proximal Promoter:-479, Mono:HC; 1:2171834, SKI||Intron 1:11701, PBMC:HC; 1:226306890, TcelhOA; 1:227009245, Mono:OA; 1:228397977, OBSCN||Intron 1:2117, Mono:OA; 1:228658646, MIR4666A||3' Proximal Enhancer: 8872, TcelhHC; 1:228658973, MIR4666A||3' Proximal Enhancer:9199, TcelhHC; 1:233749672, KCNKl||Proximal Promoter: -77, Tcel OA; 1:234667363, LOC100506795||Proximal Promoter:162, TcelhOA; 1:244214206, LOC339529||3' Proximal Enhancer: 133503,ZNF238||Proximal Promoter: -2375 |Proximal Promoter: -354, Tcel SLE; 1:24528833, LOC284632||Intron 1:2104, Mono:OA; 1:247112228, ZNF670-ZNF695||Intron 6:129887,ZNF695||Intron 5:59167, BcelhHC; 1:25069086, CLIC4||Distal Promoter: -2673, Tcel SLE; 1:25290947, RU X3|| Intron 1:554, TcelhSLE; 1:27240514, NR0B2|| Proximal Promoter:53,NUDC||5' Proximal Enhancer:-7709, TcelhOA; 1:27940619, FGR||Intron ll:12132|Intron 11:124871 Intron 11:21108, PBMC:SLE; 1:2885085, PBMC:HC; 1:29139021, OPRDl||Proximal Promoter:368, PBMC:OA; 1:3134756, Bcell:SLE,Mono:SLE; 1:3230357, PBMC:HC; 1:3230424, PBMC:HC; 1:32825803, BSDC1||3' Proximal Enhancer:34259,LOC100128071||3' Proximal Enhancer:2041,TSSK3||Proximal Promoter:-2058, Tcel SLE; 1:36581751, Tcel OA; 1:39249604, TcelhHC; 1:44117093, KDM4A||Intron 1:1297, BcelhHC; 1:45240985, BEST4||3' Proximal Enhancer: 12441,KIF2C||3' Proximal Enhancer:35496,RPS8||Proximal Promoter: -260,SNORD38A||Distal Promoter: -2528,SNORD38B||Distal Promoter: -
3076,SNORD46||Proximal Promoter:-l 178,SNORD55||Proximal Promoter:-551, Bcel OA; 1:50885352, DMRTA2||Exon 3:3767, PBMC:OA; 1:50893730, DMRTA2|| Distal Promoter: -4611, TcelhOA; 1:51982669, EPS15||Intron 1:2326, Bcel OA; 1:67807960, IL12RB2||Intron 8:34914, PBMC:HC; 1:7402983, CAMTAl||Intron 5:557600, TcelhOA; 1:75602846, LHX8||Exon 3:2280|Exon 4:8728, PBMC:OA; 1:77230619, TcelhHC; 1:77230837, TcelhHC; 1:79085162, IFI44L||Proximal Promoter:-925,
Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE 1:79085250, IFI44L||Proximal Promoter:-837, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE 1:79085586, IFI44L||Proximal Promoter:-501, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE 1:79085713, IFI44L||Proximal Promoter:-374, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE 1:79085765, IFI44L||Proximal Promoter:-322,
Bcell:SLE,PBMC:SLE,Tcell:SLE; 1:79088769, IFI44L||Intron 1:2682,
Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 1:79118191, IFI44||Intron 2:2715,IFI44L||3' Proximal Enhancer:32104, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 1:8408752, RERE||3' Proximal Enhancer:468947|3' Proximal Enhancer:74995,SLC45Al||3' Proximal Enhancer:24363, Tcel OA; 1:87817476, LM04||3' Proximal Enhancer:23326,LOC100505768||3' Proximal Enhancer: 19862, Tcel OA; 1:91488275, ZNF644||Proximal Promoter:- 1210|Proximal Promoter: -463, PBMC:SLE,Tcell:SLE; 1:949392, AGRN||5' Proximal Enhancer:-6110,ISG15||Exon 2:546, PBMC:SLE; 1:949449, AGRN||5' Proximal Enhancer:-6053,ISG15||Exon 2:603, PBMC:SLE,Tcell:SLE; 1 :949634, AGRN||5' Proximal Enhancer:-5868,ISG15||Exon 2:788, PBMC:SLE; 1 :949850, AGRN||5' Proximal Enhancer: - 5652,ISG15||Exon 2: 1004, Bcell:SLE,PBMC:SLE,Tcell:SLE; 1 :949893, AGRN||5' Proximal Enhancer: - 5609,ISG15||Exon 2: 1047, PBMC:SLE,Tcell:SLE; 20:29534074, Bcell:OA; 20:35584019, SAMHDl ||Distal Promoter: -3773, Tcell:SLE; 20:36885605, KIAA1755||Intron 1 :3569, Bcell:HC; 20:36975083, BPI||3' Proximal Enhancer:42532,LBP||Proximal Promoter: 199, Tcell:OA; 20:37462474, PPPlR16B||Intron 1 :28127, Tcell:SLE; 20:4201164, ADRA1D||3' Proximal Enhancer:28495, Bcell:HC; 20:44874567, CDH22||Intron 1 :5767, Bcell:HC; 20:47448545, PREXl ||Distal Promoter: -4125, PBMC:HC; 20:61732467, HARlA||Proximal Promoter:-176,HARlB||Intron 1 : 1204, Tcell:HC; 20:62198469, PRIC285||Exon l :638|Exon 7:7123, Mono:SLE; 20:62198872, PRIC285||Exon 7:6720|Proximal Promoter:235, Bcell:SLE,PBMC:SLE,Tcell:SLE; 20:62199034, PRIC285||Intron 6:6558|Proximal Promoter:73, PBMC:SLE,Tcell:SLE; 20:62199156, PRIC285||Intron 6:6436|Proximal Promoter: -49, PBMC:SLE,Tcell:SLE; 20:62199181, PRIC285||Intron 6:641 l |Proximal Promoter: -74, PBMC:SLE,Tcell:SLE; 20:62199190, PRIC285||Intron 6:6402|Proximal Promoter:-83, PBMC:SLE,Tcell:SLE; 20:62200091, PRIC285||Exon 6:5501 |Proximal Promoter:-984, Bcell:SLE,PBMC:SLE,Tcell:SLE; 20:62200199, PRIC285||Exon 6:5393|Proximal Promoter: -1092, Mono:SLE,PBMC:SLE,Tcell:SLE; 20:62200285, PRIC285||Exon 6:5307|Proximal Promoter:- 1178, PBMC:SLE; 20:62204908, PRIC285||5' Proximal Enhancer: -580 l |Intron 1 :684, Bcell:SLE,Mono:SLE,PBMC:SLE; 20:62212228, GMEB2||3' Proximal Enhancer:46153,PRIC285||5' Proximal Enhancer:-6636, PBMC:SLE,Tcell:SLE; 21 :34398085, OLIG2||Proximal Promoter:- 130, PBMC:OA; 21 :42218964, Tcell:OA; 21 :42791867, MX1 ||5' Proximal Enhancer:-6110|5' Proximal Enhancer:-6235|Proximal Promoter: -652, Mono:SLE; 21 :42797588, MXl ||Intron 3:5069|Proximal Promoter: -389|Proximal Promoter:-514, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 21 :42797847, MXl ||Intron 3:5328|Proximal Promoter:-130|Proximal Promoter: -255,
Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 21 :42798747, MXl ||Intron l :645|Intron l:770|Intron 3:6228, Bcell:SLE,Tcell:SLE; 21 :42799141, MXl pxon 2: 1164|Exon 4:6622|Intron 1 : 1039, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 21 :45149398, PDXK||Intron 1 : 10421, Bcell:OA; 21 :46495607, ADARBl ||Intron l : 1115,SSR4Pl ||Proximal Promoter: -2481, PBMC:SLE; 21 :47396773, COL6Al ||Distal Promoter: -4889, PBMC:SLE; 22: 18635460, USP18||Intron 1 :2703, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 22: 19742426, TBXl ||Proximal Promoter:- 1799, Tcell:SLE; 22:21399663, LOC400891 ||Proximal Promoter:-585,P2RX6P||Proximal Promoter:-1125, Bcell:OA; 22:22001120, CCDC116||3' Proximal Enhancer: 14035,MIR130B||5' Proximal Enhancer:-6472,MIR301B||5' Proximal Enhancer:-6149,SDF2L1 ||3' Proximal Enhancer:4579, Bcell:OA; 22:24979964, FAM211B||3' Proximal Enhancer:9071,GGTl ||Proximal Promoter:247, Bcell:SLE,Mono:SLE,PBMC:SLE; 22:32555310, C22orf42||Proximal Promoter:-67, Bcell:HC; 22:32572348, Tcell:OA; 22:35389501, PBMC:OA; 22:45608465, Mono:HC; 22:45737514, FAM118A||Exon 10:32434|Exon 9:31730,SMC1B||3' Proximal Enhancer:71986, PBMC:SLE; 22:46760595, CELSRl ||Exon 33: 172472,TRMU||3' Proximal Enhancer:29298, Tcell:OA; 22:46835192, CELSRl ||Exon 3:97875, Tcell:OA; 22:49087783, FAM19A5||Intron 2: 115666, Bcell:HC; 22:50984368, KLHDC7B||Proximal Promoter:-2093,SYCE3||3' Proximal Enhancer: 16960, Mono:SLE,PBMC:SLE; 22:50984393, KLHDC7B||Proximal Promoter: - 2068,SYCE3||3' Proximal Enhancer: 16935, Mono:SLE; 22:50986813, KLHDC7B||Proximal Promoter:352,SYCE3||3' Proximal Enhancer: 14515, Tcel SLE; 2: 113521451, CKAP2L||Intron 1 :803, BcelhHC; 2: 127841945, BINl ||Intron 1 :22958, PBMC:SLE; 2: 128142155, Bcel HC; 2: 128168798, PROC||5' Proximal Enhancer: -7197, PBMC:OA; 2: 1481492, TPO||Intron 6:Intron 7:63313|Intron 8:64260, Mono:OA; 2: 150176814, LYPD6||5' Proximal Enhancer:-9684, Tcel OA; 2: 157291262, GPD2||Proximal Promoter:-1637|Proximal Promoter:-702, PBMC:SLE; 2: 161188335, RBMS l||Intron 2: 161983, Mono:SLE; 2: 174881312, Mono:HC; 2: 175753137, CHNl ||Intron 5: 116844|Intron 5:Intron 6: 116970, Mono:OA; 2: 183237787, PDElA||Intron l : 149466|Intron 2: 149678, BcelhHC; 2: 190447407, SLC40Al ||Proximal Promoter:- 1870, Bcell:SLE,Mono:SLE; 2: 191894418, STAT4||Exon 24: 121568|Exon 24: 121904, Bcell:SLE,Mono:SLE; 2: 19553422, MIR4757||3' Proximal Enhancer:5233,OSRl ||Exon 2:4950, Tcel OA; 2: 198246278, Mono:OA; 2:201170806, SPATS2L||Proximal Promoter:- 178|Proximal Promoter: - 549|Proximal Promoter:203, PBMC:SLE; 2:201194453, SPATS2L||Intron 2:23098|Intron 2:23469|Intron 2:23850, PBMC:SLE,Tcell:SLE; 2:203159409, SNORDl l ||3' Proximal Enhancer: 1636,SNORDl lB||3' Proximal Enhancer:3370, Bcel OA; 2:211090171, ACADL|| Proximal Promoter:44, PBMC:OA; 2:223166989, CCDC140||Intron l :4124,PAX3||Distal Promoter:-3274, PBMC:OA; 2:231714705, Mono:HC; 2:231714995, Mono:HC; 2:233384768, CHRND||5' Proximal Enhancer: - 6153,PRSS56||Proximal Promoter: -404, PBMC:OA; 2:237072673, GBX2||3' Proximal Enhancer:3979, PBMC:OA; 2:238410067, MLPH|| Intron 2: 14190, PBMC:SLE; 2:240265915, MIR2467||3' Proximal Enhancer:7584, TcelhOA; 2:241900108, LOC200772||Intron 3:6760, BcelhSLE; 2:27073253, DPYSL5||Intron l : 1962|Intron l :2097|Intron 1 :2285, Tcel OA; 2:27529788, MPV17||3' Proximal Enhancer:16181,TRIM54||Exon 10:Exon 9:24492,UCN||3' Proximal Enhancer: 1342, PBMC:OA; 2:43398079, TcelhSLE; 2:43398339, PBMC:SLE,Tcell:SLE; 2:45165946, SIX3||Distal Promoter:-3090, PBMC:OA; 2:45234140, SIX2||Intron 1:2402, Mono:OA; 2:47319, FAM110C||Proximal Promoter: -731, Tcel OA; 2:583975, Bcel HC; 2:620044, Bcel HC; 2:64373042, PELIl||Proximal Promoter: -1437, PBMC:HC; 2:65086991, Bcel OA; 2:66671478, MEISl||Intron 6:8947, PBMC:HC; 2:7004578, CMPK2||Intron 1:1358, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 2:74645397, C2orffil||Proximal Promoter:-553,RTKN||3' Proximal Enhancer:22313|3' Proximal Enhancer:23663,WDR54||Distal Promoter: - 3487, Tcel OA; 2:74668672, RTKN|| Proximal Promoter: -9621 Proximal Promoter:388, PBMC:HC; 2:75681243, Mono:OA; 2:80229409, Bcel HC; 2:84709147, PBMC:SLE; 2:85977911, ATOH8||Distal Promoter: -2997, BcelhOA; 2:86038538, LOC284950||Distal Promoter:-3714, Mono:OA; 2:87141088, RGPDl||Distal Promoter:-3649,RGPD2||Proximal Promoter:154, BcelhOA; 2:87572542, BcelhOA; 3:10397182, ATP2B2||Intron ll:Intron 14:150086, BcelhOA; 3:107810507, CD47||Proximal Promoter:- 572, Tcel SLE; 3:107810716, CD47||Proximal Promoter:-781, PBMC:SLE,Tcell:SLE; 3:108321607, DZIP3||Intron 1:13271, PBMC:HC,PBMC:SLE; 3:116996975, TcelhOA; 3:122281881, DTX3L||Proximal Promoter:-1303,PARP9||Intron l:1266|Intron l:1313|Intron 1:1642,
Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 3:122281939, DTX3L|| Proximal Promoter:- 1245,PARP9||Intron l:1208|Intron l:1255|Intron 1:1584, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 3:122281975, DTX3L|| Proximal Promoter:-1209,PARP9||Intron l:1172|Intron l:1219|Intron 1:1548, PBMC:SLE; 3:122284215, DTX3L||Intron l:1031,PARP9||Proximal Promoter: -102 l|Proximal Promoter:- 1068|Proximal Promoter:-692, PBMC:SLE; 3:122286677, DTX3L||Intron 2:3493,PARP15||5' Proximal Enhancer:-9771,PARP9||Distal Promoter:-3154|Distal Promoter:-3483|Distal Promoter:-3530, Tcel SLE; 3:122400474, PARP14||Intron 1:803, Mono:SLE,PBMC:SLE; 3:122401300, PARP14||Intron 1:1629, Bcell:SLE,PBMC:SLE,Tcell:SLE; 3:122401343, PARP14||Intron 1:1672,
Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 3:133160722, BFSP2||Intron 1:41933, PBMC:SLE; 3:135432551, BcelhHC; 3:138668349, C3orf72||Intron l:2274,FOXL2||Proximal Promoter: -2367, Tcel OA; 3:13894328, WNT7A||Intron 3:27290, PBMC:SLE; 3:141163704, ZBTB38||Exon 8:120650, PBMC:HC; 3:145734655, TcelhOA; 3:147110378, ZIC4||Intron 2:Intron 3:14218|Intron 3: 11693| Intron 3:12929|Proximal Promoter:-161, PBMC:OA; 3:147112438, ZIC4||Intron 2:Intron 3:12158|Intron 3:10869|Intron 3:9633|Proximal Promoter: -2221, TcelhOA; 3:147130536, ZICl||Intron 2:3356,ZIC4||5' Proximal Enhancer: -5940|5' Proximal Enhancer: -7229|5' Proximal Enhancer:-8465, PBMC:OA; 3:150996563, P2RY14||Proximal Promoter:-333, BcelhSLE; 3:156394028, TIPARP || Intron l:1314|Intron l:1824|Proximal Promoter: -424,TIPARP-ASl||Proximal Promoter:-526, Bcel HC; 3:160121821, IFT80||Distal Promoter:-4501,MIR15B||Proximal Promoter: -554,MIR16-2||Proximal Promoter: - 711,SMC4||Intron 3:3475|Intron 4:4392, PBMCSLE; 3:160544991, PPM 1L|| Intron 1:70996, PBMC:OA; 3:165908381, BcelhHC; 3:168726716, Bcel HC; 3:168870287, MECOM||5' Proximal Enhancer: -5887|5' Proximal Enhancer:-6194|Distal Promoter: -4765 |Intron l:Intron 2:511276, Bcel HC; 3:179598680, PEX5L||Intron 4:155837, Mono:OA; 3:181045270, PBMC:OA; 3:193922037, Bcel OA; 3:193922375, BcelhOA; 3:193922406, Mono:OA; 3:194071770, CPN2||Proximal Promoter:287,LRRC15||3' Proximal Enhancer: 18702, Tcel OA; 3:194407750, FAM43A||Exon 1:1129, Mono:OA; 3:195632915, TNK2||Intron 1:2965, PBMC:SLE; 3:22412746, Bcell:SLE,Mono:SLE,PBMC:SLE; 3:27521365, Bcel SLE; 3:32023475, OSBPL10||Proximal Promoter:-133,ZNF860||Proximal Promoter:210, Bcel OA; 3:42976884, KRBOXl||Proximal Promoter: -949, PBMC:SLE; 3:46506374, LTF||Proximal Promoter:-1213|Proximal Promoter:224, TcelhOA; 3:48507087, ATRIP||3' Proximal Enhancer: 18870,SHISA5||3' Proximal Enhancer:34574,TREXl||Proximal Promoter:- 141, Tcel SLE; 3:48508391, ATRIP||3' Proximal Enhancer:20174,SHISA5||3' Proximal Enhancer:33270,TREXl||Exon l:Exon 2:1163, Mono:SLE; 3:55514421, WNT5A||Intron 2:6910, PBMC:OA; 3:68981895, FAM19A4|| Proximal Promoter:- 134, PBMC:OA; 3:70744125, Tcel OA; 3:72305082, Mono:SLE; 4:101715708, BcelhHC; 4:140621943, MGST2||Intron 2:Intron 3:35022, PBMC:HC; 4:15007205, CPEB2||Intron l:2908,LOC441009||Distal Promoter:-3536, Bcell:SLE,PBMC:SLE; 4:1520151, Bcel OA; 4:154092267, TRIM2|| Intron 1:17998, PBMC:OA; 4:154681066, RNF175||Proximal Promoter:321, PBMC:OA; 4:158141936, GRIA2||Proximal Promoter: 117|Proximal Promoter:201, Tcel OA; 4:165304531, PBMC:OA; 4:168824531, Bcell:OA,Mono:OA; 4:169239131, DDX60||Intron 1:827, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 4:169242366, DDX60||Proximal Promoter:-2408, Tcel SLE; 4:172734031, GALNTL6||Proximal Promoter:-543, TcelhOA; 4:17580680, LAP3||Intron 1:1754, PBMC:SLE,Tcell:SLE; 4:184018031, C4orG8||3' Proximal Enhancer:2321,WWC2||Proximal Promoter: -2431, Mono:OA; 4:184939030, STOX2||3' Proximal Enhancer: 112522, TcelhOA; 4:23936764, Mono:SLE; 4:2431998, LOC402160||Intron 2:11298, PBMC:HC; 4:3531603, LRPAPl ||Intron 1:2621, PBMC:HC; 4:40890484, APBB2||Intron ll:Intron 12:326151, TcelhOA; 4:57845134, NOAl||Proximal Promoter:-1308,POLR2B||Proximal Promoter:26, Bcel OA; 4:70080453, UGT2Bll||Proximal Promoter:-4, BcelhOA; 4:7437027, PSAPLl||Proximal Promoter:-327, Tcel OA; 4:74486558, RASSF6||Proximal Promoter: -218|Proximal Promoter: -424, Mono:OA; 4:74810142, TcelhOA; 4:7646087, Bcell:HC; 4:77119206, SCARB2||Intron 1:15846, BcelhHC; 4:83886021, LIN54||Intron 4:4596 l|Intron 4:48019, Mono:OA; 4:8396163, ACOX3||Intron 10:46289, BcelhOA; 4:89204074, PPM 1K|| Intron 1:1814, Bcell:SLE; 4:89302999, HERC6||Intron 1:3109, Tcell:SLE; 4:99851060, EIF4E||Exon l:726|Proximal Promoter:-817, Mono:HC; 5:102201137, PAM||Proximal Promoter:-389, Mono:OA; 5:110948135, LOC100505678||Intron 1:100212, BcelhOA; 5:1231351, SLC6A18||Intron 1:5882,SLC6A19||3' Proximal Enhancer:29642, PBMC:OA; 5:138725830, C5orf65||3' Proximal Enhancer:5055,MZBl||Proximal Promoter: -225,SLC23A1||5' Proximal Enhancer:-6791,SPATA24||3' Proximal Enhancer: 13946, Tcell:SLE; 5:139017367, UBE2D2||3' Proximal Enhancer:76617, PBMC:OA; 5:140249080, PCDHAl||Intron l:83205,PCDHA10||Intron l:13447,PCDHAll||Exon 1:1250,PCDHA12||5' Proximal Enhancer:-5850,PCDHA2||Intron l:74637,PCDHA3||Intron l:68298,PCDHA4||Intron l:62409,PCDHA5||Intron l:47720,PCDHA6||Intron l:41431,PCDHA7||Intron 1:35112,PCDHA8||Intron l:28174,PCDHA9||Intron 1:21724, Bcell:OA; 5:140256817, PCDHAl||Intron l:90942,PCDHA10||Intron 1:21184,PCDHA11||3' Proximal Enhancenlntron l:8987,PCDHA12||Exon 1:1887,PCDHA13||5' Proximal Enhancer:-5036,PCDHA2||Intron l:82374,PCDHA3||Intron l:76035,PCDHA4||Intron l:70146,PCDHA5||Intron l:55457,PCDHA6||Intron l:49168,PCDHA7||Intron l:42849,PCDHA8||Intron 1:3591 l,PCDHA9||Intron 1:29461, Bcell:OA; 5:140621375, PCDHB15||Distal Promoter:-3771,PCDHB18||3' Proximal Enhancer:7438,PCDHB19P||Exon 1:1687, PBMC:OA; 5:141392795, GNPDAl||Proximal Promoter:-175, Mono:OA; 5:152729842, PBMC:SLE; 5:153192843, GRIAlpxon 16:322760, Tcell:OA; 5:16785399, MYO10||Intron 4:150986, Bcell:OA; 5:172306136, ERGICl||Intron 1:44914, Tcell:HC; 5:172314133, ERGICl||Intron 1:52911, PBMC:HC; 5:173351052, CPEB4||Intron 2:35722, Mono:SLE; 5:173602861, Tcell:OA; 5:180674133, GNB2Ll||Distal Promoter:-3227,SNORD95||Distal Promoter:-3757,SNORD96A||5' Proximal Enhancer: - 5244,TRIM52||3' Proximal Enhancer: 13986, PBMC:SLE,Tcell:SLE; 5:1834527, Tcel OA; 5:35803436, SPEF2||Intron 34:185448, PBMC:SLE; 5:4512242, Tcel OA; 5:50266099, BcelhOA; 5:50678451, ISLl||Proximal Promoter: -506, Tcel OA; 5:54319996, GZMK||Proximal Promoter:- 110, Bcel SLE; 5:55117749, DDX4||3' Proximal Enhancer:55037|3' Proximal Enhancer:83905, PBMC:OA; 5:55775841, PBMC:SLE; 5:56268061, PBMC:SLE; 5:65182255, PBMC:OA; 5:66296978, MAST4||Intron 3:172375|Intron 4:404803, Mono:HC; 5:783220, TcelhOA; 5:79552537, SERINC5||Proximal Promoter: - 639, Bcel SLE; 5:79869070, ANKRD34B||Distal Promoter:-2766, TcelhOA; 5:80257268, RASGRF2||Intron 1:761, PBMC:SLE; 5:93530270, KIAAO 8251| Intron 20:424039, Bcel HC; 5:95514729, BcelhHC; 6:100676889, Tcel OA; 6:10398601, TFAP2A||Exon 7:14006|Exon 7:16869|Exon 7:21196, Tcel HC; 6:10414565, LOC100130275||Intron l:2015,TFAP2A||Intron l:5232|Intron 1:905 |Proximal Promoter:-1958, BcelhOA; 6:110300146, GPR6|| Proximal Promoter:-151, BcelhOA; 6:110300218, GPR6||Proximal Promoter:-79, Tcel OA; 6:11032802, ELOVL2||Intron 1:11822, Tcel OA; 6:119662024, MANlAl||Intron 2:8902, Mono:SLE; 6:119862526, PBMC:SLE; 6:14037614, PBMC:OA; 6:145217150, Tcel OA; 6:15300007, JARID2|| Intron 1:53481, Tcel HC; 6:161350484, Tcel OA; 6:1619687, FOXCl||3' Proximal Enhancer:9007,GMDS||3' Proximal Enhancer:556538|3' Proximal Enhancer:626181, Tcel OA; 6:1624442, GMDS||Exon 1 l:551783|Exon 11:621426, PBMC:HC; 6:164506861, BcelhOA; 6:168196493, C6orfl23||Intron 1:1046, Tcel HC; 6:17764205, KIF13A||Exon 37:Exon 38:Exon 39:Intron 37:223649, PBMC:HC; 6:25180502, Mono:SLE; 6:25652602, SCGN||Proximal Promoter: 174, PBMC:OA; 6:26330584, PBMC:SLE; 6:28912126, Bcel SLE; 6:29599390, GABBRl||Distal Promoter:-3385|Intron 2:1572, TcelhHC; 6:29620138, MOG||Distal Promoter: -4619, TcelhOA; 6:29635507, MOG||Intron 3:Intron 4:10750,ZFP57||3' Proximal Enhancer:9424, Bcell:SLE,PBMC:SLE; 6:29692035, HLA-F||Exon 3:919,HLA-F-AS1||3' Proximal Enhancer:24791, Bcel SLE; 6:29692082, HLA-F||Exon 3:966,HLA-F- AS1||3' Proximal Enhancer:24744, PBMC:SLE; 6:29692085, HLA-F||Exon 3:969,HLA-F-AS1||3' Proximal Enhancer:24741, Bcell:SLE,Mono:SLE; 6:29692092, HLA-F||Exon 3:976,HLA-F-AS1||3' Proximal Enhancer:24734, BcelhSLE; 6:29692111, HLA-F||Exon 3:995,HLA-F-AS1||3' Proximal Enhancer:24715, Mono:SLE; 6:29975239, HLA-J||Intron 3:1492,ZNRDl-ASl||Intron 5:53722, TcelhOA; 6:30067855, TRIM31||3' Proximal Enhancer: 13012, Mono:SLE; 6:30079192, TRIM31||Intron 3:1675, Bcel OA; 6:30619232, ATAT1||3' Proximal Enhancer:24570|3' Proximal Enhancer:24618|3' Proximal Enhancer:24620,C6orfl36||Exon 3:Exon 4:4417,DHX16||3' Proximal Enhancer:21598, Mono:HC; 6:31166799, HCG27||Intron 1:1263, PBMC:HC; 6:31323677, HLA-B||Intron 3:1312, Bcell:SLE,PBMC:SLE; 6:31431312, HCG26||5' Proximal Enhancer:-7693,HCP5||Proximal Promoter:356, Bcell:SLE,Mono:SLE; 6:31431407, HCG26||5' Proximal Enhancer:-7598,HCP5||Proximal Promoter:451, Bcell:SLE,PBMC:SLE; 6:31431503, HCG26||5' Proximal Enhancer:-7502,HCP5||Exon 2:547, Bcell:SLE,PBMC:SLE; 6:31431902, HCG26||5' Proximal Enhancer:-7103,HCP5||Exon 2:946, Mono:SLE; 6:31431969, HCG26||5' Proximal Enhancer:-7036,HCP5||Exon 2:1013, BcelhSLE; 6:31582837, AIFl||Proximal Promoter: -156|Proximal Promoter: -195 |Proximal Promoter:-951,PRRC2A||5' Proximal Enhancer:-5612,SNORA38||5' Proximal Enhancer:-8018, PBMC:HC; 6:31996931, C4A||Intron 27:14360,C4B||Intron 27:14360,CYP21A2||5' Proximal Enhancer:-9161,LOC100293534||Intron 27:14360, Tcell:OA; 6:32373620, BTNL2||Intron 1:1280, Mono:OA; 6:32552547, HLA-DRB 1 |Intron 1:5066, Tcell:HC; 6:32632159, HLA-DQB 1 |Intron 2:2307, Bcell:OA; 6:32805554, LOC100507463||5' Proximal Enhancer:-6308,PSMB8||3' Proximal Enhancer:6262|3' Proximal Enhancer:7158,TAPl||3' Proximal Enhancer:16194,TAP2||Exon 2:993, PBMC:SLE; 6:32808918, LOCI 00507463 ||Distal Promoter: - 2944,PSMB8||Intron 5:2898|Intron 5:3794,TAP1||3' Proximal Enhancer: 12830,TAP2||Proximal Promoter: - 2371, Tcel SLE; 6:32811251, LOC100507463||Proximal Promoter:-61 l,PSMB8||Intron l:1461|Intron 1:565,TAP1||3' Proximal Enhancer: 10497,TAP2||Distal Promoter:-4704, Mono:SLE; 6:32820355, LOC100507463||3' Proximal Enhancer:8493,PSMB8||5' Proximal Enhancer:-7643|5' Proximal Enhancer: - 8539,PSMB9||Proximal Promoter:- 1582,TAPl||Intron 1:1393, Mono:SLE; 6:33131745, COL 11A2|| Intron 62:Intron 63:Intron 65:28500, TcelhOA; 6:33679850, C6orfl25||Proximal Promoter: -346,IP6K3||3' Proximal Enhancer:34912, Mono:OA; 6:40567376, Mono:OA; 6:43214396, TTBKl||Exon 2:3175, BcelhOA; 6:44295389, TcelhOA; 6:4459669, TcelhOA; 6:45608938, TcelhOA; 6:45629759, Bcel HC; 6:68596887, Mono:OA; 6:72131020, LINC00472||Proximal Promoter: -572, PBMC:SLE; 6:75912711, COL12Al||Intron 1:2912, BcelhOA; 7:101364176, Bcel SLE; 7:104460407, Tcel OA; 7:105348517, ATXN7Ll||Intron 3:168514, PBMC:SLE; 7:123992223, BcelhOA; 7:129254604, NRFl||Intron 1:3050, BcelhHC; 7:130646051, FLJ43663||Intron 2:145738|Intron 3:147511, Mono:HC; 7:139761087, PARP12||Intron 1:2434, PBMC:SLE; 7:142494244, Tcel HC; 7:150018095, ACTR3C||Intron l:2663,C7orl29||5' Proximal Enhancer:-8842,LRRC61||Proximal Promoter:-2200, Mono:OA; 7:150026567, ACTR3C||5' Proximal Enhancer:-5809,C7orl29||Proximal Promoter: -370,LRRC61||Intron l:Intron 2:6272,RARRES2||3' Proximal Enhancer: 12196, Bcell:OA,Mono:OA,Tcell:OA; 7:150216489, GIMAP7||Intron 1:4545, Tcel HC; 7:155674426, BcelhHC; 7:155790512, Mono:OA; 7:15725322, MEOX2||Intron 1:986, PBMC:OA; 7:157620445, PBMC:SLE; 7:158381023, PBMC:OA; 7:2444010, CHST12||Intron 1:816, PBMC:SLE,Tcell:SLE; 7:2444534, CHST12||Intron 1:1340, PBMC:SLE; 7:2646782, IQCEpxon 20:Exon 21:48151, Mono:OA; 7:29923120, WIPF3||Intron 4:76951, Tcel OA; 7:30185776, C7orf41||Intron 1:11225, PBMC:SLE; 7:38370988, PBMC:OA; 7:43562162, LOC100506895||Proximal Promoter: -21, BcelhHC; 7:47846424, C7orf69||Intron l:11536,PKDlLl||Intron 52:141647, PBMC:HC; 7:64126140, ZNF107||Proximal Promoter: -370, PBMC:SLE; 7:70139561, AUTS2||Intron 5:1075656|Intron 5:1075657, PBMC:SLE,Tcell:SLE; 7:79083447, MAGI2-AS3||Intron l:Intron 2: 1175 Proximal Promoter: 172, PBMC:OA; 7:93190462, Bcel SLE; 7:94953956, PONl||Proximal Promoter: -72, PBMC:SLE; 7:95026106, PON2||3' Proximal Enhancer:38278,PON3||Proximal Promoter:- 419, PBMC:OA; 7:961384, ADAPl||Intron 3:32905, PBMC:OA; 7:965534, ADAPl||Intron 3:28755, PBMC:SLE; 7:96631680, DLX6||Distal Promoter:-3609,DLX6-ASl||Intron 1:11697, Tcel OA; 7:97361241, TACl||Proximal Promoter: -29, PBMC:OA; 7:98739782, SMURFl||Intron 1:1961, PBMC:SLE; 7:99773786, GAL3ST4||5' Proximal Enhancer:-7413,GPC2||Intron 2:1204,STAG3||Proximal Promoter:- 1751, TcelhOA; 8:104177564, LOC100499183||3' Proximal Enhancer:6804, TcelhOA; 8:10488231, RPlLl||Intron 1:24386, Mono:SLE; 8:106330173, ZFPM2|| Proximal Promoter:-973, Mono:OA; 8:11338675, PBMC:OA; 8:11567691, GATA4||Intron 2:5975, TcelhOA; 8:1365175, Mono:OA; 8:144070338, LOC100133669||Intron 1:29469, BcelhSLE; 8:144098888, LOC100133669||Intron l:919,LY6E||Proximal Promoter:-1013, PBMC:SLE; 8:144099482, LOC 100133669| |Proximal Promoter: 325,LY6E| |Proximal Promoter: -419,
Bcell:SLE,PBMC:SLE,Tcell:SLE; 8:144102584, LOC100133669||Distal Promoter: -2777,LY6E||Intron 2:2683, Mono:SLE,PBMC:SLE,Tcell:SLE; 8:144103587, LOC100133669||Distal Promoter:- 3780,LY6E||Exon 4:3686, Bcell:SLE,PBMC:SLE,Tcell:SLE; 8:144105210, LOC100133669||5' Proximal Enhancer:-5403,LY6E||3' Proximal Enhancer:5309, PBMC:SLE; 8:145025059, MIR661||5' Proximal Enhancer:-5612,PLEC||5' Proximal Enhancer:-6154|5' Proximal Enhancer: -6949|5' Proximal Enhancer:- 8367|Intron 1:22638|Intron l:3029|Intron 2:25854|Proximal Promoter:-15, Mono:OA; 8:145086427, SPATC1 IProximal Promoter: -154, Bcel OA; 8:1649143, DLGAP2|| Intron 11:199575, Mono:HC; 8:21549935, GFRA2||Exon 7:Exon 8:Exon 9:96411, Bcel SLE; 8:22503577, BIN3||Intron l:23084,FLJ14107||Distal Promoter:-3855, PBMC:SLE; 8:23560319, NKX2-6||Exon 2:3792, TcelhOA; 8:25901422, EBF2||Intron 1:1218, Tcel OA; 8:2591207, Mono:OA; 8:27850175, BcelhOA; 8:37119428, Tcel SLE; 8:42266931, SLC20A2||3' Proximal Enhancer:130137,VDAC3||3' Proximal Enhancer: 17653, BcelhHC; 8:54764515, ATP6V1H||5' Proximal Enhancer:-8665|5' Proximal Enhancer: - 8968,RGS20||Proximal Promoter:148, Bcel HC; 8:582908, Bcel SLE; 8:599963, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 8:600039, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 8:600233, Bcell:SLE,Mono:SLE,Tcell:SLE; 8:600429, Bcel SLE; 8:600488, Bcell:SLE,Mono:SLE; 8:61777711, CHD7||Exon 38:186388, PBMC:SLE; 8:61777859, CHD7||Exon 38:186536, PBMC:SLE; 8:66751182, PDE7A||Intron 1:2787, Bcell:SLE,Mono:SLE,PBMC:SLE; 8:67592861, C8orf44||Exon 3:13075,C8orf44-SGK3||Intron 2:13075, Bcell:SLE,Tcell:SLE; 8:67839134, SNHG6|| Proximal Promoter: - 1357,SNORD87||Distal Promoter:-4350, Tcel OA; 8:92528313, Bcel HC; 8:9759720, LOC157627||Exon 1:1119,MIR124-1||3' Proximal Enhancer: 1262, Mono:OA; 9:100394654, NCBPl||Proximal Promoter:- 1050,TSTD2||Intron 1: 1308, Bcell:SLE,PBMC:SLE; 9: 100850391, NANS||3' Proximal Enhancer:31433,TRIM14||Intron 5:31089|Intron 5:31097, Bcell:SLE,Mono:SLE,PBMC:SLE; 9: 101471921, GABBR2|| Proximal Promoter: -442, Tcell:OA; 9:124463457, DAB2IP||Intron 3:134059, Bcell:OA; 9: 133792985, FIBCDl||Intron 4:21254|Intron 5:21470, PBMC:OA; 9: 134139878, FAM78A||Intron 1:12028, PBMC:SLE; 9: 138518416, GLT6Dl||Intron 3:12970, PBMC:OA,Tcell:OA; 9: 138549731, LCN9||5' Proximal Enhancer:-5436, Tcell:OA; 9: 140703637, Mono:SLE; 9:32525008, DDX58||Intron 1: 1314, Tcell:SLE; 9:37649417, FRMPDl||Proximal Promoter:-1634, Bcell:OA; X: 135863102, ARHGEF6||Proximal Promoter:401, Tcell:OA; X: 149106647, CXorf40B||Proximal Promoter:69,LOC100272228||Proximal Promoter:- 118, Mono:OA; X:149742400, MTMl||Intron 1:5354, Bcell:HC; X: 15353772, FIGF||3' Proximal Enhancer:48763,PIGA||Proximal Promoter: -96,PIR-FIGF||3' Proximal Enhancer: 155660, Mono:OA; X: 154255174, FUNDC2||Proximal Promoter: 111 , Mono:OA; X: 17755305, NHS||3' Proximal Enhancer: 101893,SCMLl||Proximal Promoter: -286, BcelhOA; X: 17878715, RAI2||Intron l:742|Proximal Promoter:232, BcelhOA; X:21392644, CNKSR2||Proximal Promoter: 109, Mono:OA; X:21393508, CNKSR2||Intron 1:973, Bcell:OA; X:2836114, ARSD||Exon 5: 11302, Tcell:OA; X:51361885, Mono:OA; X:69509686, ARR3||3' Proximal Enhancer:21502,KIF4A||Proximal Promoter:-192,PDZDl l||Proximal Promoter: 112,RAB41||3' Proximal Enhancer:7665, Bcell:OA; X:83757504, HDX||Proximal Promoter:-17, Mono:OA
Table 2B
Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:100137031, PYROXD2||3' Proximal Enhancer: 37947, BcelhHC; 10: 101732382, PBMC:notRA; 10:101843063, CPNl||Proximal Promoter: -1421, PBMCnotRA; 10:102295134, HIF1 AN || Proximal Promoter: -506,NDUFB8||5' Proximal Enhancer:-5498, TcelhOA; 10:102381532, Tcel OA; 10: 102984681, FLJ41350||Distal Promoter:-4669,LBXl||3' Proximal Enhancer:4036, TcelhOA; 10: 102997382, FLJ41350||Intron 2:8032,LBX1||5' Proximal Enhancer:-8665, PBMC:OA; 10:103484797, Bcel HC; 10:104169733, FBXL15||5' Proximal Enhancer:-9837,NFKB2||3' Proximal Enhancer: 1430213' Proximal Enhancer:15395|3' Proximal Enhancer: 15505,PSD||Intron 10:9168, PBMC:OA_SLE_HC,PBMC:SLE; 10:104194843, CUEDC2||Proximal Promoter:-2420,MIR146B||Proximal Promoter:-1425, Tcell:OA_SLE_HC; 10:104436140, ARL3||Exon 6:38050, PBMC:HC; 10: 105357975, NEURL||3' Proximal Enhancer: 104241,SH3PXD2A|| Exon 14:257189, Wholeblood:notRA; 10: 105730465, SLK||Intron 1:2996, Tcel HC; 10: 105846002, Bcell:OA_SLE_HC; 10:106028329, GST01||3' Proximal Enhancer:13862|3' Proximal Enhancer: 14378,GST02||5' Proximal Enhancer:-6557|Proximal Promoter:- 301,MIR4482-l||Proximal Promoter:- 166, Bcell:OA_SLE_HC; 10:106029337, GST01||3' Proximal Enhancer: 14870|3' Proximal Enhancer: 15386,GST02||5' Proximal Enhancer:-5549|Intron 1:707,MIR4482- l||Proximal Promoter:-l 174, Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 10:106068573, GST02||3' Proximal Enhancer:33687|3' Proximal Enhancer:39943,ITPRIP||3' Proximal Enhancer:25090, PBMC:HC; 10:110226691, Mono:SLE; 10: 111152929, PBMC:OA_SLE_HC; 10:111659903, XPNPEPl||Intron 2:Intron 3:23408, PBMC:HC; 10:112170649, Mono:HC; 10: 112507322, RBM20||Intron 1:103168, PBMC:SLE; 10: 113987376, PBMC:HC; 10: 113987401, PBMC:HC; 10:11443364, PBMC:OA_SLE_HC; 10:115024317, PBMC:notRA; 10: 115804095, ADRBl||Proximal Promoter:290, PBMC:OA; 10:116301354, ABLIMl||Intron 6:116704|Intron 6:143060, PBMC:HC,Tcell:HC; 10:116581248, FAM160Bl||Proximal Promoter:-254, PBMC:HC; 10:117997745, GFRAl||Intron 3:34074|Intron 4:3505 l|Intron 4:35381, PBMC:OA_SLE_HC,PBMC:notRA; 10: 118084587, C10ori96||Exon 2:648, PBMC:notRA; 10:118459383, HSPA12A||Intron 4:42702, PBMC:SLE; 10: 120282778, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE; 10:12085641, UPF2||Proximal Promoter: -472|Proximal Promoter:-801, PBMC:HC; 10: 120968739, GRK5||Intron 1: 1543, Mono:OA_SLE_HC; 10: 121028978, GRK5||Intron 1:61782, PBMC:HC; 10: 121127614, GRK5||Intron 2: 160418,MIR4681||5' Proximal Enhancer:-9869, PBMC:HC; 10:122262397, PPAPDC1A|| Intron 1:45932, PBMC:notRA; 10:122356491, PPAPDC1A||3' Proximal Enhancer: 140026,
PBMC:OA_SLE_HC,PBMC:notRA; 10: 122524702, LOC283089||Intron 2:85989, PBMC:notRA; 10:123748615, TACC2||Proximal Promoter:-73, PBMC:notRA; 10:123872229, TACC2||Intron 3:Intron 5:123541, Tcell:OA; 10:123924042, TACC2||Intron l:938|Intron 4:Intron 7:175354, Tcell:HC; 10:124030740, BTBD16||Proximal Promoter:-80, PBMC:notRA; 10:124181965, MIR3941||3' Proximal Enhancer:5485,PLEKHAl||Intron 8:30147|Intron 8:47872|Intron 9:36381, PBMC:SLE; 10:124402673, DMBTl||Exon 40:Exon 52:Exon 53:82493, PBMC:OA; 10:1245261, ADARB2||Intron 8:534409, PBMC:HC; 10:124757121, IKZF5||Intron 3:11190,PSTK||3' Proximal Enhancer: 17566, PBMC:OA_SLE_HC; 10:125117367, PBMC:notRA; 10:125218684, PBMC:OA; 10:125423240, GPR26||Distal Promoter: -2630, PBMC:notRA; 10:12629812, CAMKlD||Intron 2:238230,MIR4480||3' Proximal Enhancer:9061, Tcell:HC; 10:126390317, FAM53B||Intron 2:42613, PBMC:HC; 10:126428818, FAM53B||Intron 1:4112, PBMC:SLE,Tcell:SLE; 10:126916492, PBMC:notRA; 10:127587253, FANKl||Intron 1:2146, Wholeblood:notRA; 10:127779842, ADAM12||Intron 11:297285, PBMC:OA_SLE_HC; 10: 12810556, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA; 10:128947230, DOCKl||Intron 27:353208,FAM196A||Intron 5:47192, PBMC:notRA; 10:129533731, FOXI2||Proximal Promoter:- 1806, PBMC:notRA; 10:129691429, CLRN3|| Proximal Promoter:-218, PBMC:notRA; 10:129795003, PTPRE||Intron 2:89679, PBMC:HC; 10:129949058, Tcell:HC; 10:130268832, Bcell:HC; 10:130279912, PBMC:HC,PBMC:OA_SLE_HC; 10:130303915, PBMC:notRA; 10:13089772, Mono:OA; 10:131214173, Mono:OA; 10:131682269, PBMC:HC,PBMC:OA_SLE_HC; 10:131682386, PBMC:HC,PBMC:OA_SLE_HC; 10:131697669, PBMC:OA_SLE_HC; 10:131762052, PBMC:HC; 10:131812486, PBMC:notRA; 10:131912837, CTAGE7P||3' Proximal Enhancer:8565,LOC387723||Distal Promoter:-3756, PBMC:notRA; 10:132883127, TCERG1L||3' Proximal Enhancer:226857, PBMC:OA_SLE_HC; 10:133048930, TCERGlL||Intron 4:61054, PBMC:OA_SLE_HC; 10:133449638, PBMC:notRA; 10:133528587, PBMCnotRA; 10:133558971, PBMC:notRA; 10:133647534, PBMC:HC; 10:133786713, BNIP3||Intron 2:8722, PBMC:HC; 10:133786923, BNIP3||Intron 2:8512, Tcell:OA_SLE_HC; 10:133949209, JAKMIP3|| Intron 4:30897, PBMC:OA_SLE_HC; 10:133956824, JAKMIP3||Intron 10:38512,
Bcell:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 10:133956982, JAKMIP3|| Intron 10:38670, PBMC:OA_SLE_HC,PBMC:SLE; 10:134093274, STK32C||Intron 1:28203, Mono:OA; 10:134109919, STK32C||Intron 1:11558, Wholeblood:notRA; 10:134110222, STK32C||Intron 1:11255, PBMC:HC; 10:134150506, LRRC27||Intron 2:4766|Intron 2:4893 |Proximal Promoter:- 104, Tcell:HC; 10:134188873, LRRC27||3' Proximal Enhancer: 38263 |Exon ll:43133|Exon 11:43260, PBMC:HC; 10:134220016, PWWP2B||Intron 2:9315, Wholeblood:notRA; 10:134230885, PWWP2B||Exon 3:20184, Mono:HC; 10:134407912, INPP5A||Intron 1:56560, PBMC:HC,Tcell:HC; 10:134442032, INPP5A||Intron 2:90680, PBMC:OA; 10:134657052, TTC40||Intron 44:99037, PBMC:notRA; 10:134726665, TTC40||Exon 18:29424, Wholeblood:notRA; 10:134729332, TTC40||Intron 17:26757, PBMC:notRA; 10:134775542, PBMC:HC; 10:134775610, PBMC:HC; 10:134775949, PBMC:HC; 10:134837806, PBMCnotRA; 10:134853084, PBMC:SLE; 10:134965215, KNDC1||5' Proximal Enhancer:-8755, PBMC:OA_SLE_HC; 10:134994186, KNDCl||Intron 3:20216, PBMC:OA_SLE_HC; 10:13515358, BEND7||Intron 5:Intron 6:29618, PBMC:notRA; 10:13516370, BEND7||Intron 5:Intron 6:28606, PBMC:OA_SLE_HC; 10:135200523, MTG1||5' Proximal Enhancer:-7097,PAOX||Intron 3:Intron 4:7783, PBMC:notRA; 10:13526193, BEND7||Intron 4:Intron 5:18783, Mono:OA_SLE_HC; 10:135265980, LOC619207||Proximal Promoter:-1451, PBMC:notRA; 10:135436467, FRG2B||3' Proximal Enhancer:3832, Wholeblood:notRA; 10:13831250, FRMD4A|| Intron 5:541616,
PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 10:13858592, FRMD4A|| Intron 3:514274, BcelhOA; 10:1401818, ADARB2||Intron 3:377852, PBMC:HC,PBMC:notRA; 10:1406218, ADARB2||Intron 2:373452, Wholeblood:notRA; 10:1411072, ADARB2|| Intron 2:368598,
PBMC:OA_SLE_HC,PBMC:notRA; 10:1416920, ADARB2|| Intron 2:362750, Wholeblood:notRA; 10:1422865, ADARB2||Intron 1:356805, PBMC:HC; 10:1438548, ADARB2|| Intron 1:341122, PBMC:notRA; 10:1451648, ADARB2|| Intron 1:328022, PBMC:notRA; 10:14620934, FAM107B|| Intron 2:195962, Tcel HC; 10:14650660, FAM107B||Intron 2:166236, PBMC:HC; 10:15025840, PBMC:notRA; 10:15038349, PBMC:OA_SLE_HC; 10:16561351, ClQL3||Intron 1:2653,PTER||3' Proximal Enhancer:82385, PBMC:HC,PBMC:OA_SLE_HC; 10:16561393, ClQL3||Intron 1:2611,PTER||3' Proximal Enhancer: 82427, Bcell:OA_SLE_HC; 10:16561412, ClQL3||Intron 1:2592,PTER||3' Proximal Enhancer: 82446, Bcell:OA_SLE_HC; 10:16859367, CUBN||3' Proximal Enhancer:312449,RSUl||Proximal Promoter:86, PBMC:notRA; 10:17486972, TcelhOA; 10:18549536, CACNB2|| Intron 2:119795|Intron 2:11993 l|Proximal Promoter: -47, PBMCnotRA; 10:18550033, CACNB2|| Intron 2:120292|Intron 2:120428|Proximal Promoter:450, Wholeblood:notRA; 10:18550223, CACNB2||Exon l:640|Intron 2:120482|Intron 2:120618, PBMC:HC; 10:18629602, CACNB2|| Intron l:80019|Intron 2:199861|Intron 2:199997|Proximal Promoter:-ll, PBMC:HC; 10:20268452, PLXDC2||Intron 1:163081, Mono:SLE; 10:21683093, PBMC:notRA; 10:21688798, PBMC:OA; 10:21799314, C10orfl40||3' Proximal Enhancer: 15297, PBMC:HC; 10:22717154, LOC100499489||3' Proximal Enhancer:9704, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 10:22766861, Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 10:22767076, PBMC:SLE; 10:22894054, PIP4K2A||Intron 3: 109449, PBMCnotRA; 10:23463015, Bcell:OA; 10:23480316, PTFlA||Proximal Promoter:- 1143, PBMC:HC; 10:23492470, PTF1A||3' Proximal Enhancer: 11011, PBMC:HC; 10:25755241, GPR158||Intron 4:290952, PBMCnotRA; 10:27756752, Mono:OA; 10:28588024, PBMC:HC; 10:29018952, Mono:OA_SLE_HC; 10:29273678, PBMC:notRA; 10:29769658, SVILpxon 27:255072|Exon 29: 154243, PBMC:notRA; 10:29834523, MIR604||Proximal Promoter: -497, SVIL||Intron 6:89378|Intron 8: 190207, PBMCnotRA; 10:29874759, PBMC:notRA; 10:30711382, Mono:SLE; 10:31108190, Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 10:31121906, Tcel HC; 10:31872296, Mono:HC; 10:32345864, KIF5B||Proximal Promoter: -493, PBMC:SLE; 10:32345866, KIF5B||Proximal Promoter: -495, PBMC:SLE,Tcell:OA_SLE_HC; 10:3248143, PBMC:OA; 10:3281074, PBMC:notRA; 10:334773, DIP2C||Intron 32:400835, PBMC:HC; 10:33483109, NRP1 ||3' Proximal Enhancer: Intron l l :Intron 12: 140724, PBMC:notRA; 10:3500383, PBMC:notRA; 10:35894430, GJD4||Proximal Promoter:93, PBMC:HC,PBMC:OA_SLE_HC; 10:36054798, PBMC:notRA; 10:37414261, ANKRD30A|| Proximal Promoter: -523, BcelhOA; 10:37940493,
PBMC:HC,PBMC:OA_SLE_HC; 10:37943880, PBMC:notRA; 10:38691492, SEPT7L||Proximal Promoter:288, Mono:HC,PBMC:HC,PBMC:OA_SLE_HC; 10:38691799, SEPT7L||Proximal Promoter:-19, PBMC:HC,PBMC:OA_SLE_HC; 10:38692317, SEPT7L||Proximal Promoter:-537,
PBMC:HC,PBMC:OA_SLE_HC; 10:4002490, PBMC:OA_SLE_HC; 10:42673902, Wholeblood:notRA; 10:42859004, LOC441666||Intron 1 :4489, Wholeblood:notRA; 10:42862876, LOC441666||Intron 1 :617, PBMC:notRA; 10:42862978, LOC441666||Intron 1 :515, Wholeblood:notRA; 10:42863068, LOC441666||Proximal Promoter:425, PBMC:notRA,Wholeblood:notRA; 10:42863173, LOC441666||Proximal Promoter:320, PBMC:notRA,Wholeblood:notRA; 10:42863444, LOC441666||Proximal Promoter:49, Wholeblood:notRA; 10:42863508, LOC441666||Proximal Promoter:- 15, PBMC:notRA,Wholeblood:notRA; 10:42863539, LOC441666||Proximal Promoter:-46, PBMC:notRA; 10:42970987, LOC84856||Proximal Promoter:49, Tcell:HC,Tcell:OA_SLE_HC; 10:43186868, PBMC:notRA; 10:43248870, PBMC:notRA; 10:43522143, PBMC:OA; 10:43605906, RET||Intron 6:33390, PBMC:OA; 10:43622663, RET||Exon 19:Intron 19:50147, PBMC:OA; 10:43941753, ZNF487P||Intron 1 :9180, PBMC:notRA; 10:44186174, PBMC:HC; 10:44806146, PBMC:SLE; 10:45072520, PBMCSLE; 10:45406764, TMEM72||Proximal Promoter: l,TMEM72-ASl ||Intron 2:48373, Tcell:OA_SLE_HC; 10:45650346, LOC100133308||Proximal Promoter:-302,LOC338579||Proximal Promoter:237,MIR3156-l ||5' Proximal Enhancer: -9115, PBMC:notRA; 10:45798249, OR13Al ||Exon 4: 12807, Mono:SLE; 10:45958759, MARCH8||Intron 4:72060|Intron 4:Intron 5: 131595, PBMC:HC; 10:46221282, FAM21C||Proximal Promoter:-1365, PBMC:OA_SLE_HC; 10:468347, DIP2C||Intron 5:267261, BcelhHC; 10:47062881, PBMC:HC; 10:47083283, PPYRl ||Proximal Promoter:-250, Bcel SLE; 10:47083392, PPYRl ||Proximal Promoter: -141, PBMC:HC; 10:48416899, GDF 10||3' Proximal Enhancer:22239,GDF2||Proximal Promoter:-46, PBMC:HC; 10:48760449, PTPN20A||Intron l :Intron 4:Intron 5:Intron 6:67132|Intron 2:Intron 5:Intron 6:Intron 7:67475|Intron 6:46536,PTPN20B||Intron l :Intron 4:Intron 5:Intron 6:67132|Intron 2:Intron 5:Intron 6:Intron 7:67475|Intron 6:46536, PBMC:HC,PBMC:notRA; 10:49348564, Mono:HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC,Tcell:OA_SLE_HC;
10:49659559, ARHGAP22||Intron 6:42133|Intron 7: 105164|Intron 8: 153617|Intron 8:200888|Intron 9:204751, PBMC:SLE; 10:49815243, ARHGAP22||Intron l :45204|Intron 2:49067|Proximal Promoter:- 2067, Bcell:OA_SLE_HC; 10:50221200, VSTM4||3' Proximal Enhancer: 102359, Mono:HC,PBMC:OA; 10:50336460, FAM170B||3' Proximal Enhancer:5605,LOC100506733||Intron 1 :6577, Bcell:OA_SLE_HC; 10:50970863, OGDHL|| Proximal Promoter:-438, PBMC:OA_SLE_HC; 10:50976646, OGDHL||5' Proximal Enhancer: -6221, PBMC:OA; 10:516163, DIP2C||Intron 3:219445, PBMC:notRA; 10:51826695, FAM21A||Proximal Promoter:-988,FLJ31813||Exon 1 :868, PBMC:notRA; 10:52390957, SGMS1 ||5' Proximal Enhancer: -7220, PBMC:notRA; 10:52487619, PBMC:notRA; 10:52500425, ASAH2B|| Intron 1 :718, PBMCnotRA; 10:56057923, PCDH15||Intron 7:Intron 8:Intron 9:503128, PBMC:HC; 10:5606380, PBMC:SLE; 10:5735349, FAM208B||Intron 1 :8549, Bcell:OA_SLE_HC; 10:5807561, FAM208B||3' Proximal Enhancer:80761,GDI2||Exon 10:Exon 11 :47951, PBMC:notRA; 10:587122, DIP2C||Intron 1 : 148486, PBMC:OA_SLE_HC; 10:5882576, PBMC:OA_SLE_HC; 10:593275, DIP2C||Intron 1 : 142333, PBMC:OA_SLE_HC; 10:601783, DIP2C||Intron 1 : 133825, PBMC:notRA; 10:603950, DIP2C||Intron 1 : 131658, Wholeblood:notRA; 10:604032, DIP2C||Intron 1 : 131576, Wholeblood:notRA; 10:60936866, PHYHIPL||Intron l :519|Proximal Promoter:-360, PBMC:OA; 10:61596106, CCDC6||Intron 2:70308, BcelhOA SLE HC; 10:62671136, RHOBTBl ||Exon 3:Exon 4:32897|Exon 4:89600|Exon 4:90062, PBMC:SLE; 10:63423079, C10orfl07||Proximal Promoter:361, Mono:OA; 10:64431533, ZNF365||Exon 7: 151327|Exon 8:297618, PBMCnotRA; 10:679171, DIP2C||Intron 1 :56437, Bcell:OA_SLE_HC; 10:68687951, CT NA3||Intron 7:737465|Intron 7:767998,LRRTM3||Exon 2:2160, Mono:OA_SLE_HC; 10:69609793, PBMC:OA_SLE_HC; 10:69634185, PBMC:notRA; 10:70319774, TETl||Proximal Promoter:-342, Tcell:HC; 10:70805603, PBMC:OA_SLE_HC; 10:71005638, HKDCl||Intron 7:25580, BcelhHC; 10:716157, C10orfl08||3' Proximal Enhancer: 20141, PBMC:notRA; 10:72215990, Bcell:OA,Mono:OA; 10:72545473, C10orf27||Proximal Promoter: -316, BcelhHC; 10:72647652, PCBDl||Intron 1:889,SGPL1||3' Proximal Enhancer:71949, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 10:72648693, PCBDl||Proximal Promoter:-152,SGPLl||3' Proximal Enhancer:72990, PBMC:OA_SLE_HC; 10:73038012, PBMC:notRA; 10:73350048, CDH23||Intron 9:193358, PBMC:notRA; 10:73497629, C10orfl05||Proximal Promoter: -48,C10orf54||3' Proximal Enhancer:35708,CDH23||3' Proximal Enhancer:Intron 32:340939, PBMC:HC; 10:73499965, C10orfl05||Proximal Promoter:-2384,C10orf54||3' Proximal Enhancer:33372,CDH23||3' Proximal Enhancenlntron 34:343275, PBMC:HC; 10:73516760, C10orf54||Intron 3: 16577, PBMC:HC; 10:73529624, C10orf54||Intron 1:3713, PBMC:OA_SLE_HC,PBMC:SLE; 10:736083, PBMC:OA; 10:75121857, TTC18||Distal Promoter:-3240, PBMC:notRA; 10:75405260, MYOZl||Distal Promoter: - 3745,SYNP02L||Exon 2:5527|Exon 4: 10572, PBMC:HC; 10:75488242, BMSlP4||Exon 2:2030, PBMC:notRA; 10:75490334, BMSlP4||Proximal Promoter:-62, PBMC:notRA; 10:75619420, CAMK2G||Intron 3:14929, PBMC:HC; 10:75692227, Bcell:OA_SLE_HC; 10:76947956, SAMD8||3' Proximal Enhancer:76564, PBMC:HC; 10:77165673, ZNF503||Distal Promoter:-4160,ZNF503-AS2||Intron l:2160|Intron 1:4388, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 10:77167091, ZNF503||5' Proximal Enhancer:-5578,ZNF503-AS2||Exon 2:3578|Exon 2:5806,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC; 10:77542314, C10orfl l||Proximal Promoter: - 204, PBMC:notRA; 10:79622515, DLG5||Intron 2:63833, PBMC:OA_SLE_HC; 10:80757927, LOC283050||Intron 3:Intron 4:Intron 5:69278, PBMC:HC; 10:8089733, FLJ45983||3' Proximal Enhancer:5714,GATA3||5' Proximal Enhancer: -6933, PBMC:OA; 10:81114059, PPIFpxon 6:6840, PBMC:OA_SLE_HC; 10:81173663, ZCCHC24||Intron 2:31720,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 10:8145066, PBMC:OA_SLE_HC; 10:81680307, LOC100288974||Intron 3: 15654,MBLlP||Proximal Promoter:374, Wholeblood:notRA; 10:81888928, PLAC9||Distal Promoter:-3329, PBMC:notRA; 10:81892109, PLAC9||Proximal Promoter:-148, PBMC:OA_SLE_HC; 10:8203261, PBMC:notRA; 10:82119561, DYDCl||Distal Promoter:- 3061,DYDC2||Intron 2:3004, PBMC:notRA; 10:82296191, SH2D4B||Distal Promoter: -4383|Proximal Promoter: -1466, Mono:HC; 10:835505, PBMC:notRA; 10:8559030, Bcell:OA_SLE_HC; 10:88391658, PBMC:notRA; 10:91012862, LIPA||Proximal Promoter:-1202, BcelhOA; 10:91173811, IFIT5||Proximal Promoter:-513, Bcell:SLE,PBMC:OA_SLE_HC; 10:91175366, IFIT5||Intron 1: 1042, PBMC:OA_SLE_HC,Tcell:SLE; 10:91453851, FLJ37201||Exon 2:3834,KIF20B||5' Proximal Enhancer:- 7515, PBMC:HC; 10:92916289, NUDT9Pl||Distal Promoter:-3452, Bcell: OA SLE HC ; 10:93299523, PBMC:notRA; 10:94179809, MARK2P9||Exon 2:601, PBMC:notRA; 10:94180383, MARK2P9||Proximal Promoter:27, PBMC:OA; 10:95363, TUBB8||Proximal Promoter: -185, Wholeblood:notRA; 10:95721442, PIPSL||Proximal Promoter:230, PBMC:notRA; 10:97073199, SORBSl||Exon 21:Exon 22:Exon 28:Exon 31:127738|Exon 25:Exon 26:247972, PBMC:notRA; 10:97201172, SORBSl||Intron 2: 119999|Proximal Promoter:-235, Tcell:OA_SLE_HC; 10:97471606, ENTPDl||Proximal Promoter:71, PBMC:notRA; 10:97515372, ENTPDl||Intron l:43837|Proximal Promoter:-300|Proximal Promoter:-36,LOC728558||Exon 6:334620, TcelhSLE; 10:97515377, ENTPDl||Intron l:43842|Proximal Promoter:-295|Proximal Promoter: - 31,LOC728558||Exon 6:334615, TcelhSLE; 10:97849795, Mono:OA; 10:98064175, DNTT||Proximal Promoter:91, PBMC:SLE; 10:98069610, DNTT||Intron 1:5526, Bcell:OA_SLE_HC,Bcell:SLE; 10:980765, BcelhHC; 10:98948259, ARHGAP19-SLITl||Intron 11:104171, PBMC:notRA; 10:98977821, ARHGAP19||3' Proximal Enhancer:74609,ARHGAP19-SLITl||Intron 11:74609, PBMC:notRA; 10:99160096, RRP12||Exon 2:1031, Wholeblood:notRA; 10:99278449, UBTDl||Intron 1: 19682, PBMC:notRA; 10:99326436, ANKRD2||5' Proximal Enhancer: -5819,UBTDl||Intron 1:67669, Bcell:OA_SLE_HC; 10:99338074, ANKRD2||Exon 3:5819,HOGAl||5' Proximal Enhancer: - 6027,UBTD1||3' Proximal Enhancer:79307, PBMC:notRA; 10:99478719, LOC100270710||Proximal Promoter:-817,MARVELDl||3' Proximal Enhancer:5255, PBMC:HC; 10:99561384, PBMC:HC; 10:99766975, CRTACl||Intron 2:23610, Bcel OA; 11:100558484, ARHGAP42||Proximal Promoter:78, BcelhOA; 11:101918710, CI lorf70|| Intron 2:542, PBMCnotRA; 11: 102401438, MMP7||Proximal Promoter:40, PBMC:HC; 11: 10332052, ADM||3' Proximal Enhancer:5411, Bcell:OA_SLE_HC; 11:10477821, AMPD3||Distal Promoter:-4856|Intron 1:1156|Intron l:5598|Intron l:5954|Proximal Promoter:341, PBMC:notRA; 11:10531091, AMPD3||3' Proximal Enhancer:48414|3' Proximal Enhancer:53611|3' Proximal Enhancer:54426|3' Proximal Enhancer:58868|3' Proximal Enhancer:59224,MIR4485||Proximal Promoter:-1218,MTRNR2L8||Proximal Promoter:-368,RNF141||3' Proximal Enhancer:31683, PBMC:notRA; 11:10531665, AMPD3||3' Proximal Enhancer:48988|3' Proximal Enhancer:54185|3' Proximal Enhancer:55000|3' Proximal Enhancer:59442|3' Proximal Enhancer:59798,MIR4485||Proximal Promoter:-1792,MTRNR2L8||Proximal Promoter:-942,RNF141||3' Proximal Enhancer:31109, PBMC:notRA; 11:10674182, MRVIl||Intron l:Intron 2:41353|Intron 2:40939|Proximal Promoter:-334, PBMC:notRA; 11:108680123, DDX10||Intron 13:144308, Bcell:OA_SLE_HC; 11:110198965, PBMC:HC; 11:111250566, POU2AFl||Proximal Promoter:-409, Tcell:OA_SLE_HC; 11:111692181, ALG9|| Intron 13:49823|Intron 13:50124, PBMC:notRA; 11:11177888, PBMC:OA_SLE_HC,PBMC:SLE; 11:112088765, BC02||Exon 12:41677|Exon 12:42558,PTS||5' Proximal Enhancer:-8322, PBMC:notRA; 11:112096781, BC02||3' Proximal Enhancer:49693|3' Proximal Enhancer:50574,PTS||Proximal Promoter:-306, PBMC:OA; 11:112693829, PBMC:OA_SLE_HC; 11:113817020, HTR3B||Exon 9:41503, PBMC:notRA; 11:114191367, NMT||3' Proximal Enhancer:24833, PBMC:SLE; 11:114493826, PBMC:notRA; 11:115571126, PBMC:HC; 11:115765072, Bcell:SLE; 11:115931334, Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 11:116371188, PBMC:HC,PBMC:OA_SLE_HC; 11:116455589, BcelhOA SLE HC; 11:116801299, SIK3||Intron 3:167694, PBMC:SLE,Tcell:SLE; 11:117688335, FXYD2||3' Proximal Enhancer:10472|3' Proximal Enhancer:7124,FXYD6-FXYD2||3' Proximal Enhancer: 59411, Bcell:OA; 11:117695828, FXYD2||Intron l:2979|Proximal Promoter:-369,FXYD6-FXYD2||Intron 6:51918, PBMC:HC; 11:117748187, FXYD6||Proximal Promoter:-441|Proximal Promoter:14,FXYD6-FXYD2||Proximal Promoter:-441, Mono:OA_SLE_HC; 11:117857630, IL10RA|| Intron l:Intron 2:525, PBMC:HC; 11:117857990, IL10RA||Intron l:Intron 2:885, PBMC:HC; 11:118100782, AMICAl||Distal Promoter:- 4973,MPZL3||Intron 5:22229, PBMC:HC; 11:118286105, ATP5L||3' Proximal Enhancer: 14002, PBMC:HC; 11:118474243, ARCN1||3' Proximal Enhancer:31142,PHLDBl||Distal Promoter:-2969|Distal Promoter: -4062, PBMC:notRA; 11:118576628, Tcell:OA_SLE_HC; 11:118781763, BCL9L||Proximal Promoter:-150,MIR4492||Proximal Promoter:347, PBMC:HC; 11:118790354, BCL9L||5' Proximal Enhancer:-8741,MIR4492||3' Proximal Enhancer: 8938, PBMC:SLE; 11:118842484, FOXRl||Proximal Promoter:68, Wholeblood:notRA; 11:120078840, OAF||Distal Promoter: -2906, PBMC:notRA; 11:120516366, TcelhOA; 11:121297716, Mono:OA; 11:1220171, PBMC:OA_SLE_HC; 11:122022999, MIR100||Proximal Promoter: 17,MIRLET7A2||5' Proximal Enhancer:-5698, Bcel OA; 11:122275841, Bcell:OA_SLE_HC; 11:12263892, MICAL2||Exon 19:131755, Mono:HC; 11:12303499, MICALCL||Distal Promoter:-4947, Mono:OA; 11:123849141, OR10Sl||Proximal Promoter: -743, BcelhHC; 11:123899065, OR10G7||3' Proximal Enhancer: 10643,OR10G8||Proximal Promoter:-1264,OR10G9||3' Proximal Enhancer:5346, PBMC:notRA; 11:123985650, VWA5A|| Proximal Promoter: -460, Mono:HC; 11:124387114, PBMC:notRA; 11:1248959, MUC5B||Exon 7:4665,
PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 11:125260943, PKNOX2|| Intron 6:226385, PBMC:SLE; 11:125649040, PATE2|| Proximal Promoter:-326,PATE3||5' Proximal Enhancer:-8965, PBMC:notRA; 11:128388475, ETSl||Intron l:3730|Intron 3:68978, PBMC:HC; 11:128760609, Cllorf45||3' Proximal Enhancer:14983|3' Proximal Enhancer: 15355|3' Proximal Enhancer: 15517, KCNJ5|| Proximal Promoter:- 703, PBMC:notRA; 11:130416290, PBMC:notRA; 11:130710076, Bcell:OA_SLE_HC; 11:131160689, PBMC:notRA; 11:131241788, NTM||Intron 1:1418, PBMC:notRA; 11:131526811, NTM||Intron 1:286441, PBMC:notRA; 11:131561541, NTM||Intron 1:321171, Wholeblood:notRA; 11:131780094, NTM||Intron l:539724|Proximal Promoter:-617, PBMC:HC; 11:132016295, NTM||Exon 2:235584|Exon 3:775925, Mono:OA_SLE_HC; 11:132107476, NTM||Intron 3:326765|Intron 4:867106,
PBMC:OA_SLE_HC,PBMC:SLE; 11:132217395, PBMC:HC; 11:133782453, IGSF9B||3' Proximal Enhancer:44427, Mono:OA_SLE_HC; 11:133784410, IGSF9B||3' Proximal Enhancer:42470, PBMC:notRA; 11:133800800, IGSF9B||Intron 11:26080, PBMC:OA_SLE_HC; 11:134137345, ACAD8||3' Proximal Enhancer:13912,GLBlL3||5' Proximal Enhancer:-8929, TcelhOA; 11:134257514, B3GATl||Exon 2:Exon 3:24298, Mono:OA; 11:134605862, PBMC:notRA; 11:134608598, PBMC:notRA; 11:13485289, BTBD10||Proximal Promoter: -451, PBMC:notRA; 11:13938802, PBMC:HC; 11:1413145, BRSK2||Intron 1:2017, TcelhHC; 11:14495049, COPBl||Intron 14:26355|Intron 14:26366|Intron 14:26392, PBMC:HC,PBMC:OA_SLE_HC; 11:1463541, BRSK2||Intron 4:52413, PBMC:HC,Tcell:HC; 11:1463554, BRSK2||Intron 4:52426, TcelhHC; 11:1463620, BRSK2||Intron 4:52492, TcelhHC; 11:1463662, BRSK2||Intron 4:52534, TcelhHC; 11:14927549, Tcel SLE; 11:16921230, PLEKHA7||Intron 3:114733, PBMC:notRA; 11:1750302, IFITM10||3' Proximal Enhancer:21522, PBMC:HC; 11:1750353, IFITM10||3' Proximal Enhancer:21471, PBMC:HC,PBMC:OA_SLE_HC; 11:18211133, PBMC:notRA; 11:18230799, LOC494141||Proximal Promoter:-32|Proximal Promoter:115, PBMC:notRA; 11:18300953, HPS5||Exon 22:Exon 23:42768,SAA1||3' Proximal Enhancer: 13146, Wholeblood:notRA; 11:18429080, LDHA||Exon 7:Exon 8:13145|Exon 8:11268,LDHC||Distal Promoter: -4772, PBMC:notRA; 11:19223635, CSRP3||Proximal Promoter: -1051 Proximal Promoter: -46, PBMC:OA; 11:19367621, NAV2||Distal Promoter: -4649, PBMC:notRA; 11:1952756, T NT3||Intron 7:Intron 8:11958, PBMC:HC; 11:19699299, PBMC:notRA; 11:19831490, PBMC:notRA; 11:20181911, DBXl||Proximal Promoter:-41, PBMC:OA_SLE_HC; 11:2020391, H19||Proximal Promoter:-1326,MIR675||Proximal Promoter:- 2330,MRPL23-AS1||5' Proximal Enhancer:-9241, PBMC:notRA; 11:2183420, INS||Proximal Promoter: - 981,INS-IGF2||Proximal Promoter:-981,TH||3' Proximal Enhancer:9615, Tcell:OA_SLE_HC; 11:2243685, BcelhHC; 11:2292373, ASCL2||Proximal Promoter:- 191, PBMC:OA; 11:2295852, ASCL2||Distal Promoter:-3670, PBMC:OA_SLE_HC,Wholeblood:notRA; 11:23919652, Bcell:SLE,PBMC:HC; 11:259533, PSMD13||3' Proximal Enhancer:22726, BcelhSLE; 11:285037, ATHLl||Distal Promoter: - 4100,NLRP6||Intron 7:6468, PBMC:HC; 11:28588618, PBMC:notRA; 11:289966, ATHLl||Exon 2:829,IFITM5||3' Proximal Enhancer:9560,NLRP6||3' Proximal Enhancer: 11397, PBMC:HC; 11:2907334, CDKNlC||Proximal Promoter:-339,SLC22A18AS||3' Proximal Enhancer: 17841, PBMCnotRA; 11:2907670, CDKNlC||Proximal Promoter:-675,SLC22A18AS||3' Proximal Enhancer: 17505, PBMC:HC; 11:2919808, SLC22A18||Distal Promoter:-3703|Proximal Promoter:-1142,SLC22A18AS||Intron 3:5367, PBMC:OA; 11:300286, ATHL1||3' Proximal Enhancer: 11149,IFITM2||5' Proximal Enhancer:- 7820,IFITM5||Proximal Promoter:-760, PBMC:HC; 11:30038692, KCNA4|| Proximal Promoter:- 115, PBMC:OA; 11:300404, ATHL1||3' Proximal Enhancer: 11267,IFITM2||5' Proximal Enhancer:- 7702,IFITM5||Proximal Promoter:-878, Bcell:OA_SLE_HC,PBMC:notRA; 11:3035856, CARS||Intron 16:Intron 17:42825, PBMC:HC; 11:30502936, MPPED2||Intron 3:99104|Intron 4: 104994, Mono:SLE; 11:3073408, CARS||Intron 1:5273, PBMC:HC; 11:308231, IFITM1||5' Proximal Enhancer:- 5759,IFITM2||Proximal Promoter: 125,IFITM5||5' Proximal Enhancer:-8705, PBMC:notRA; 11:312518, IFITMl I |Proximal Promoter:-1472,IFITM2||3' Proximal Enhancer:4412,IFITM3||3' Proximal Enhancer:8396, T cell: SLE; 11:312560, IFITMl ||Proximal Promoter:-1430,IFITM2||3' Proximal Enhancer:4454,IFITM3||3' Proximal Enhancer: 8354,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:SLE,Tcell:SLE; 11:312841, IFITMl ||Proximal Promoter: - 1149,IFITM2||3' Proximal Enhancer:4735,IFITM3||3' Proximal Enhancer: 8073,
Bcell:SLE,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:SLE; 11:313120, IFITMl ||Proximal Promoter:- 870,IFITM2||3' Proximal Enhancer:5014,IFITM3||3' Proximal Enhancer: 7794,
Bcell:OA_SLE_HC,Bcell:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 11:313267, IFITMl ||Proximal Promoter:-723,IFITM2||3' Proximal Enhancer:5161,IFITM3||3' Proximal Enhancer:7647, Bcell:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:313354, IFITMl ||Proximal Promoter:-636,IFITM2||3' Proximal Enhancer:5248,IFITM3||3' Proximal Enhancer:7560, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:SLE; 11:313478, IFITMl ||Proximal Promoter: - 512,IFITM2||3' Proximal Enhancer:5372,IFITM3||3' Proximal Enhancer: 7436,
Mono:OA_SLE_HC,Tcell:SLE; 11:313527, IFITMl ||Proximal Promoter: -463,IFITM2||3' Proximal Enhancer:5421,IFITM3||3' Proximal Enhancer:7387, PBMC:SLE; 11:313624, IFITMl ||Proximal Promoter:-366,IFITM2||3' Proximal Enhancer:5518,IFITM3||3' Proximal Enhancer:7290, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 11 :314493, IFITMl ||Intron
1:503,IFITM2||3' Proximal Enhancer:6387,IFITM3||3' Proximal Enhancer: 6421, Mono:SLE; 11:3145609, OSBPL5||Intron 3:40973, PBMC:HC; 11:315102, IFITMl||Exon 2: 1112,IFITM2||3' Proximal Enhancer:6996,IFITM3||3' Proximal Enhancer:5812,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:315118, IFITMl||Exon 2: 1128,IFITM2||3' Proximal Enhancer:7012,IFITM3||3' Proximal Enhancer:5796, Bcell:OA_SLE_HC,Mono:SLE,PBMC:HC,Tcell:OA_SLE_HC; 11:315262, IFITMl||Exon
2:1272,IFITM2||3' Proximal Enhancer:7156,IFITM3||3' Proximal Enhancer:5652,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 11:315908, IFITMl ||3' Proximal Enhancer:1918,IFITM2||3' Proximal Enhancer:7802,IFITM3||3' Proximal Enhancer:5006, Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 11:316456, IFITM1||3' Proximal Enhancer:2466,IFITM2||3' Proximal Enhancer:8350,IFITM3||3' Proximal Enhancer:4458, PBMC:SLE; 11:3168455, OSBPL5||Intron 1: 18127, PBMC:notRA; 11:3175007, OSBPL5||Intron 1: 11575, PBMC:HC; 11:317767, IFITM1||3' Proximal Enhancer:3777,IFITM2||3' Proximal Enhancer:9661,IFITM3||3' Proximal Enhancer: 3147, Tcel SLE; 11:3178024, OSBPL5||Intron 1:8558, PBMC:HC; 11:3189207, OSBPL5||Distal Promoter: - 2625, PBMC:HC; 11:319555, IFITM1||3' Proximal Enhancer:5565,IFITM3||3' Proximal Enhancer: 1359, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 11:320940, IFITM1||3' Proximal
Enhancer:6950,IFITM3||Proximal Promoter: -26, PBMC:SLE; 11:32909110, QSER1||5' Proximal Enhancer:-5681, PBMC:notRA; 11:33097876, CSTF3||3' Proximal Enhancer:85161,LINC00294||Proximal Promoter: 181,TCPl lLl||3' Proximal Enhancer: 36316|3' Proximal Enhancer:36914, PBMC:notRA; 11:33744567, CD59||Intron l:Intron 2:Intron 3: 13458|Proximal Promoter:-294|Proximal Promoter:-69, PBMC:OA; 11:33744977, CD59||Intron l:Intron 2:Intron 3: 13048|Proximal Promoter:-479|Proximal Promoter: -704, Bcell:OA_SLE_HC,Tcell:OA_SLE_HC; 11:34460336, CAT||Proximal Promoter:- 135, Mono:OA; 11:35164485, CD44||Intron 1:4069, Mono:HC,PBMC:HC; 11:3598521, PBMC:notRA; 11:3647419, TRPC2|| Proximal Promoter:-294, Bcell:OA_SLE_HC,PBMC:HC; 11:3648013, TRPC2||Proximal Promoter:300, PBMC:HC; 11:39868490, PBMC:notRA; 11:40316514, LRRC4C||Proximal Promoter:-850, Bcel OA; 11:43094025, PBMC:OA_SLE_HC; 11:43291043, HNRNPKP3||Proximal Promoter: -124, PBMC:notRA; 11:43364829, API5||Exon l l:Exon 13:Exon 14:Exon 15:31325, PBMCnotRA; 11:44881716, TSPAN18||Intron 1:95741, Bcell:OA_SLE_HC; 11:44927976, TSPAN18||Exon 3: 142001, Mono:OA; 11:45376874, Bcell:OA_SLE_HC; 11:45726188, BcelhHC; 11:45744972, PBMC:SLE; 11:45921557, Cl lorf94||3' Proximal
Enhancer:7276,MAPK8IPl||Intron 2:14511,PEX16||3' Proximal Enhancer: 18117, PBMC:notRA; 11:45951803, GYLTL1B||3' Proximal Enhancer:8608,PHF21A||Exon 18:191182, PBMCSLE; 11:4631906, TRIM68||Proximal Promoter: -2417, Tcel SLE; 11:46366643, DGKZ||Intron l: 12189|Proximal Promoter: - 173|Proximal Promoter: -2312, Tcell:OA_SLE_HC; 11:46366833, DGKZ||Intron 1: 123791 Proximal Promoter: -2122|Proximal Promoter: 17, Tcell:OA_SLE_HC; 11:46366840, DGKZ||Intron l:12386|Proximal Promoter:-2115|Proximal Promoter:24, Tcell:OA_SLE_HC; 11:46368045, DGKZ||Intron l: 1229|Intron l: 13591|Proximal Promoter: -910, PBMC:SLE,Tcell:OA_SLE_HC; 11:46389249, DGKZpxon 3:20294|Exon 3:22433|Exon 3:34795|Exon 4:6105,MIR4688||5' Proximal Enhancer:-8702, PBMC:notRA; 11:46408399, AMBRA1||3' Proximal Enhancer:204515,CHRM4||Proximal Promoter:-292,MDK||3' Proximal Enhancer:5097|3' Proximal Enhancer:5181|3' Proximal Enhancer:5782, BcelhHC; 11:47276469, ACP2||5' Proximal Enhancer:-6012,NRlH3||Distal Promoter: -2998|Intron l:6021|Intron 2:6619, PBMC:HC; 11:47415397, Bcell:OA_SLE_HC; 11:47416886, PBMC:OA_SLE_HC; 11:47639458, MTCH2||Exon 13:24748, Mono:SLE; 11:47736254, AGBL2||Exon 2:674,FNBP4||3' Proximal Enhancer:52739, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:48238296, OR4Bl||Proximal Promoter:-65, Wholeblood:notRA; 11:48284249, OR4Xl||Proximal Promoter:-1163, PBMC:OA_SLE_HC; 11:48345361, OR4C3||Proximal Promoter:-1131, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 11:48509778, OR4A47||Proximal Promoter:-566, PBMC:OA_SLE_HC; 11:49017551, PBMC:HC,PBMC:OA_SLE_HC; 11:49872414, PBMC:notRA; 11:49914049, PBMC:OA_SLE_HC; 11:49917069, PBMC:notRA; 11:50238009, LOC441601||3' Proximal Enhancer: 19624, PBMC:notRA; 11:50257496, LOC441601||Proximal Promoter:137, Mono:HC,PBMC:HC,Tcell:HC; 11:5346163, OR51B2|| Proximal Promoter:-581, PBMC:OA_SLE_HC; 11:5372944, OR51B5||Intron l:153938,OR51B6||Proximal Promoter:207, Bcel HC; 11:5617926, TRIM6|| Intron l:596|Proximal Promoter: 62,TRIM6- TRIM34||Proximal Promoter:62, PBMC:SLE; 11:56381067, OR5Ml||Proximal Promoter:-89, PBMC:notRA; 11:5645703, TRIM34||5' Proximal Enhancer:-7781|Intron l:4530|Proximal Promoter: - 503,TRIM6-TRIM34||Intron 7:27839, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC; 11:5645913, TRIM34||5' Proximal Enhancer:-7571|Intron l:4740|Proximal Promoter: -293,TRIM6-TRIM34||Intron 7:28049, PBMC:OA_SLE_HC,PBMC:SLE; 11:56467944, OR9Gl||Proximal Promoter:81,OR9G9||Proximal Promoter:81, Tcell:OA_SLE_HC; 11:5667836, TRIM34||3' Proximal Enhancer: 14352|3' Proximal Enhancer:21630|3' Proximal Enhancer:26663,TRIM6-TRIM34||3' Proximal
Enhancer:49972,TRIM78P||Intron 1:3425, PBMC:SLE; 11:57089821, SSRP1||3' Proximal Enhancer:13530,TNKSlBPl||Intron 1:2592, Bcel HC; 11:5710654, TRIM22||Proximal Promoter: - 162,TRIM5||Distal Promoter:-4315, PBMC:SLE; 11:5716255, TRIM22||Intron 1:5439,TRIM5||5' Proximal Enhancer:-9916, Bcell:OA_SLE_HC,Bcell:SLE,PBMC:SLE; 11:58494370, GLYAT||Intron 1:5077, PBMC:notRA; 11:58965571, DTX4||Intron 7:25760, PBMC:HC; 11:58978082, DTX4||3' Proximal Enhancer:38271,MPEGl||Exon 1:2412, Mono:HC; 11:59824038, MS4A3||Proximal Promoter:- 62,PLAC1L||3' Proximal Enhancer: 16291, PBMC:HC; 11:59824089, MS4A3||Proximal Promoter: - 11,PLAC1L||3' Proximal Enhancer: 16342, PBMC:HC; 11:59824116, MS4A3||Proximal Promoter: 16,PLAC1L||3' Proximal Enhancer: 16369, PBMC:HC; 11:59824161, MS4A3||Proximal Promoter:61,PLAClL||3' Proximal Enhancer: 16414, PBMC:HC; 11:59836817, MS4A3||Intron 3:Intron 4:Intron 5:12717, PBMC:HC; 11:59841290, MS4A3||3' Proximal Enhancer: 17190, PBMC:notRA; 11:59951557, MS4A6A||Intron l:582|Proximal Promoter:-753, PBMC:HC; 11:60049097, MS4A4A||Intron 1: 1084, PBMC:notRA; 11:60106260, MS4A6E||Intron 2:3906, PBMC:notRA; 11:60534991, MS4A15||Intron l:Intron 2: 10652, Wholeblood:notRA; 11:60608291, CCDC86||Proximal Promoter:- 1137, PBMC:notRA; 11:60617807, CCDC86||Exon 4:8379,PTGDR2||3' Proximal Enhancer:5637, PBMC:notRA; 11:60775715, CD6||Intron 3:36603, Wholeblood:notRA; 11:60775831, CD6||Intron 3:36719, Wholeblood:notRA; 11:60776124, CD6||Exon 4:37012, Wholeblood:notRA; 11:61159602, TMEM216||Proximal Promoter:-229|Proximal Promoter:-262, PBMC:SLE; 11:61281763, LRRC10B||3' Proximal Enhancer:5492,MIR4488||3' Proximal Enhancer:5696,SYT7||Exon 10:Exon 9:66581, PBMC:notRA; 11:61388864, RPLP0P2||Intron 1:6357, PBMC:OA_SLE_HC; 11:62092739, Wholeblood:notRA; 11:626128, CDHR5|| Proximal Promoter:-1061,SCT||3' Proximal Enhancer: 1045, PBMC:notRA; 11:6291339, CCKBR||Exon 3:10436, PBMC:notRA; 11:6291625, CCKBR||Intron 3:10722, PBMC:notRA; 11:6291879, CCKBR||Exon 4:10976, PBMC:notRA; 11:6291927, CCKBR||Exon 4:11024, PBMC:notRA; 11:6291951, CCKBR||Exon 4:11048, PBMC:notRA; 11:6292311, CCKBR||Exon 5:11408, PBMC:notRA; 11:6292490, CCKBR||Exon 5:11587, PBMC:notRA; 11:6292511, CCKBR||Exon 5:11608, PBMC:notRA; 11:63033729, PBMC:notRA; 11:63272909, LGALS12||Distal Promoter: -2549|Proximal Promoter:-614, PBMC:HC; 11:63330918, HRASLS2||Proximal Promoter:-63, BcelhOA SLE HC; 11:63331821, HRASLS2||Proximal Promoter: -966, PBMC:HC; 11:63529891, Cl lori 5||Exon 5:6222,RTN3||3' Proximal Enhancer: 80970, PBMC:HC; 11:64543849, SFl||Intron 2: 1383|Intron 2:2089|Intron 2:2467, TcelhOA; 11:64642516, EHDl||Intron 1:3675, PBMC:SLE; 11:64794610, ARL2||3' Proximal Enhancer:13026,ARL2-SNX15||Intron 3:13026,SNX15||Proximal Promoter:-269, PBMC:SLE; 11:64808081, ARL2-SNX15||3' Proximal Enhancer:26497,NAALADLl ||3' Proximal Enhancer:17928,SAC3Dl||Proximal Promoter: -294,SNX15||3' Proximal Enhancer: 13202, Tcel SLE; 11:64808083, ARL2-SNX15||3' Proximal Enhancer:26499,NAALADLl ||3' Proximal Enhancer:17926,SAC3Dl||Proximal Promoter:-292,SNX15||3' Proximal Enhancer: 13204, PBMC:SLE; 11:65152051, FRMD8||Proximal Promoter:-1989,SLC25A45||Proximal Promoter:-1909, Tcel SLE; 11:65194933, NEAT1||3' Proximal Enhancer:4665, PBMC:SLE; 11:65195995, NEAT1||3' Proximal Enhancer:5727, PBMC:notRA; 11:65249342, Mono:SLE; 11:65314021, LTBP3||Exon 16:11678,SCYL1||3' Proximal Enhancer:21474, PBMC:OA_SLE_HC; 11:65321591, LTBP3||Exon 2:4108, PBMC:OA_SLE_HC; 11:65324768, LTBP3||Intron 1:931, PBMCSLE; 11:65341001, EHBPlLl||Distal Promoter: -2507,FAM89B||Exon 2:1182,LOC254100||Distal Promoter:-3117,SSSCAl||3' Proximal Enhancer:3059, PBMC:SLE; 11:65344604, EHBPlLl||Intron 1:1096,FAM89B||3' Proximal Enhancer:4785,LOC254100||5' Proximal Enhancer:-6720,SSSCA1||3' Proximal Enhancer:6662, PBMC:SLE; 11:65378622, MAP3Kll||Intron 1:3098,PCNXL3||5' Proximal Enhancer:-5160, PBMC:HC; 11:65554678, DKFZp761E198||5' Proximal Enhancer:-6856,OVOLl||Proximal Promoter:174, PBMC:OA; 11:65601754, SNX32||Proximal Promoter:345, PBMC:OA_SLE_HC,PBMC:SLE; 11:65687892, Cllorf68||Proximal Promoter:- 136 l,DRAPl||Exon 4:1165, Tcel SLE; 11:65770024, BANFl||Proximal Promoter:475,CST6||5' Proximal Enhancer: -9437,EIFlAD||Proximal Promoter: -387, PBMC:notRA; 11:65816646, GAL3ST3|| Proximal Promoter:5,SF3B2||Distal Promoter: -3169, PBMC:OA; 11:6598119, DNHD1||3' Proximal Enhancer: 79594, PBMC:HC; 11:66104993, B3GNT1||3' Proximal Enhancer: 10168,BRMS11 |Exon 10:7589,RINl||Proximal Promoter: -993,
PBMC:OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 11:66362959, CCDC87||Proximal Promoter:- 2405,CCS||Intron 2:2270, PBMC:OA_SLE_HC; 11:67053829, ADRBKl||Exon
21:19925,ANKRD13D||Distal Promoter:-2932|Distal Promoter:-2986, PBMC:SLE; 11:67070738, ANKRD13D||3' Proximal Enhancer:13923|3' Proximal Enhancer: 13977,SSH3||Proximal Promoter: -180, Mono:OA; 11:67079729, ANKRD13D||3' Proximal Enhancer:22914|3' Proximal Enhancer:22968,LOC100130987||5' Proximal Enhancer:-5580,SSH3||Exon 14:8811, PBMCSLE; 11:67139546, CLCFl||Intron l:1660|Intron 1:2102, PBMC:SLE; 11:67142001, CLCFl||Proximal Promoter: -353 IProximal Promoter: -795, PBMC:HC; 11:67174843, CARNS1||5' Proximal Enhancer: - 8305,PPP1CA||5' Proximal Enhancer:-5467,RAD9A||3' Proximal Enhancer: 14068|3' Proximal Enhancer:15421,TBClD10C||Intron 8:3432, PBMC:HC; 11:67203360, COR01B||3' Proximal Enhancer:7623|3' Proximal Enhancer:7932,PTPRCAP||Exon 2:1793,RPS6KB2||3' Proximal Enhancer: 7426, PBMC:HC; 11:67203434, COR01B||3' Proximal Enhancer:7549|3' Proximal
Enhancer:7858,PTPRCAP||Exon 2:1719,RPS6KB2||3' Proximal Enhancer: 7500, PBMC:HC; 11:67205869, COR01B||Exon ll:5114|Exon 12:5423,PTPRCAP||Proximal Promoter:-716,RPS6KB2||3' Proximal Enhancer:9935, TcelhHC; 11:67206263, COR01B||Exon 10:4720|Exon ll:5029,PTPRCAP||Proximal Promoter:-1110,RPS6KB2||3' Proximal Enhancer: 10329, PBMC:HC,Tcell:HC; 11:67206308, COR01B||Exon 10:4675|Exon ll:4984,PTPRCAP||Proximal Promoter:-l 155,RPS6KB2||3' Proximal Enhancer: 10374, Tcel HC; 11:67211017, COR01B||Proximal Promoter:-34|Proximal Promoter:275,GPR152||3' Proximal Enhancer:9183,PTPRCAP||5' Proximal Enhancer:-5864,RPS6KB2||3' Proximal Enhancer:15083, Bcell:OA_SLE_HC; 11:67251154, AIP||Intron 1:650,PITPNM1||3' Proximal Enhancer:21689, PBMC:HC; 11:67251939, AIP||Intron 1:1435,PITPNM1||3' Proximal Enhancer:20904, PBMC:HC; 11:67254381, AIP||Intron 1:3877,PITPNM1||3' Proximal Enhancer: 18462, Bcell:OA_SLE_HC,PBMC:HC; 11:67417958, AC Y3|| Proximal Promoter:172, PBMC:HC; 11:67418106, ACY31 IProximal Promoter:24, PBMC:HC; 11:67418113, AC Y3|| Proximal Promoter:17, PBMC:HC,PBMC:notRA; 11:67418140, AC Y3|| Proximal Promoter:-10, PBMC:HC; 11:67418148, ACY31 IProximal Promoter:-18, Mono:OA_SLE_HC,PBMC:HC; 11:67418213, AC Y3|| Proximal Promoter: - 83, Mono:HC; 11:67418291, ACY3|| Proximal Promoter:- 161, PBMC:HC,PBMC:OA_SLE_HC; 11:67418310, ACY3|| Proximal Promoter: -180, PBMC:HC,PBMC:OA_SLE_HC; 11:67418315, ACY3||Proximal Promoter:- 185, PBMC:HC,PBMC:OA_SLE_HC; 11:67418358, ACY3|| Proximal Promoter: -228, Mono:OA_SLE_HC; 11:67418365, ACY3||Proximal Promoter: -235, PBMC:HC; 11:67432957, ALDH3B2||Exon 7:15728|Exon 7:9145, Wholeblood:notRA; 11:67761514, UNC93Bl||Intron 9:10079, PBMC:OA_SLE_HC,Tcell:SLE; 11:67804055, ALDH3B1||3' Proximal Enhancer:26266|3' Proximal Enhancer:28008,MIR4691||3' Proximal Enhancer:2692,NDUFS8||Exon 7:5972,TCIRG1||5' Proximal Enhancer:-6391|Proximal Promoter: -2406, Tcel HC; 11:68451699, GAL||Proximal Promoter:-283, PBMC:HC; 11:68607622, CPTlA||Intron 1:1777, PBMC:SLE; 11:68607737, CPTlA||Intron 1:1662, Tcell:OA_SLE_HC; 11:68866761, TPCN2||3' Proximal Enhancer:50412, PBMC:HC; 11:69063136, MYEOV||Exon 3:1515,
Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE; 11:69240844, PBMC:HC; 11:69261044, PBMC:HC; 11:69987633, AN01||Intron 11:56118|Intron 11:63226, PBMC:HC; 11:70228615, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 11:70245893, CTTN||Intron 1:1282, PBMC:SLE; 11:70333993, SHANK2|| Intron 21:601815|Intron 9:173930, Mono:OA; 11:70391215, SHANK2||Intron 14:544593|Intron 2:116708, PBMC:SLE; 11:7041511, NLRP14||Proximal Promoter: - 188,ZNF214||Proximal Promoter:75, PBMC:OA; 11:70433293, SHANK2||Intron 14:502515|Intron 2:74630, PBMC:HC; 11:70672511, SHANK2||Intron 8:263297, PBMC:HC; 11:70708216, SHANK2||Intron 8:227592, PBMC:notRA; 11:70733251, PBMC:OA_SLE_HC; 11:71147213, DHCR7||Intron 8: 12264, PBMC:notRA,Tcell:OA_SLE_HC; 11:71352122, PBMC:notRA; 11:71420485, PBMC:notRA; 11:71524734, PBMC:notRA; 11:71567175, LOC100133315||3' Proximal Enhancer:72318, Wholeblood:notRA; 11:72379867, Bcell:HC; 11:72912441, PBMC:HC; 11:73036179, ARHGEF 17||Intron 1: 16517, PBMC:notRA; 11:73760904, C2CD3||Intron 26:121160, PBMC:notRA; 11:74860985, SLC02B1||5' Proximal Enhancer: -9858|Proximal Promoter: -1046, Mono:HC; 11:74861433, SLC02B1||5' Proximal Enhancer:-9410|Proximal Promoter:-598, PBMC:notRA; 11:75062225, Tcell:OA_SLE_HC; 11:7517263, OLFMLl||Intron 2:10664, Bcell:OA; 11:755658, TALD01||Intron 1:8227, PBMC:OA_SLE_HC; 11:75943228, PBMC:HC; 11:76320970, Tcell:SLE; 11:76340765, Tcell:SLE; 11:76495749, TSKU||Intron 1:1465, PBMC:SLE,Tcell:SLE; 11:76498701, TSKU||Intron 1:4417, PBMC:SLE,Tcell:SLE; 11:7694524, CYB5R2||Proximal Promoter:297, Bcell:HC; 11:77118761, PAKl||Intron 1:66347, PBMC:HC; 11:7715991, OVCH2||Intron 13:11950, PBMC:notRA; 11:7728370, OVCH2||Proximal Promoter:-429, Mono:OA_SLE_HC; 11:77314957, AQPl l||Intron 2:14278, PBMC:HC; 11:77741873, KCTD14||5' Proximal Enhancer:-7553,NDUFC2-KCTD14||Intron 2:Intron 3:49392, Mono:OA_SLE_HC,Mono:SLE; 11:79651476, PBMC:OA_SLE_HC; 11:8052536, TUB||5' Proximal Enhancer:-7643, Bcell:HC; 11:8385712, PBMC:HC; 11:85596390, CCDC83||Intron 4:30247, PBMC:notRA; 11:85873778, PBMC:notRA; 11:86085932, CCDC81||Proximal Promoter: 155, Bcell:SLE; 11:87224821, PBMC:HC; 11:88241946, GRM5||Exon 9:539294|Exon 9:554870, PBMC:OA; 11:89430562, FOLHlB||Intron 13:38098, PBMC:notRA; 11:89477675, PBMC:OA; 11:93467095, Cl lorf54||5' Proximal Enhancer:-7697,MIR1304||Proximal Promoter:-165,SNORAl||Proximal Promoter:-
1796,SNORA18||Proximal Promoter:-332,SNORA25||Distal Promoter:-3283,SNORA32||Distal Promoter:- 2830,SNORA40||3' Proximal Enhancer: 1307,SNORA8||Proximal Promoter:-1430,SNORD5||Proximal Promoter:-629,SNORD6||Proximal Promoter:-2356,TAFlD||3' Proximal Enhancer:7608, PBMC:HC; 11:94138452, GPR83||Distal Promoter: -3867, PBMC:OA; 11:94823751, ENDODl||Intron 1:778, PBMC:OA_SLE_HC; 11:94883474, Mono:OA; 11:95433344, PBMC:SLE; 11:9597577, WEEl||Exon 2:1344|Exon 2:2350, PBMC:notRA; 12:10086277, CLEC2A||Proximal Promoter:-1297, PBMC:notRA; 12:102224140, GNPTAB|| Intron 1:505, PBMC:notRA; 12:10252119, CLEC1A|| Proximal Promoter:-514, BcelhHC; 12: 103312819, P AH || Proximal Promoter: -1438, Mono:HC; 12:103325781, PBMC:HC,PBMC:OA_SLE_HC; 12:104659306, TXNRDl||Intron 3:49748, PBMC:notRA; 12: 105630720, APPL2||Distal Promoter:-3537|Proximal Promoter:-712, PBMC:SLE; 12: 107380263, CRY1||3' Proximal Enhancer:107335,MTERFD3||Intron 1:666, Tcell:OA_SLE_HC; 12:107774298, BTBDl l||Intron 1:62102, BcelhHC; 12:107855547, BTBDl l||Intron 1:143351, Bcel SLE; 12:109017367, SELPLGpxon 2: 10303|Exon 2:8487, PBMC:notRA; 12: 109250438, SSHl||Intron 1:921,
PBMC:OA_SLE_HC,PBMC:SLE; 12:109250515, SSHl||Intron 1:844, PBMC:notRA; 12:1098663, ERCl||Proximal Promoter:- 1740, PBMC:HC; 12: 110228049, TRPV4||Intron 10:Intron 9:24583|Intron 12:24552|Intron 12:43163, PBMC:OA_SLE_HC; 12:110605944, IFT81||Exon 12:Intron 11:43805, Tcel OA; 12: 11062991, TAS2R13||Proximal Promoter:-830, PBMC:HC,PBMC:notRA; 12: 110888857, ARPC3||Proximal Promoter:-699,GPN3||3' Proximal Enhancer: 17232|3' Proximal Enhancer: 17669, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:OA_SLE_HC; 12: 110942599, RAD9B||Intron 2:2595,VPS29||Distal Promoter:-2683, PBMC:notRA; 12:111099321, HVCNl||Intron 3:27625|Intron 3:28296, PBMC:OA_SLE_HC; 12:11149362, TAS2R20||Exon 1:1112,TAS2R50||5' Proximal Enhancer: -9851, PBMC:notRA; 12: 11176386, TAS2R19||Proximal Promoter:-1216,TAS2R31||3' Proximal Enhancer:7620, PBMC:notRA; 12: 11287271, TAS2R30||Proximal Promoter:-428, PBMC:notRA; 12:113229534, RPH3A||Proximal Promoter:-14, PBMC:HC; 12:113229647, RPH3A||Proximal Promoter:99, PBMC:OA_SLE_HC; 12:113345598, OASl||Intron 1:860,RPH3A||3' Proximal Enhancer: 116050, Bcell:SLE,PBMC:SLE,Tcell:SLE; 12:113355675, OASl||Exon 5:Intron 5:10937, PBMC:OA_SLE_HC; 12:113373737, OAS3||Distal Promoter:-2511, PBMC:notRA; 12: 113495619, DTXl||Proximal Promoter:-42, Tcell:OA_SLE_HC; 12: 113495701, DTXl||Proximal Promoter:40, PBMC:SLE,Tcell:OA_SLE_HC; 12: 113527336, DTXl||Intron 2:31675,RASAL1||3' Proximal Enhancer:46223|3' Proximal Enhancer:46708, Tcel HC; 12:113655841, IQCD||Intron l:3039,TPCNl||Distal Promoter:-3418, PBMC:OA_SLE_HC; 12:113684389, TPCNl||Intron 2:Intron 3:25130, Mono:OA; 12: 114851495, LOC255480||3' Proximal Enhancer:5496,TBX5||5' Proximal Enhancer:-5248|5' Proximal Enhancer:-7606|5' Proximal Enhancer:-9792, PBMC:notRA; 12: 115133324, Wholeblood:notRA; 12:115136308, PBMC:OA; 12: 117013718, MAPlLC3B2||Exon 2:16533, PBMC:notRA; 12:117099208, PBMC:notRA; 12:117188015, RNFT2||Exon 4:11920, Tcell:OA_SLE_HC; 12:117299508, HRK||Intron 1:19724,RNFT2||3' Proximal Enhancer: 123413, PBMC:SLE,PBMC:notRA; 12:117348108, FBXW8|| Proximal Promoter: -652, PBMC:notRA; 12:117540072, TESC||Distal Promoter: - 2821, Tcell:OA; 12:118588556, PEBP1||3' Proximal Enhancer:14687,TAOK3||Exon 21:222194, PBMC:notRA; 12:11992925, ETV6||Intron 3:190138, PBMC:HC; 12:120539137, CCDC64||3' Proximal Enhancer:111490,RAB35||Intron 3:15506, Bcell:OA_SLE_HC; 12:120730932, SIRT4||5' Proximal Enhancer:-9191, PBMC:notRA; 12:121088311, CABPl||Intron l:9890|Proximal Promoter:-59, Mono:OA_SLE_HC; 12:121092968, CABPl||Intron l:14547|Intron 1:4598, PBMC:notRA; 12:121570752, P2RX7||Proximal Promoter: 122|Proximal Promoter: 131 , PBMC:SLE; 12:121647654, P2RX4||Proximal Promoter: -9, PBMC:notRA; 12:121893769, KDM2B|| Intron 12:124595|Intron 12:125151, PBMC:SLE; 12:122012243, KDM2B||Intron 4:6121|Intron 4:6677, PBMC:notRA; 12:122019076, KDM2B||Proximal Promoter:-156|ProximalPromoter:-712, PBMC:OA_SLE_HC,PBMC:SLE; 12:12224457, BCL2L14||Intron l:580|Proximal Promoter:56, PBMC:OA_SLE_HC; 12:122444580, WDR66||3' Proximal Enhancer:88118, PBMC:HC; 12:122467179, BCL7A||Intron 1:7319, PBMC:HC; 12:122512410, MLXIP||Distal Promoter: - 4241, PBMCnotRA; 12:122712137, DIABLO||Proximal Promoter:-69,VPS33A||3' Proximal Enhancer:38931, Tcell:HC; 12:122990019, RSRC2||Exon 10:Exon ll:21541,ZCCHC8||Distal Promoter: - 4476, Mono:HC; 12:123009494, KNTCl||Proximal Promoter:-2314,RSRC2||Intron 1:2066, PBMC:HC,PBMC:OA_SLE_HC; 12:123012351, KNTCl||Intron l:543,RSRC2||Proximal Promoter: -791, PBMC:notRA; 12:123469669, ARL6IP4||3' Proximal Enhancer:4790,OGFOD2||3' Proximal Enhancer:10316,PITPNM2||Exon 25:125306, Mono:SLE; 12:123503709, MIR4304||5' Proximal Enhancer: - 8434,PITPNM2||Intron 2:91266, PBMC:HC; 12:123519157, Bcell:OA_SLE_HC; 12:123548027, Bcell:SLE; 12:123560479, LOC100507091||5' Proximal Enhancer:-5451, PBMC:HC; 12:123707827, MPHOSPH9||Proximal Promoter:- 1386, PBMC:HC; 12:123757018, CDK2APl||Proximal Promoter:-331, Bcell:OA; 12:124344196, DNAH10||Intron 37:97155, Tcell:OA; 12:124422135, CCDC92||Exon 5:35028,DNAH10||3' Proximal Enhancer: 175094, PBMC:SLE; 12:124422259, CCDC92||Exon 5:34904,DNAH10||3' Proximal Enhancer: 175218, PBMCSLE; 12:124702334, ZNF664-FAM101A||Intron 3:244573, Mono:HC; 12:124810173, FAM101A||3' Proximal Enhancer:36464,NCOR2||Intron 47:Intron 48:241837,ZNF664-FAM101A||3' Proximal Enhancer:352412, PBMC:notRA; 12:124831017, NCOR2||Intron 32:Intron 33:220993, PBMC:OA_SLE_HC,PBMC:notRA; 12:124864594, NCOR2||Intron 19:187416, Mono:OA; 12:124929963, NCOR2||Intron 9:122047, PBMC:OA_SLE_HC; 12:125023115, NCOR2||Intron 1:28895, PBMC:HC; 12:12518875, LOH12CRl||Intron 2:8856,LOH12CR2||5' Proximal Enhancer:-8874, Mono:OA_SLE_HC; 12:125398014, UBC||Exon 2:1573, PBMC:notRA; 12:125538377, PBMC:HC; 12:125570010, AACS||Intron 3:20086, Mono:OA; 12:126018364, TMEM 132B| |Intron 4:207203, PBMC:notRA; 12:126465510, LOC400084||Intron 1:2410, PBMC:notRA; 12:127209583, LOC387895||3' Proximal Enhancer:47225, TcelhOA; 12:127226034, LOC100507206||Intron l:4482,LOC387895||Intron 3:30774, PBMC:OA_SLE_HC; 12:129326769,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 12:129337339, GLTlDl||Proximal Promoter: -741, PBMC:notRA; 12:129429698, GLTlDl||Intron 4:91618, PBMC:notRA; 12:12963527, DDX47||Distal Promoter: -2752, PBMC:notRA; 12:130087444, TMEM 132D| |Intron 2:300768, PBMC:notRA; 12:130092534, TMEM132D||Intron 2:295678, PBMC:notRA; 12:130335340, TMEM132D||Intron 1:52872, PBMC:OA_SLE_HC; 12:130434412, PBMC:OA_SLE_HC; 12:130450777, PBMC:notRA; 12:130604991, PBMC:notRA; 12:130680612, PBMC:OA; 12:130968528, RIMBP2||Intron 2:33882, PBMC:notRA,Wholeblood:notRA; 12:131324319, STX2||Proximal Promoter:-508, PBMC:SLE; 12:131387360, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 12:131590460, GPR133||Intron 17:152009, PBMC:HC; 12:131606752, GPR133||Intron 20:168301, Wholeblood:notRA; 12:132551483, PBMC:HC; 12:132831695, GALNT9|| Intron 5:74210, Bcell:OA_SLE_HC; 12:132832250, GALNT9|| Intron 5:73655, PBMC:notRA; 12:132859441, GALNT9||Intron 2:46464,LOC100130238||3' Proximal Enhancer: 7465, TcelhOA; 12:132859722, GALNT9||Intron 2:46183,LOC100130238||3' Proximal Enhancer: 7746, PBMC:OA_SLE_HC; 12:132887349, Mono:OA_SLE_HC,Tcell:HC; 12:132929908, PBMC:notRA; 12:132935480, Bcell:SLE,Mono:OA_SLE_HC; 12:132950559, PBMC:HC; 12:132962614, PBMC:notRA; 12:132972807, PBMC:notRA; 12:133020327, PBMCnotRA; 12:133021135, Mono:HC,Tcell:HC; 12:133022423, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC; 12:133022550, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 12:133022677, PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 12:133022760, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 12:133022853, Tcell:HC,Tcell:OA_SLE_HC; 12:133022955, PBMC:HC; 12:133125057, FBRSLl||Intron 5:57901, PBMC:HC; 12:133147971, FBRSLlpxon 9:80815, Wholeblood:notRA; 12:133322256, ANKLE2|| Intron 5:16195, PBMC:HC,PBMC:OA,Tcell:HC; 12:133429949, CHFR||Intron ll:Intron 9:34255, Tcell: OA SLE HC ; 12:133435861, CHFR||Intron 5:Intron 7:28343, PBMC:HC,PBMC:OA_SLE_HC; 12: 133516439, ZNF605||Intron 2: 164531 Intron 3: 16429, PBMC:notRA; 12: 133526195, ZNF605||Intron l :6673|Intron 1 :6697, PBMC:notRA; 12: 14132940, GRIN2B|| Proximal Promoter:82, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 12: 14134486, GRIN2B||Proximal Promoter:-1464, Tcell:OA_SLE_HC; 12: 14413090, Bcell:SLE,Mono:SLE,PBMC:HC; 12: 14413185,
Mono:SLE,PBMC:HC; 12: 14420864, PBMC:notRA; 12: 14547229, ATF7IP||Intron 1 :28619, PBMC:OA_SLE_HC,PBMC:SLE; 12: 14927076, H2AFJ|| Proximal Promoter:-193,HIST4H4||Distal Promoter:-3011, Mono:OA; 12: 15038788, MGP||Proximal Promoter:65, PBMC:notRA; 12: 15114732, ARHGDIB||Proximal Promoter:- 170, PBMC:notRA; 12: 1609034, ERC1 ||3' Proximal Enhancer:50863 l,LOC100292680||Proximal Promoter: -622,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 12: 1612770, ERC1 ||3' Proximal
Enhancer:512367,LOC100292680||Exon 2:3114, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC;
12: 16762831, LM03||Distal Promoter:-2747|Distal Promoter:-3097|Distal Promoter:-3295|Distal Promoter:-3927|Distal Promoter:-4518|Proximal Promoter:-1683, PBMC:notRA; 12: 19310593, PLEKHA51 |Intron 3:27968, Bcell:OA; 12:2017649, Wholeblood:notRA; 12:24650901, PBMCnotRA; 12:248500, IQSEC3||Exon 3:61959|Exon 4:72452,LOC574538||Intron 7:9832, Tcell:HC; 12:248889, IQSEC3||Intron 3:62348|Intron 4:72841,LOC574538||Intron 7:9443, PBMC:HC; 12:249109, IQSEC3 ||Intron 3:62568|Intron 4:73061,LOC574538||Intron 7:9223, PBMC:HC; 12:25151263, C12orf77||Proximal Promoter:-890, Mono:HC; 12:25304568, CASCl ||Intron 3:Intron 5:Intron 6:Intron 7:43526, Mono:HC; 12:25436262, PBMC:OA_SLE_HC,PBMC:SLE; 12:25705953, IFLTDl ||Intron l :95535|Proximal Promoter:225|Proximal Promoter:233|Proximal Promoter:264, Bcell:OA_SLE_HC; 12:26274368, BHLHE41 ||Exon 5:3635, PBMC:OA; 12:26881038, ITPR2||Intron 2: 105093, Bcell:HC; 12:26951217, ITPR2||Intron 1 :34914, Mono:OA; 12:27170664, MED21 ||Distal Promoter:- 4818,TM7SF3||Distal Promoter:-3325, PBMC:HC; 12:27861039, MRPS35||Distal Promoter: -2666, PBMC:notRA; 12:2881762, LOC283440||Proximal Promoter:-927, PBMC:OA_SLE_HC; 12:29303160, PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 12:29303184, PBMC:SLE,Tcell:SLE; 12:2944310, LOC100507424||Proximal Promoter:-1671,NRIP2||Proximal Promoter:-89, PBMC:OA_SLE_HC; 12:29568207, Mono:OA_SLE_HC,Mono:SLE; 12:297831, SLC6A12||3' Proximal Enhancer:24782|3' Proximal Enhancer:25032|3' Proximal Enhancer:25540, PBMC:OA_SLE_HC; 12:3070406, TEAD4||Intron l : 1659|Intron 2: 1929, PBMCSLE; 12:31767203, Tcell:OA; 12:31816638, AMN1 ||3' Proximal Enhancer:65470,METTL20||Intron 2: 16545|Intron 2:4030|Intron 2:4518, Tcell:OA; 12:32675207, FGD4||Intron 1 :20167, PBMC:HC; 12:33593177, SYT10||Proximal Promoter: -423, Mono:OA; 12:34317569, PBMCnotRA; 12:34372490, Tcell:HC; 12:34547604, PBMC:HC; 12:34753697, BcelhOA SLE HC; 12:3489096, BcelhOA SLE HC; 12:3680597, PRMT8|| Intron 6:80173, PBMC:HC; 12:38532129, PBMC:HC; 12:38545085, PBMC:SLE; 12:41831532, PDZRN4||Intron 3:249283|Proximal Promoter:-8, PBMC:notRA; 12:42679156, PBMC:notRA; 12:42680748, PBMCnotRA; 12:42681908, PBMC:notRA; 12:43031000, PBMC:notRA; 12:4403352, CCND2||Intron 4:20451, Wholeblood:notRA; 12:4671597, RAD51AP1 ||3' Proximal Enhancer:23648, Mono:OA_SLE_HC; 12:4671731, RAD51AP1 ||3' Proximal Enhancer:23782, Mono:HC; 12:47479795, AMIG02||5' Proximal Enhancer: -6061, PBMC:OA; 12:47626844, FAM113B||Intron 1 : 16793, PBMC:notRA; 12:48690974, Mono:HC; 12:48921782, OR8Sl ||Exon 2:2368, PBMC:notRA; 12:48965123, LALBA||Proximal Promoter:-1294, Bcell:HC; 12:49332783, ARF3||Exon 5: 18469, Mono:OA; 12:51442472, LETMD 11 |Proximal Promoter: 373 |Proximal Promoter:391, Wholeblood:notRA; 12:51636921, DAZAP2||Exon 3:Exon 4:Exon 5:Intron 3:4414,SMAGP||3' Proximal Enhancer:27073|3' Proximal Enhancer:27281, PBMC:HC; 12:51818049, SLC4A8||Proximal Promoter: -544, PBMC:notRA; 12:52281482, ANKRD331 |Proximal Promoter: -310, PBMC:notRA; 12:52281676, ANKRD3311 Proximal Promoter:-l 16, PBMC:notRA; 12:52281810, ANKRD3311 Proximal Promoter: 18, PBMCSLE; 12:52509901, PBMC:notRA; 12:52639388, KRT7||Exon 7: 12435, PBMC:notRA; 12:53170909, KRT76||Proximal Promoter:220, Mono:OA; 12:53359155, PBMC:notRA; 12:53441582, EIF4B||3' Proximal Enhancer:41521,LOC283335||Intron 2:6640,TENCl ||Intron l :773|Proximal Promoter:- 1150|Proximal Promoter:-2252, Bcell:OA_SLE_HC; 12:53492662, IGFBP6|| Intron l : 1227,SOAT2||Distal Promoter: -4611,
PBMC:OA,PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 12:53592259, ITGB7||Intron 3:8741,ZNF740||3' Proximal Enhancer: 17725, Bcel SLE; 12:53808156, AMHR2||5' Proximal Enhancer: -9482,SPl ||Exon 6:33729|Exon 6:34178, Bcell:OA_SLE_HC; 12:54069197, ATP5G2||Intron l : 1315|Intron 1 :912, Wholeblood:notRA; 12:54071090, ATP5G2||Proximal Promoter:-578|Proximal Promoter: -981, PBMC:OA; 12:54475010, FLJ12825||Intron l :22973,LOC100240735||Intron 1 :597, PBMC:notRA; 12:54583464, SMUGl||Proximal Promoter:-686|Proximal Promoter: -723, PBMC:notRA; 12:54653091, Bcel OA; 12:55944274, OR6C4||Proximal Promoter: -736, Tcel OA; 12:56036796, OR10P1 ||3' Proximal Enhancer:6121, PBMC:HC; 12:56040208, OR10P1 ||3' Proximal Enhancer:9533, PBMC:notRA; 12:56414442, IKZF4||Proximal Promoter:-246, PBMC:HC; 12:56555325, MYL6||Exon 6:Exon 7:3281,MYL6B||3' Proximal Enhancer:9122,SMARCC2||3' Proximal Enhancer:28026, PBMC:notRA; 12:56732723, IL23A||Proximal Promoter:61,PAN2||5' Proximal Enhancer:-5190|Distal Promoter:- 4886,STAT2||3' Proximal Enhancer:21314, Mono:HC; 12:56882535, GLS2||Proximal Promoter: -354, Wholeblood:notRA; 12:57421088, MY01A||3' Proximal Enhancer:22813|3' Proximal Enhancer:23461, PBMC:SLE; 12:57617297, NXPH4||Intron 1 :6720,SHMT2||5' Proximal Enhancer: -6058|5' Proximal Enhancer:-6530|5' Proximal Enhancer:-6813|5' Proximal Enhancer:-6845, PBMC:notRA; 12:58003965, ARHGEF251 |Proximal Promoter:-1252|Proximal Promoter: 3, DTX3||3' Proximal
Enhancer:5362,PIP4K2C||3' Proximal Enhancer: 19024,SLC26A10||5' Proximal Enhancer: -9727, TcelhOA; 12:58236712, Tcell: OA SLE HC ; 12:59730539, Mono:OA_SLE_HC; 12:60673288, PBMC:SLE; 12:62685785, USP15||Intron 1 :31665, Tcell:OA_SLE_HC; 12:6277045, Tcell:OA_SLE_HC,Tcell:SLE; 12:62855292, MON2||5' Proximal Enhancer: -5304, PBMC:notRA; 12:6308774, CD9||Proximal Promoter: - 707, PBMC:HC; 12:6416539, PLEKHG6||5' Proximal Enhancer:-5277|Distal Promoter:-3062|Distal Promoter: -3559, PBMCnotRA; 12:6435752, PLEKHG6||Intron 13: 13936|Intron 14: 15654|Intron 14: 16151,TNFRSF1A||3' Proximal Enhancer: 15531, PBMC:notRA; 12:66122497, PBMC:notRA; 12:66138190, PBMC:notRA; 12:6619164, NCAPD2|| Intron 3: 15867,SCARNA10||Proximal Promoter:-223, PBMC:SLE; 12:6659524, IFF01 ||Intron 3:Intron 4:5725,NOP2||3' Proximal Enhancer: 17956, TcelhHC; 12:67272574, Mono:SLE; 12:6741882, ACRBP||3' Proximal Enhancer: 14698, LP AR5|| Intron l :3415|Proximal Promoter:- 1067, BcelhHC; 12:6799541, C12orf53||3' Proximal Enhancer: 10055|3' Proximal Enhancer: 10468,ZNF384||Proximal Promoter:- 1000|Proximal Promoter:-803, BcelhHC; 12:68201286, PBMC:OA; 12:69139618, NUP107||3' Proximal Enhancer:58888,SLC35E3||Proximal Promoter: -317, PBMC:SLE; 12:69139650, NUP107||3' Proximal Enhancer:58920,SLC35E3||Proximal Promoter: -285, PBMC:SLE; 12:69742232, LYZ||Proximal Promoter:99, PBMC:HC; 12:69769552, YEATS4||Intron 6: 16021, PBMC:OA_SLE_HC; 12:7066614, MIR141 ||5' Proximal Enhancer: - 6645,MIR200C||5' Proximal Enhancer:-6247,PHB2||3' Proximal Enhancer: 13277|3' Proximal Enhancer: 13302,PTPN6||Intron 9: 10875|Intron 9:6181, SCARNA12||3' Proximal Enhancer: 10155, PBMC:HC; 12:72149658, RAB21 ||Intron 1 : 1001, PBMC:OA_SLE_HC; 12:72245061, MRS2P2||Proximal Promoter:-298,TBClD15||Intron 1 : 11575, PBMC:notRA; 12:7245510, ClR||Proximal Promoter: - 467,C1RL||3' Proximal Enhancer: 16359, PBMC:OA; 12:7260776, ClRL||Intron 2: 1093,MATL2963||Proximal Promoter:-127, PBMC:notRA; 12:739280, NINJ2||Intron 1 :33475, PBMC:notRA; 12:739980, NINJ2||Intron 1 :32775, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 12:740100, NINJ2||Intron 1 :32655, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 12:75601711, KCNC2||Exon 2: 1800, PBMC:OA; 12:75780994, GLIPRlL2||Distal Promoter:-3894, PBMC:notRA; 12:7593007, CD163Ll ||Intron 2:3742, Wholeblood:notRA; 12:76176280, PBMC:notRA; 12:76354015, PBMC:HC; 12:7900651, CLEC4C||Intron 1 : 1418, BcelhOA; 12:80308778, PPPlR12A||Intron 1 : 19953 |Intron l :20200|Intron 2:20457|Proximal Promoter:- 1087, PBMC:OA; 12:83321412, TMTC2||Intron 3:240479, PBMC:notRA; 12:8333010, FAM66C||Proximal Promoter:206,ZNF705A||3' Proximal Enhancer: 7861, PBMC:notRA; 12:8403616, FAM86FP||5' Proximal Enhancer:-8074, PBMC:notRA; 12:86658860, MGAT4C|| Intron 3:573821, PBMC:HC; 12:86995819, PBMC:notRA; 12:8833355, PBMC:notRA; 12:89968675, PBMC:HC; 12:91775374, PBMC:HC; 12:9227209, A2M||Exon 29:41349,C12orG3||5' Proximal Enhancer:-9543,LOC144571 ||3' Proximal Enhancer:9437, PBMC:notRA; 12:9231867, A2M||Exon 25:36691, Bcell:OA_SLE_HC; 12:93530780, LOC643339||Intron 3:240732, PBMC:HC; 12:93895324, MRPL42||Exon 6:Exon 7:34059, PBMC:notRA; 12:94915694, PBMC:notRA; 12:95228201, KRT19P2||Proximal Promoter:-28,MIR492||Proximal Promoter:28, PBMC:notRA; 12:9559402, PBMC:OA_SLE_HC; 12:95594566, FGD6||Intron 2: 16674, BcelhHC; 12:95841289, PBMC:HC; 12:96367302, AMDHD1 ||3' Proximal Enhancer:30232,HAL||Exon 21 :22769, Mono:HC; 12:96590115, ELK3||Intron 1 : 1909, PBMC:HC; 12:96604497, ELK3||Intron 1 : 16291, PBMC:OA_SLE_HC; 12:98107291, PBMC:notRA; 12:98151379, PBMC:notRA; 13: 100004097, FKSG29||Proximal Promoter:424,MIR623||Distal Promoter: -4287, PBMC:HC; 13: 100149311, TM9SF2||Distal Promoter:-4416, PBMC:HC; 13: 100394412, Mono:OA_SLE_HC; 13: 100517027, PBMC:HC,PBMC:OA_SLE_HC; 13: 100637241, ZIC2||Exon 2:3216, PBMC:OA; 13: 100638446, ZIC2||Exon 3:4421, PBMC:notRA; 13: 100642408, ZIC2||3' Proximal Enhancer: 8383, PBMC:notRA; 13: 100781335, PCCA||Intron 3:Intron 4:40067, PBMC:HC; 13: 101910744, NALCN||Intron 11 : 158069, Tcell:OA_SLE_HC; 13: 101910811, NALCN||Exon 11 : 158002, PBMC:HC; 13: 102520143, FGF14||Intron 3:48852|Intron 3:533981, PBMC:HC; 13: 105484300, PBMC:notRA; 13: 105791890, Mono:OA_SLE_HC; 13: 106117425, DAOA||Proximal Promoter:- 1139|Proximal Promoter:-790|Proximal Promoter:-938,DAOA- ASl ||Intron 5:40605, BcelhHC; 13: 107344392, PBMC:notRA; 13: 108110276, FAM155A||Intron 1 :409184, BcelhOA SLE HC; 13: 108954054, TNFSF13B||Intron 2:Intron 3:32078, PBMC:HC,PBMC:notRA; 13: 109439124, MY016||Intron 5: 157554|Intron 5: 190625, PBMC:OA_SLE_HC; 13: 109833854, MY016||Intron 34:552284|Intron 34:585355, Mono:HC; 13: 110386267, Mono:OA,PBMC:HC; 13: 110431612, IRS2||Intron 1 :7302, BcelhOA; 13: 110892021, COL4Al ||Intron 2:67475, Mono:OA_SLE_HC; 13: 111297551, CARKD||3' Proximal Enhancer:29621 |3' Proximal Enhancer:29745,CARS2||Intron 12:60929, Wholeblood:notRA; 13: 111318160, CARS2||Intron 8:40320, PBMC:HC; 13: 111358924, CARS2|| Proximal Promoter: -444,ING1 ||5' Proximal Enhancer:-6158|5' Proximal Enhancer:-6685|5' Proximal Enhancer:-6700|5' Proximal Enhancer:-8434, PBMC:notRA; 13: 111704375, PBMC:OA; 13: 112063695, PBMC:HC,PBMC:OA_SLE_HC; 13: 112319172, PBMC:HC; 13: 112324767, PBMC:OA; 13: 112508324, PBMC:OA_SLE_HC; 13: 112679965, PBMC:notRA; 13: 112707805, PBMC:HC; 13: 112721778, SOXl ||Proximal Promoter:-134, PBMC:OA; 13: 112722333, SOXl ||Proximal Promoter:421, BcelhOA; 13: 112729515, SOXl||3' Proximal Enhancer:7603, PBMC:notRA; 13: 113001355, PBMC:HC; 13: 113097259, SPACA7||3' Proximal Enhancer:66609, PBMC:notRA; 13: 113313905, C13orG5||Intron 1 : 12548, PBMC:notRA; 13: 113411561, ATP 11A|| Intron 1 :66919, PBMC:OA_SLE_HC; 13: 113419790, ATPl lA||Intron 1 :75148, PBMC:HC; 13: 113528751, ATPl lA||Intron 27: 184109, BcelhSLE; 13: 113841719, PCID2||Intron 7:21310, PBMC:HC; 13: 114161463, TMC03||Intron 6: 16156, PBMC:HC; 13: 114166135, TMC03||Intron 7:20828, PBMC:HC; 13: 114184462, TMC03||Intron 8:39155, PBMC:HC; 13: 114261934, TFDPl ||Intron 2:22879|Intron 2:22932, PBMC:HC; 13: 114741241, RASA3||3' Proximal Enhancer: 156854, PBMCnotRA; 13: 114764621, RASA3||Intron 20: 133474, PBMC:HC,PBMC:notRA; 13: 114773785, RASA3||Intron 17: 124310, PBMC:OA_SLE_HC; 13: 114774991, RASA3||Intron 16: 123104, PBMC:notRA; 13: 114783503, RASA3||Intron 11 : 114592, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC; 13: 114814333, RASA3||Intron 3:83762, Mono:SLE,PBMC:SLE; 13: 114814401, RASA3||Intron 3:83694, Mono:SLE,PBMC:OA_SLE_HC; 13: 114828264, RASA3||Intron 2:69831, PBMC:HC; 13: 114839662, RASA3||Intron 1 :58433, PBMC:HC; 13: 114843624, RASA3||Intron 1 :54471, PBMC:notRA; 13: 114844592, RASA3||Intron 1 :53503, PBMC:OA_SLE_HC; 13: 114872606, RASA3||Intron 1 :25489, PBMCnotRA; 13: 114879659, RASA3||Intron 1 : 18436, Tcell:HC; 13: 114883479, RASA3||Intron 1 : 14616, PBMC:SLE; 13: 114890515, RASA3||Intron 1 :7580, PBMC:notRA; 13: 114890566, RASA3||Intron 1 :7529, PBMC:HC; 13: 114900021, RASA3||Proximal Promoter:-1926, PBMC:OA_SLE_HC,PBMC:notRA; 13: 114908901, PBMC:HC; 13: 114923588, PBMC:SLE; 13: 114927933, Tcell:OA_SLE_HC; 13: 19692444, PHF2Pl ||Proximal Promoter: -21, PBMC:notRA; 13: 19921076, ANKRD26P3||Proximal Promoter:-1963,LINC00421 ||3' Proximal Enhancer: 1888, PBMC:OA; 13:20135998, PBMC:notRA; 13:20703415, GJA3||3' Proximal Enhancer:31768, PBMC:OA_SLE_HC; 13:20796216, GJB6||Exon 3:9156|Exon 3:Exon 4:Exon 5: 10318, PBMC:HC; 13:20933879, PBMC:HC; 13:21010146, CRYLl ||Intron 4:89866,MIR4499||Proximal Promoter: -2161, BcelhOA; 13:21182994, IFT88||Intron 13:Intron 15:41787, PBMC:notRA; 13:21480411, XP04||Distal Promoter: -3498, PBMCnotRA; 13:21833918, PBMC:notRA; 13:21838110, PBMC:notRA; 13:21872349, PBMC:notRA; 13:21896301, PBMC:notRA; 13:23310635, PBMCnotRA; 13:24144985, TNFRSF19||5' Proximal Enhancer:-8513|Proximal Promoter:477, PBMC:SLE; 13:24471776, ClQTNF9B||Proximal Promoter:-651,ClQTNF9B-ASl ||3' Proximal Enhancer:8185|3' Proximal Enhancer:8749,MIPEP||5' Proximal Enhancer:-8189, PBMC:notRA; 13:24520348, Mono:OA_SLE_HC; 13:24824078, Tcell:OA_SLE_HC; 13:25319768, PBMC:notRA; 13:27338713, GPR12||Distal Promoter: - 3791, PBMC:notRA; 13:28369514, GSX1 ||3' Proximal Enhancer:2735, TcelhOA; 13:28492265, PDXl ||Proximal Promoter:-1902, PBMC:OA; 13:28555064, PRHOXNB|| Intron 1 :7710, PBMC:OA_SLE_HC,PBMC:SLE; 13:28555387, PRHOXNB|| Intron 1 :7387, PBMC:SLE; 13:28558413, PRHOXNB||Intron 1 :4361, PBMC:OA_SLE_HC,PBMC:SLE; 13:28562902, PRHOXNB|| Proximal Promoter:-128, PBMC:notRA; 13:28875661, FLTl ||Exon 30: 193604,PAN3||3' Proximal Enhancer: 163019, BcelhOA; 13:29329153, Mono:OA; 13:30707585, PBMC:notRA; 13:30982971, PBMC:HC; 13:31473080, C13orG3||5' Proximal Enhancer:-7231,LOC100507064||Intron 2:33665, Tcell:OA_SLE_HC; 13:32531145, EEFlDP3||Intron 3: 110226, PBMC:HC,PBMC:notRA; 13:33780283, STARD13||Intron 1 :79618|Intron 5:470649|Proximal Promoter: -96, PBMC:HC; 13:33860016, TcelhOA; 13:34371837, Mono:HC; 13:38231017, TRPC4||Intron 5:Intron 6:212922, PBMC:HC,PBMC:OA_SLE_HC; 13:41366576, LOC100616668||3' Proximal Enhancer: 129310,SLC25A15||Intron 1 :3030, PBMC:OA_SLE_HC; 13:41384019, LOC100616668||Intron 5:Intron 7: 111867,MIR621 ||Proximal Promoter: - 882,SLC25A15||Exon 7:20473, PBMC:notRA; 13:41931181, NAA16||Intron 10:Intron 9:45841, Bcell:OA_SLE_HC; 13:42028532, C13orfl5||Distal Promoter:-3009, PBMC:notRA; 13:43151796, TNFSFl l ||Intron l :3506|Intron 3: 14925, PBMC:OA; 13:43355739, C13orG0|| Proximal Promoter:54, Mono:OA_SLE_HC; 13:43450419, PBMC:OA; 13:46425929, SIAH3||Proximal Promoter:-83, PBMC:OA_SLE_HC,PBMC:SLE; 13:47126300, LRCH1 || Proximal Promoter:-995, BcelhHC; 13:47214871, LRCHl ||Intron 1 :87576, PBMC:OA,PBMC:OA_SLE_HC; 13:48073444, TcelhOA; 13:48575897, SUCLA2||Proximal Promoter:-435, Wholeblood:notRA; 13:49005868, LPAR6||Distal Promoter: -4825|Intron l : 12972,RBl ||Intron 17: 127986, PBMC:HC,PBMC:OA_SLE_HC; 13:49019222, LPAR6||Proximal Promoter: -382,RBl ||Intron 17: 141340, PBMC:notRA; 13:49117085, RCBTB2||5' Proximal Enhancer:-9769, PBMC:HC; 13:49227121, Mono:OA; 13:50414468, PBMC:HC; 13:50425353, PBMC:HC; 13:51020511, PBMC:notRA; 13:51416639, DLEU7||Intron 1 : 1246, Mono:HC; 13:51416749, DLEU7||Intron 1 : 1136, BcelhHC; 13:51466941, PBMC:HC; 13:52165356, WDFY2||Intron 1 :6873, PBMC:HC; 13:53171401, PBMC:notRA; 13:53174319, PBMC:HC; 13:53422871, PCDH8||Proximal Promoter: -96, PBMC:OA; 13 :53442030, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 13:54708344, PBMC:HC,PBMC:notRA; 13:60733965, PBMC:notRA; 13:67801125, PCDH9||Exon 2:3343, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC; 13:67801551, PCDH9||Exon 2:2917, Mono:SLE; 13:76334583, LM07||Intron 4: 140014|Proximal Promoter:-213, Mono:SLE,PBMC:SLE; 13:76334707, LM07||Intron 4: 140138|Proximal Promoter:-89, Mono:SLE; 13:76334728, LM07||Intron 4: 140159|Proximal Promoter:-68, Mono:SLE; 13:77292011, Mono:OA; 13:79234251, RNF219||Proximal Promoter: -937, PBMC:SLE; 13:79234353, RNF219||Proximal Promoter: - 1039, PBMC:SLE; 13:79234435, RNF219||Proximal Promoter:- 1121, PBMC:SLE; 13:80911808, SPRY2||Exon 2:3278, PBMC:SLE; 13:84660622, PBMC:HC,PBMC:notRA; 13:88329151, SLITRK5||Exon 2:4282, PBMC:OA_SLE_HC; 13:91370196, Bcell:OA; 13:92001764, MIR17||Proximal Promoter: - 1094,MIR17HG| |Intron 1 : 1691 ,MIR18A| |Proximal Promoter: - 1240,MIR19A| (Proximal Promoter: - 1380,MIR19B 11 |Proximal Promoter: - 1681 ,MIR20A| |Proximal Promoter: -
1554,MIR92Al ||Proximal Promoter:-1803, PBMC:SLE; 13:94107224, GPC6||Intron 1 :228147, PBMC:notRA; 13:94568320, GPC6||Intron 3:689243, Bcell:HC; 13:95652307, PBMC:notRA; 13:95954534, ABCC4||Proximal Promoter:-847, PBMC:OA_SLE_HC; 13:97126731, HS6ST3||Intron 1 :383639, Bcell:OA; 13:98112404, RAP2A||Intron 1 :25930, Mono:HC; 13:99095003, STK24||3' Proximal Enhancer: 134393|3' Proximal Enhancer:79338, PBMC:notRA; 13:99174875, STK24||Intron l :54521 |Proximal Promoter:-534, Mono:HC; 13:99869897, MIR548AN||Intron 4: 188657,UBAC2||Intron l : 16735|Intron 1 : 17219, Mono:OA; 14: 100540291, EVL||Intron 1 :8541, PBMC:HC; 14: 101123867, LINC00523||Proximal Promoter:263, PBMC:OA_SLE_HC,PBMC:SLE; 14: 101292967, MEG3||Intron 1 :523, PBMC:notRA; 14: 101908865, Tcell:HC; 14: 102171582, PBMC:notRA; 14: 102176671, PBMC:notRA; 14: 102682062, WDR20||3' Proximal Enhancer:Intron 2:Intron 3:75874, Wholeblood:notRA; 14: 103018726, PBMC:notRA,Wholeblood:notRA; 14: 103659071, LOC100131366||Distal Promoter:-3706, PBMC:OA; 14: 104010839, TRMT61A||3' Proximal Enhancer: 15331, Wholeblood:notRA; 14: 104095156, KLCl ||Proximal Promoter:-368, PBMC:notRA; 14: 104119516, KLCl ||Intron 1 :23992, PBMC:notRA; 14: 104734272, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 14: 104734368, PBMC:OA_SLE_HC; 14: 104736574, Bcel HC; 14: 104917314, PBMC:notRA; 14: 105011965, PBMC:OA_SLE_HC; 14: 105036133, C14oril 80||5' Proximal Enhancer:-9922, PBMC:notRA; 14: 105041159, C14orfl 80||Distal Promoter: -4896, PBMC:OA_SLE_HC; 14: 105106665, PBMC:HC; 14: 105108721, PBMC:notRA; 14: 105332627, KIAA0284||Intron 1 :978, PBMC:OA_SLE_HC; 14: 105555223, PBMC:HC; 14: 105708343, BRF l ||Intron l:5879|Intron l :7398|Intron 4:Intron 5:58986|Intron 5:73571,BTBD6||5' Proximal Enhancer: - 6535, PBMC:HC; 14: 105779952, PACS2||Intron 1 : 12783 |Proximal Promoter:-799, PBMC:HC; 14: 105855008, PACS2||Intron 18:87839|Intron 18:Intron 19:74257,TEX22||5' Proximal Enhancer: -9911, Mono:HC; 14: 105860954, PACS2||Exon 24:93785|Exon 24:Exon 25:80203,TEX22||Distal Promoter:-3965, Mono:HC,Tcell:HC; 14: 106095194, PBMC:OA; 14: 106135024, PBMC:notRA; 14: 106320748, PBMC:HC; 14: 106410628, BcelhHC; 14: 106436764, ADAM6||Exon 2: 1594, PBMC:notRA; 14: 107210810, Wholeblood:notRA; 14: 19647166, PBMC:notRA; 14: 19745841, PBMC:OA; 14:20482899, OR4K14||Proximal Promoter:453, Wholeblood:notRA; 14:21152213, ANG||Distal Promoter: - 4718|Proximal Promoter:-122,RNASE4||Distal Promoter:-4718|Proximal Promoter:-158, PBMC:notRA; 14:21153451, ANG||Distal Promoter:-3480|Intron 1 : 1116,RNASE4||Distal Promoter:-3480|Intron 1 : 1080, PBMC:HC; 14:21199099, PBMC:notRA; 14:21483641, NDRG2||3' Proximal Enhancer: 10294|3' Proximal Enhancer:9623, PBMC:HC; 14:21738473, HNRNPC|| Proximal Promoter:-835, Mono:HC; 14:22362410, BcelhOA SLE HC; 14:22902298, PBMC:HC,PBMC:OA_SLE_HC; 14:22938675, PBMC:OA_SLE_HC; 14:22958399, PBMC:HC; 14:22993190, PBMC:HC; 14:23317496, MMP14||3' Proximal Enhancer: 11704, PBMC:HC; 14:23531625, ACINl ||Exon 14:Exon 15:33198|Exon 8:Exon 9:9154,CDH24||Distal Promoter: - 4878, PBMC:HC; 14:23588325, CEBPE||Proximal Promoter:495,SLC7A8||3' Proximal Enhancer:35285|3' Proximal Enhancer:64524, PBMC:HC; 14:23588616, CEBPE||Proximal Promoter:204,SLC7A8||3' Proximal Enhancer: 34994|3' Proximal Enhancer:64233, PBMC:HC; 14:23821149, EFS||3' Proximal Enhancer: 13693,SLC22A17||Intron 2:931 |Proximal Promoter:330, Wholeblood:notRA; 14:24520788, DHRS4L1 ||3' Proximal Enhancer: 15079,LRRC16B||Proximal Promoter:-417, PBMC:HC; 14:24641706, IP04||3' Proximal Enhancer: 16418,IRF9||3' Proximal Enhancer: 11285,REC8||Proximal Promoter:473, PBMC:SLE; 14:24641852, IP04||3' Proximal Enhancer: 16272,IRF9||3' Proximal Enhancer: 11431,REC8||Intron l :Intron 2:619, PBMC:SLE,Tcell:SLE; 14:24642317, IP04||3' Proximal Enhancer: 15807,IRF9||3' Proximal Enhancer: 11896,REC8||Intron 3:Intron 4: 1084,
PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 14:24676542, CHMP4A||3' Proximal Enhancer:6494,MDPl ||3' Proximal Enhancer:8734,NEDD8||3' Proximal Enhancer:25034,NEDD8-MDPl ||3' Proximal Enhancer:25034,TSSK4||Exon 3: 1617, PBMC:HC; 14:25046121, CTSG||Proximal Promoter:-655, PBMC:HC; 14:28733613, PBMC:HC; 14:30585046, PBMC:notRA; 14:31711014, PBMC:notRA; 14:31915923, C14oril26||Exon 3: 10757, PBMCnotRA; 14:31927974, C14orfl26||Proximal Promoter: - 1294, PBMC:HC; 14:32413698, PBMC:notRA; 14:32896478, AKAP6||Intron 1 :98000, PBMC:notRA; 14:34270437, NPAS3||Exon l l :Exon 12:861979, PBMC:notRA; 14:35032169, SNX6||Exon 13:67146|Exon 14:67197, PBMC:OA_SLE_HC; 14:35184556, CFL2||Proximal Promoter:-1533|Proximal Promoter:-527|Proximal Promoter:-795, PBMC:OA_SLE_HC; 14:35835511, PBMC:HC; 14:36971168, SFTA3||Intron 1 : 11822, PBMC:HC; 14:37051693, NKX2-8||Proximal Promoter:93, Bcell:OA; 14:37506088, Mono:OA_SLE_HC,Mono:SLE; 14:39856160, FBX033||3' Proximal Enhancer:45544, PBMC:notRA; 14:42662538, Mono:HC; 14:44004546, PBMC:notRA; 14:45267997, PBMC:SLE; 14:45381239, C14orl28||3' Proximal Enhancer: 14733, Bcell:OA_SLE_HC; 14:47120845, RPL10L||Proximal Promoter: 183, PBMC:notRA; 14:47411755, MDGA2||Intron 9:400683 |Intron 9:732402, Mono:OA; 14:47872288, MDGA2|| Intron 1 :271869, PBMC:HC,PBMC:OA_SLE_HC; 14:48095779, MDGA2||Intron 1 :48378, PBMC:notRA; 14:50468241, C14orfl 82||Intron 1 :5997, PBMC:HC; 14:50474530, C14orfl 821| Proximal Promoter:-292, PBMC:notRA; 14:51026681, ATLl ||Intron l :26882|Proximal Promoter:-61, PBMC:HC; 14:51134070, SAVl ||Intron 1 :953, PBMC:OA_SLE_HC; 14:51172257, PBMC:notRA; 14:51606299, PBMC:notRA; 14:51955005, FRMD6||Proximal Promoter: - 849, Bcel HC; 14:51974848, FRMD6|| Intron 1 : 18994, PBMC:HC; 14:52326905, GNG2|| Proximal Promoter:-116, PBMC:SLE; 14:52733216, PTGDR|| Proximal Promoter:- 1214, Mono:SLE; 14:52816915, PBMC:SLE; 14:53331182, FERMT2||Exon 12:86633, Bcel HC; 14:54410717, BMP4||3' Proximal Enhancer: 10553|3' Proximal Enhancer: 12837, PBMC:OA_SLE_HC; 14:54507223, Bcell:OA_SLE_HC; 14:54948899, GMFBpxon 3:6845, PBMC:notRA; 14:56281968, PBMC:HC; 14:58599692, C14orG7||Intron 3: 19155, PBMC:notRA; 14:58621892, C14orG7||Distal Promoter:-3045, PBMC:notRA; 14:59066094, PBMC:HC; 14:59238729, PBMC:notRA; 14:60632532, DHRS7||Proximal Promoter:-321, PBMC:OA_SLE_HC; 14:60633047, DHRS7||Proximal Promoter:-836, PBMC:SLE; 14:60864465, PBMC:notRA; 14:60974499, SIX6||Proximal Promoter:-1438, PBMC:HC; 14:61793064, PRKCH||Intron 1 :4550, PBMC:HC; 14:61801201, PRKCH||Intron 1 : 12687, PBMC:HC; 14:61928727, PRKCH||Intron 9: 140213, PBMC:HC; 14:62583787, FLJ43390||Proximal Promoter:-287, PBMC:OA; 14:64932678, AKAP5||Proximal Promoter:462,MTHFDl ||3' Proximal Enhancer:77920, Tcell:OA_SLE_HC; 14:66480528, PBMC:notRA; 14:67983484, TMEM229B||Proximal Promoter:-1463, PBMC:OA_SLE_HC; 14:68973466, RAD51B||3' Proximal Enhancenlntron 10:686971, PBMC:HC; 14:69159219, Bcell:OA_SLE_HC,Bcell:SLE; 14:69256677, ZFP36Ll ||Exon 2:3954|Exon 3:6283, PBMC:HC; 14:69256690, ZFP36Ll ||Exon 2:3941 |Exon 3:6270, PBMC:HC; 14:70077191, KIAA0247||Proximal Promoter:-1118, Tcell:OA_SLE_HC; 14:71372869, PCNX||Proximal Promoter:-1252, PBMCnotRA; 14:71555837, PCNX||Intron 29: 181716, PBMC:notRA; 14:72141840, SIPAlLl ||Intron 9: 145799, PBMC:notRA; 14:72399846, RGS6||Intron l : 1030|Intron l :691 |Proximal Promoter:61, PBMC:notRA; 14:72990359, RGS6||Intron 14:591543|Intron 14:Intron 15:590574|Intron 15:591204, Bcell:OA_SLE_HC; 14:73373205, PBMC:HC,Tcell:HC; 14:73719302, PAPLN||Intron 9: 15098, PBMC:OA_SLE_HC; 14:73929570, NUMB||Distal Promoter:-4284, PBMC:OA_SLE_HC; 14:74704714, VSX2||Proximal Promoter:-1460, PBMC:notRA; 14:74891361, SYNDIC 1L|| Intron 1 : 1444, Bcel HC; 14:74892986, SYNDIGlL||Proximal Promoter:-181, PBMC:OA; 14:75179363, FCFl ||Proximal Promoter:- 486,KIAA0317||Proximal Promoter:444, PBMC:notRA; 14:75596637, NEK9||Distal Promoter: - 2859,TMED10||3' Proximal Enhancer:46712, PBMC:notRA; 14:75741733, FOS||Distal Promoter: -3747, PBMC:SLE; 14:75764329, LOC731223||3' Proximal Enhancer: 3223, PBMC:HC; 14:76734327, PBMC:notRA; 14:76734368, PBMC:notRA; 14:76734493, PBMC:notRA; 14:76734550, PBMC:notRA; 14:76816747, Tcell:OA_SLE_HC; 14:76819370,
Mono:OA,PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC,Tcell:OA; 14:77609774, ZDHHC22||Proximal Promoter: -1640, PBMC:OA_SLE_HC; 14:77767735, POMT2||Intron 5: 19490, PBMCnotRA; 14:77781561, GSTZ1 ||5' Proximal Enhancer:-5668|5' Proximal Enhancer:-6144,POMT2||Intron 1 :5664, PBMC:notRA; 14:78447545, Mono:OA; 14:81392851, CEP128||Intron 1 : 13033, PBMC:notRA; 14:86086389, FLRT2||Intron 1 :89902, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 14:88472437, GPR65||Intron 1 :970, PBMC:HC; 14:88831516, PBMC:notRA; 14:89493095, Mono:OA_SLE_HC; 14:89976587, PBMC:SLE; 14:90995484, PBMC:notRA; 14:91860613, CCDC 88C|| Intron 3:23575, PBMC:HC; 14:91884912, CCDC88C||Proximal Promoter:-724, PBMC:notRA; 14:92333771, FBLN5||3' Proximal Enhancer:80275,TC2N||Proximal Promoter: 109, PBMC:SLE; 14:92334029, FBLN5||3' Proximal Enhancer:80017,TC2N||Proximal Promoter:-149, PBMC:HC; 14:92339595, FBLN5||Intron 10:74451,TC2N||5' Proximal Enhancer:-5715, PBMC:HC; 14:92435629, TRIPl l ||Exon 21 :70774, Tcell:OA_SLE_HC; 14:92585304, CPSF2||Distal Promoter: -2993, NDUFBl ||Intron 1 :2849, PBMC:HC; 14:92788580, SLC24A4|| Proximal Promoter:- 157 l |Proximal Promoter:-344|Proximal Promoter: -956, PBMC:OA_SLE_HC; 14:92927875, SLC24A4||Intron 12: 137724|Intron 12: 138951 |Intron 13: 138339, PBMC:OA_SLE_HC; 14:93315488, GOLGA5||3' Proximal Enhancer:54839, PBMC:HC; 14:93604463, PBMC:notRA; 14:94385395, FAM181A||5' Proximal Enhancer:-8292|5' Proximal Enhancer:-8293|5' Proximal Enhancer:-8335|Proximal Promoter: 156,FAM181A-ASl||Intron 4:7323,
PBMC:OA_SLE_HC,PBMC:SLE; 14:94577101, IFI27||Proximal Promoter:23,IFI27Ll ||3' Proximal Enhancer:29463, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 14:94981685, SERPINA12||Intron 2:2496, Wholeblood:notRA; 14:95358041, PBMC:notRA; 14:95826830, PBMC:HC; 14:95826853, PBMC:HC,Tcell:HC; 14:95826997, TcelhHC; 14:96038687, PBMC:OA_SLE_HC; 14:96526884, C14orfl32||Intron 1 :21223 Intron 1 :21224, PBMC:SLE; 14:96563269, C14orfl32||3' Proximal Enhancer:57608|3' Proximal Enhancer:57609,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 14:96655464, PBMC:HC; 14:96955063, AK7||Exon 18:96616, PBMC:notRA; 14:98444476, C14orf64||Proximal Promoter:-15, PBMC:HC; 14:98445245, C14orf64||Proximal Promoter:-784, PBMCnotRA; 14:98919898, PBMC:notRA; 14:99707721, BCLl lB||Intron 2:30101, PBMCnotRA; 14:99708736, BCLl lB||Intron 2:29086, PBMC:notRA; 14:99728984, BCLl lB||Intron 1 :8838, Mono:OA; 15: 100171683, MEF2A||Intron l :Intron 2:Intron 3:65551 |Proximal Promoter: -1499, TcelhHC; 15: 100672379, AD AMT S 17 Intron 1 1 :209804, PBMC:notRA; 15: 101084507, CERS3||Proximal Promoter:418, PBMC:HC; 15: 101085341, CERS3||Proximal Promoter: -416, Mono:OA; 15: 101509442, LRRKl ||Intron 2:49983, PBMC:HC,Tcell:HC; 15: 101547756, LRRKl ||Intron 6:88297, PBMC:HC; 15: 101784653, CHSYl ||Intron 1 :7484, PBMC:notRA; 15: 102290915, TcelhHC; 15:20737822, GOLGA6L6||Exon 9:9292, PBMC:notRA; 15:20786824, GOLGA8C||3' Proximal Enhancer: 19151, PBMC:SLE; 15:22383188, OR4N4||Exon 1 :716, PBMC:notRA; 15:22413307, OR4N3P||Proximal Promoter:- 154, PBMC:notRA; 15:22798986, Mono:HC; 15:23454199, GOLGA8E||3' Proximal Enhancer: 19130, PBMC:OA_SLE_HC,PBMC:SLE; 15:23810334, MIR4508||Distal Promoter:-3056,MKRN3||Proximal Promoter:- 1 19, PBMC:OA_SLE_HC; 15:24506388, PBMC:notRA; 15:25298516, SNORD1 16-l ||3' Proximal Enhancer: 1894,SNORDl 16-2||Proximal Promoter:-839,SNORD1 16-3||Distal Promoter:-3489,SNORDl 16-4||5' Proximal Enhancer: - 6167,SNORD1 16-5||5' Proximal Enhancer:-8962,SNORDl 16-7||5' Proximal Enhancer:-8962,SNORDl 16- 9||Distal Promoter:-3489, Mono:OA_SLE_HC; 15:25301860, SNORD1 16-l ||3' Proximal Enhancer:5238,SNORD1 16-2||3' Proximal Enhancer:2505|5' Proximal Enhancer:-831 1,SNORD1 16- 3||Proximal Promoter:-145,SNORDl 16-4||Distal Promoter: -2823,SNORD116-5||5' Proximal Enhancer:- 5618,SNORD1 16-6||5' Proximal Enhancer:-831 1,SNORD1 16-7||5' Proximal Enhancer:-5618,SNORDl 16- 9||Proximal Promoter: -145, TcelhOA; 15:25325293, SNORD1 16-10||3' Proximal Enhancer:6034,SNORD1 16-l l ||3' Proximal Enhancer:4219,SNORDl 16-12||3' Proximal
Enhancer:3097,SNORDl 16-13||3' Proximal Enhancer: 1090,SNORDl 16-14||Proximal
Promoter:6,SNORDl 16-15||Proximal Promoter:-l 139,SNORDl 16-16||Distal Promoter:-2620,SNORD1 16- 17||5' Proximal Enhancer:-6379|Distal Promoter:-3440,SNORD1 16-18||5' Proximal Enhancer: - 5237,SNORD1 16-19||5' Proximal Enhancer:-6379|Distal Promoter:-3440,SNORD1 16-20||5' Proximal Enhancer:-7514,SNORD1 16-21 ||5' Proximal Enhancer:-8656,SNORDl 16-22||5' Proximal Enhancer: - 9775,SNORD1 16-3||3' Proximal Enhancer:7041,SNORDl 16-8||3' Proximal Enhancer:9716,SNORDl 16- 9||3' Proximal Enhancer: 7041, PBMC:notRA; 15:25428676, SNORD1 15-10||3' Proximal Enhancer:4789|5' Proximal Enhancer:-7886|Distal Promoter:-4006|Proximal Promoter: -2101, SNORD1 15-1 1 ||5' Proximal Enhancer:-5884,SNORD1 15-12||3' Proximal Enhancer:4789|5' Proximal Enhancer:-7886|Proximal Promoter: -2101,SNORD1 15-13||5' Proximal Enhancer: -9791,SNORDl 15-29||5' Proximal Enhancer:- 5884,SNORD1 15-3||3' Proximal Enhancer: 8603, SNORD1 15-36||5' Proximal Enhancer:-5884,SNORDl 15- 4\\3' Proximal Enhancer:6698,SNORDl 15-43||5' Proximal Enhancer:-5884,SNORD115-5||3' Proximal Enhancer:4792|5' Proximal Enhancer:-7889|Proximal Promoter:-2104,SNORD1 15-6||3' Proximal Enhancer:3033,SNORD1 15-7||3' Proximal Enhancer: 1 145,SNORDl 15-8||Proximal Promoter: - 776,SNORD1 15-9||3' Proximal Enhancer:4789|5' Proximal Enhancer: -7886|Proximal Promoter:-2101, PBMC:notRA; 15:25429326, SNORD1 15-10||3' Proximal Enhancer:5439|5' Proximal Enhancer: - 7236|Distal Promoter:-3356|Proximal Promoter:-1451,SNORDl 15-1 1 ||5' Proximal Enhancer: - 5234,SNORD1 15-12||3' Proximal Enhancer:5439|5' Proximal Enhancer:-7236|Proximal Promoter:- 1451,SNORD1 15-13||5' Proximal Enhancer: -914 l,SNORDl 15-29||5' Proximal Enhancer: - 5234,SNORD1 15-3||3' Proximal Enhancer:9253,SNORDl 15-36||5' Proximal Enhancer:-5234,SNORDl 15- 4\\3' Proximal Enhancer:7348,SNORDl 15-43||5' Proximal Enhancer:-5234,SNORD115-5||3' Proximal Enhancer:5442|5' Proximal Enhancer:-7239|Proximal Promoter:-1454,SNORDl 15-6||3' Proximal Enhancer:3683,SNORD1 15-7||3' Proximal Enhancer: 1795,SNORDl 15-8||Proximal Promoter: - 126,SNORD1 15-9||3' Proximal Enhancer:5439|5' Proximal Enhancer: -7236|Proximal Promoter: -1451, PBMC:notRA; 15:25434030, SNORD1 15-10||3' Proximal Enhancer: 1348|3' Proximal Enhancer:3253|Distal Promoter: -2532,SNORDl 15-1 l ||Proximal Promoter:-530,SNORD1 15-12||3' Proximal Enhancer:3253|Distal Promoter: -2532,SNORD115-13||Distal Promoter: -4437,SNORDl 15-14||5' Proximal Enhancer: - 6037,SNORD1 15-29||Proximal Promoter:-530,SNORD1 15-36||Proximal Promoter:-530,SNORD1 15- 43||Proximal Promoter: -530,SNORD1 15-5||3' Proximal Enhancer:3250|Distal Promoter:-2535,SNORDl 15- 6\\3' Proximal Enhancer:8387,SNORDl 15-7||3' Proximal Enhancer:6499,SNORDl 15-8||3' Proximal Enhancer:4578,SNORD115-9||3' Proximal Enhancer:3253|Distal Promoter:-2532, PBMC:OA_SLE_HC; 15:25434150, SNORDl 15-10||3' Proximal Enhancer: 1468|3' Proximal Enhancer:3373|Proximal Promoter:- 2412,SNORD115-l l||Proximal Promoter: -410,SNORD115-12||3' Proximal Enhancer:3373|Proximal Promoter: -2412,SNORD115-13||Distal Promoter: -4317,SNORDl 15-14||5' Proximal Enhancer: - 5917,SNORDl 15-29||Proximal Promoter: -410,SNORD115-36||Proximal Promoter: -410, SNORDl 15- 43||Proximal Promoter:-410,SNORD115-5||3' Proximal Enhancer: 33701 Proximal Promoter:- 2415,SNORD115-6||3' Proximal Enhancer:8507,SNORDl 15-7||3' Proximal Enhancer:6619,SNORDl 15- 8||3' Proximal Enhancer:4698, SNORDl 15-9||3' Proximal Enhancer: 33731 Proximal Promoter:-2412, PBMC:OA; 15:25441418, SNORDl 15-10||3' Proximal Enhancer:4856|3' Proximal Enhancer:8736,SNORD115-l l||3' Proximal Enhancer:6858,SNORDl 15-12||3' Proximal
Enhancer:4856,SNORD115-13||3' Proximal Enhancer:2951,SNORDl 15-14||3' Proximal
Enhancer: 1351, SNORDl 15-15||5' Proximal Enhancer: -9990,SNORD115-16||Distal Promoter: - 3176,SNORD115-17||5' Proximal Enhancer:-5051|5' Proximal Enhancer:-6955|5' Proximal Enhancer: - 8085,SNORD115-18||5' Proximal Enhancer:-5051|5' Proximal Enhancer:-6955|5' Proximal Enhancer: - 8085,SNORD115-19||5' Proximal Enhancer:-5051|5' Proximal Enhancer:-6955|5' Proximal Enhancer: - 8085,SNORD115-20||5' Proximal Enhancer:-9990,SNORD115-21||5' Proximal Enhancer: - 9990,SNORD115-29||3' Proximal Enhancer:6858,SNORDl 15-36||3' Proximal Enhancer:6858,SNORDl 15- 43||3' Proximal Enhancer:6858,SNORDl 15-5||3' Proximal Enhancer:4853, SNORDl 15-9||3' Proximal Enhancer:4856, PBMC:notRA; 15:25478725, SNORDl 15-1 l||Distal Promoter:-2506,SNORD115- 29||Distal Promoter:-2506,SNORD115-30||3' Proximal Enhancer:8376,SNORD115-31||3' Proximal Enhancer:6470,SNORD115-32||3' Proximal Enhancer:4612,SNORDl 15-33||3' Proximal
Enhancer:2741, SNORDl 15-34||3' Proximal Enhancer: 1192,SNORD115-35||Proximal Promoter:- 668,SNORDl 15-36||Distal Promoter:-2506,SNORD115-37||Distal Promoter:-4407,SNORD115-38||5' Proximal Enhancer:-6259,SNORDl 15-39||5' Proximal Enhancer:-8167,SNORDl 15-43||Distal Promoter: - 2506, PBMC:notRA; 15:25490492, SNORDl 15-10||Proximal Promoter:-1999,SNORD115-l l||3' Proximal Enhancer:9261|Distal Promoter:-3852,SNORD115-29||3' Proximal Enhancer:9261|Distal Promoter: - 3852,SNORD115-36||3' Proximal Enhancer:9261|Distal Promoter:-3852,SNORDl 15-37||3' Proximal Enhancer:7360,SNORD115-38||3' Proximal Enhancer:5508,SNORDl 15-39||3' Proximal
Enhancer:3600,SNORD115-40||3' Proximal Enhancer: 1732,SNORD115-41||Proximal Promoter:- 132,SNORD115-42||Proximal Promoter:-1999,SNORD115-43||3' Proximal Enhancer:9261|Distal Promoter: -3852,SNORD115-44||5' Proximal Enhancer:-5513, PBMCnotRA; 15:25941836, ATP10A||Intron 13:166513, Bcell:HC,Mono:SLE; 15:26049779, ATP 10A|| Intron 1:58570, PBMC:OA_SLE_HC; 15:26107410, Mono:SLE,PBMC:SLE; 15:27111604, GABRA5|| Proximal Promoter: -26 l|Proximal Promoter:-668, PBMC:OA_SLE_HC; 15:27214606, GABRG31 |Proximal Promoter: -1822, Wholeblood:notRA; 15:27902080, PBMC:OA_SLE_HC; 15:28053930, OCA2||Intron 23:290528, PBMC:OA; 15:28567519, HERC2|| Proximal Promoter:-224, PBMC:notRA; 15:29980500 PBMC:notRA; 15:30486767, DKFZP434L187||Proximal Promoter: -1471, Bcell:OA,Bcell:OA_SLE_HC 15:31090995, PBMC:OA_SLE_HC; 15:31515761, LOC283710||Exon 3:7289, PBMC:notRA: 15:31732992, PBMC:HC; 15:33534982, Mono:HC; 15:34634263, C15orf55||Distal Promoter:- 3802,NOP10||Exon 2: 1099,SLC12A6||5' Proximal Enhancer:-5218|Distal Promoter:-3998|Distal Promoter: - 4302, PBMC:notRA; 15:34781891, PBMC:notRA; 15:35529521, ANP32APl||Proximal Promoter:-5, PBMC:notRA; 15:36524258, PBMC:notRA; 15:36723660, PBMC:notRA; 15:37391424, MEIS2||Intron l:1317|Intron l:Intron 2:2076|Proximal Promoter:-862|Proximal Promoter: 173, PBMC:notRA; 15:37427791, PBMC:notRA; 15:37782940, PBMC:notRA; 15:39037809, BcelhOA; 15:39310779, Mono:OA_SLE_HC,PBMC:HC; 15:39713049, PBMC:notRA; 15:39759194, Bcel OA; 15:40443853, BUB1B||5' Proximal Enhancer:-9356, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 15:40531952, PAK6||Intron l:22324|Proximal Promoter:-82, PBMC:notRA; 15:41135847, SPINTl||Proximal Promoter: - 398|Proximal Promoter:-795, TcelhSLE; 15:41222276, DLL4||Exon 2:746, PBMC:OA; 15:41411926, INO80||Distal Promoter:-3586, BcelhHC; 15:41709584, RTFl||Proximal Promoter:283, PBMCnotRA; 15:42061865, MAPKBPl||Distal Promoter: -4766, TcelhHC; 15:42064259, MAPKBPl||Proximal Promoter: -2372, PBMC:notRA; 15:42652294, CAPN3||Exon 1:597,GANC||3' Proximal Enhancer: 85929, PBMC:HC; 15:43585817, TGM7||Exon 2:8636, PBMC:SLE; 15:43941407, CATSPER2||Proximal Promoter: -368, PBMC:notRA; 15:44579510, CASC4|| Proximal Promoter:- 1398, PBMC:OA_SLE_HC; 15:44969481, PATL2|| Proximal Promoter:-395, PBMC:HC; 15:45028098, TRIM69||Proximal Promoter:- 461, PBMC:OA; 15:45507901, PBMC:notRA; 15:45669010, GATM||Exon 2: 1970,LOC145663||Proximal Promoter:-1887, PBMC:HC; 15:49342629, SECISBP2L||Distal Promoter: -3869, PBMC:notRA; 15:49517594, GALK2||Intron 3:55173, PBMC:notRA; 15:49675495, C15orG3||Intron 11:237623, PBMC:notRA; 15:50108785, Mono:SLE; 15:52358353, MAPK6||Exon 6:46943, PBMC:SLE; 15:52554171, MY05C||Intron 9:33824, Mono:HC,PBMC:HC; 15:54052305, WDR72||Proximal Promoter:- 446, PBMC:notRA; 15:57052190, PBMC:HC; 15:57592083, LOC283663||Proximal Promoter: -479, PBMC:notRA; 15:57595298, LOC283663||Intron 1 :2736, BcelhOA; 15:58357891, ALDH1A2|| Proximal Promoter:230, PBMC:OA; 15:59499030, LDHAL6B||Proximal Promoter:-l 1, PBMC:HC; 15:59700360, PBMC:HC; 15:59950093, BNIP2||3' Proximal Enhancer:31549,GTF2A2||Proximal Promoter:-356, Tcell:HC; 15:61972967, PBMC:notRA; 15:62654536, PBMC:notRA; 15:62684736, PBMC:SLE; 15:62899159, PBMC:notRA; 15:63179548, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 15:63349192, TPMl pxon 2:8557|Exon 3: 14355, Bcell:OA; 15:63758958, PBMC:HC,PBMC:notRA; 15:63774509, PBMC:notRA; 15:65118189, PIF l ||Proximal Promoter:-351, Tcell:OA; 15:65843003, PTPLADl ||Intron 1 :20177, PBMC:notRA; 15:66331911, MEGFl l ||Intron 5:214164,MIR4311 ||Proximal Promoter:-659, PBMC:OA_SLE_HC; 15:66680551, MAP2Kl ||Intron 1 : 1341, PBMC:HC; 15:66914759, PBMC:HC; 15:66947066, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 15:66947171,
PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 15:66947564, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 15:66947568, PBMC:HC; 15:67006698, SMAD6||Intron 2: 12025 |Intron 2:5769, Tcell:HC; 15:67012832, SMAD6||Intron 3: 11903|Intron 3:Intron 4: 18159, Mono:SLE,PBMC:SLE; 15:67122959, Mono:OA; 15:68470500, PIASl ||Intron 11 : 123929, PBMC:notRA; 15:69373260, LINC00277||Proximal Promoter:71, Bcell:SLE; 15:69744466, KIF23||3' Proximal Enhancer:37840,RPLPl ||Proximal Promoter: -692, TcelhOA SLE HC; 15:69841231, PBMC:notRA; 15:70391035, PBMC:OA_SLE_HC; 15:71005778, UACA||Intron 1 :50072, PBMC:HC; 15:71747687, THSD4||Intron 6:313900, PBMC:notRA; 15:72567956, CELF6||3' Proximal Enhancer:30700|3' Proximal Enhancer:44331 |3' Proximal Enhancer:44569,PARP6||Distal Promoter: -4328, PBMC:notRA; 15:72977851, BBS4||Proximal Promoter: - 668,HIGD2B||Intron 1 :639, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 15:73344233, NE01 ||Proximal Promoter: -591, PBMC:notRA; 15:74266972, STOMLl ||3' Proximal Enhancer: 17663, PBMC:notRA,Wholeblood:notRA; 15:74285128, PML||Proximal Promoter:-1885,STOMLl ||Proximal Promoter: -493, Wholeblood:notRA; 15:75077691, CSK||Intron l :Intron 2:3267,MIR4513||3' Proximal Enhancer:3407, PBMC:HC; 15:75614965, PBMC:notRA; 15:77896785, LING01 ||3' Proximal Enhancer:27924, PBMC:OA_SLE_HC; 15:79725642, KIAA1024||Intron 1 :785, PBMC:OA_SLE_HC; 15:80260753, BCL2Al ||Intron 1 :2890, PBMC:notRA; 15:80696264, ARNT2|| Proximal Promoter:-427, Tcell:OA; 15:81475061, Bcell:OA_SLE_HC; 15:83241867, CPEBl ||Intron 2:74861 |Proximal Promoter: - 1294, Bcell:OA_SLE_HC; 15:83477872, FSD2||Distal Promoter: -3066,WHAMM||Proximal Promoter: -100, Bcell:HC; 15:83952774, BNCl ||Intron 1 :694, PBMC:OA; 15:84319908, ADAMTSL3||Distal Promoter:- 2929, Bcell:HC; 15:84363061, ADAMTSL31 |Intron 2:40224, PBMC:notRA; 15:86192745, AKAP13||Intron 10:268875, PBMC:notRA; 15:88119834, LINC00052||Proximal Promoter:-325, PBMC:OA_SLE_HC; 15:89181425, AEN||3' Proximal Enhancer: 16899,ISG20||Proximal Promoter:-613, PBMC:notRA; 15:89455860, MFGE8||Intron 1 :803,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 15:89561135, Tcell:OA; 15:89956781, Tcell:HC; 15:89992598, PBMC:notRA; 15:90115219, C15orf42||Distal Promoter:-3598, PBMC:OA_SLE_HC; 15:90796557, TTLL13||Exon 4:3794, PBMC:HC; 15:90927939, IQGAPl ||Distal Promoter: -3533, PBMC:HC; 15:91642909, SV2B||Proximal Promoter: -272|Proximal Promoter: -629, PBMC:OA; 15:93256789, PBMC:notRA; 15:93790914, PBMC:notRA; 15:96346592, PBMC:HC; 15:96874031, MIR 14691 | Proximal Promoter:-2458,NR2F2||Distal Promoter: -2537|Intron l :4875|Proximal Promoter:-1762|Proximal Promoter:-79, PBMC:OA; 15:97307874, PBMC:notRA; 15:97311928, PBMC:OA_SLE_HC,PBMC:SLE; 15:97814549, PBMC:notRA; 15:98197914,
Mono:HC,PBMC:HC,Tcell:HC; 15:98647776, PBMC:notRA; 15:99153795, Wholeblood:notRA; 15:99343918, PBMC:HC; 15:99975141, PBMC:OA_SLE_HC,PBMC:SLE; 15:99975310, PBMC:OA_SLE_HC,PBMC:SLE; 15:99975334, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 15:99975470, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 15:99979013, Mono:HC; 16: 1052756, Tcell:SLE; 16: 10647275, EMP2|| Intron 1 :27264, PBMCnotRA; 16: 10755037, TEKT5||Intron 5:33765, PBMC:notRA; 16: 10909361, FAM18A||Intron 2:3260, PBMC:HC; 16: 11435867, RMI2||Distal Promoter:- 3443, PBMC:SLE; 16: 11603344, PBMC:OA_SLE_HC; 16: 1170618, Bcell:HC; 16: 11759492, S N||Distal Promoter: -2796, PBMC:SLE; 16: 12060182, TNFRSF 17||Exon 2: 1219, Mono:HC; 16: 12142335, SNX29||Exon 7:71734, PBMC:notRA; 16: 12501787, SNX29||Intron 18:431186, PBMCnotRA; 16: 1255116, CACNAlH||Exon 11 :51876, PBMC:OA; 16: 12896895, Tcell:OA_SLE_HC; 16: 1361806, UBE2I||Intron l :2179|Intron 1 :2653, PBMC:OA_SLE_HC; 16: 14381731,
PBMC:OA_SLE_HC,PBMC:SLE; 16: 14394816, MIR193B||Distal Promoter:-3007,MIR365A||5' Proximal Enhancer:-8325, Tcell:OA_SLE_HC; 16: 1473469, C16orf 1 ||Intron 3:5876,UNKL||5' Proximal Enhancer: - 8764, PBMC:notRA; 16: 15073109, PDXDCl ||Intron 1 :4277, PBMC:notRA; 16: 15489619, MPV17L||Proximal Promoter:9, PBMC:notRA; 16: 1575979, IFT140||Exon 21 :86130,TMEM204||5' Proximal Enhancer: -8251, PBMC:HC; 16: 1583810, IFT140||Intron 19:78299,TMEM204||Proximal Promoter:-420, TcelhHC; 16: 16083164, ABCCl ||Intron 1 :39731, PBMC:HC; 16: 1609529, IFT140||Intron 18:52580,TMEM204||3' Proximal Enhancer:25299, Tcell:OA_SLE_HC; 16: 1611342, IFT140||Intron 18:50767,TMEM204||3' Proximal Enhancer:27112, PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 16: 1611973, IFT140||Intron 18:50136,ΤΜΕΜ204||3' Proximal Enhancer:27743,
PBMC:SLE,Tcell:OA_SLE_HC; 16: 16170085, ABCCl ||Intron 14: 126652, PBMC:HC; 16: 18799106, ARL6IP1 ||3' Proximal Enhancer: 1375 l,RPS15A||Intron 3:2550, Bcel HC; 16: 18800193, ARL6IP1 ||3' Proximal Enhancer: 12664,RPS15 A||Intron 2: 1463, PBMC:OA; 16: 19098198, COQ7||3' Proximal Enhancer: 18960|3' Proximal Enhancer: 19282, PBMC:notRA; 16: 19129228, ITPRIPL2||Exon l :Exon 2:3975, PBMC:OA_SLE_HC; 16: 1988798, RPL3L||3' Proximal Enhancer: 15881,SEPXl ||Exon 4:4496, PBMC:HC; 16:2048750, SYNGR3||3' Proximal Enhancer:8805,ZNF598||Exon 11 : 11013, PBMC:SLE; 16:20774873, ACSM3||Proximal Promoter: -438, PBMC:OA_SLE_HC,PBMC:SLE; 16:20890534, DCUNlD3||Intron 1 :21027, PBMC:notRA; 16:21169179, DNAH3||Intron l : 1583,TMEM159||Proximal Promoter: -732, PBMC:HC; 16:21569546, PBMC:notRA; 16:21658497, IGSF6||Exon 2:5490,METTL9||Intron 4:47642, PBMC:HC; 16:21665002, IGSF6||Proximal Promoter: - 1015,METTL9||Intron 4:54147, Mono:HC; 16:21767742, OTOA||Intron 17:51459|Intron 22:71993|Intron 26:77908, PBMC:notRA; 16:2210434, RAB26||3' Proximal Enhancer: 11784,SNORD60||5' Proximal Enhancer:-5328,TRAF7||Intron 1 :4636, Bcel HC; 16:2287763, DNASE 1 L21 |Intron 5: 1296,E4F1 ||3' Proximal Enhancer: 14197,ECIl ||3' Proximal Enhancer: 13839, BcelhSLE; 16:22926538, HS3ST2||Exon 2: 100679, Mono:OA_SLE_HC; 16:23316324, SC NlB||Intron 1 :2734, Tcell:OA_SLE_HC; 16:2334163, ABCA3||Intron 25:56584,MIR4717||3' Proximal Enhancer:9543, PBMC:HC; 16:23850404, PRKCB||Intron 2:3105, Mono:HC; 16:24857601, SLC5Al l ||Proximal Promoter:50, Tcel OA; 16:25075152, PBMC:notRA; 16:2657766, LOC652276||Intron 1 :4382,PDPK1 ||3' Proximal Enhancer:69797, Mono:HC; 16:26720703, Bcel HC; 16:27210995, JMJD5||Distal Promoter: -381 l |Distal Promoter:-4300, PBMC:SLE; 16:2732724, ERVK13-1 ||5' Proximal Enhancer:-9284,KCTD5||Proximal Promoter:230, PBMC:notRA; 16:27412496, IL21R||Proximal Promoter: -986, PBMC:HC; 16:27414281, IL21R||Intron 1 :799, PBMC:SLE; 16:27414418, IL21R||Exon 2:Intron 1:936, PBMC:HC; 16:27414536, IL21R||Exon 2:Intron 1 : 1054, PBMC:HC; 16:2746544, KCTD5||Intron 2: 14050, PBMC:OA_SLE_HC; 16:281201, ITFG3||Distal Promoter: -3599,LUC7L||Proximal Promoter: -1752, PBMCnotRA; 16:28205389, XP06||Intron 1 : 17801, PBMC:HC; 16:28273096, PBMC:notRA; 16:28511362, APOBR||3' Proximal Enhancer:5393,CLN3||5' Proximal Enhancer:-7739|5' Proximal Enhancer:-7959,IL27||Intron 4:6793, Mono:OA; 16:2892912, PRSS22||3' Proximal Enhancer: 15259,PRS S30P||Proximal Promoter:- 160, PBMCSLE; 16:2908934, PRSS22||Proximal Promoter:-763, PBMC:SLE; 16:29118967, RRN3P2|| Intron 15:32805, PBMC:notRA; 16:29196027, Mono:HC; 16:29227937, PBMC:notRA; 16:30101680, PPP4C||3' Proximal Enhancer: 14297,TBX6||Intron 3: 1525,YPEL3||3' Proximal Enhancer: 584113' Proximal Enhancer: 5857, BcelhOA; 16:30106682, GDPD3||3' Proximal Enhancer: 18196,PPP4C||3' Proximal Enhancer: 19299,TBX6||Distal Promoter:-3477,YPEL3||Exon l :839|Exon 2:855, PBMC:SLE; 16:30347333, LOC595101 ||Proximal Promoter:-638, PBMC:notRA; 16:30616649, ZNF689||Exon 3:5033, PBMC:HC; 16:31439106, COX6A2||Exon 3:643,ITGAD||3' Proximal Enhancer:34474,ZNF843||3' Proximal Enhancer: 15242, PBMC:HC,Tcell:HC; 16:318717, ITFG3||3' Proximal Enhancer:33917,RGSl l ||Exon 17:7197, Wholeblood:notRA; 16:31884740, ZNF267||Proximal Promoter:-338, Tcel HC; 16:3243552, PBMC:OA; 16:32857551, Wholeblood:notRA; 16:3334273, ZNF263||Intron 1 :787, PBMC:notRA; 16:33357151, PBMCnotRA; 16:33483299, PBMC:HC; 16:33483591, PBMC:notRA; 16:33938155, Wholeblood:notRA; 16:33952673, LINC00273||3' Proximal Enhancer:9830,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 16:34209247, Wholeblood:notRA; 16:34787597, PBMC:notRA; 16:3511787, NAA60||Intron l :3796|Intron 2: 18120,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 16:3533812, C16orf90||3' Proximal Enhancer: 11609,NAA60||Intron 5:25821 |Intron 6:40145, PBMC:notRA; 16:3988694, PBMC:HC; 16:3988869, PBMC:HC; 16:4183883, Bcel HC; 16:420230, MRPL28||Proximal Promoter:339,TMEM8A||3' Proximal Enhancer: 11720, PBMC:notRA; 16:4397291, COR07||3' Proximal Enhancer:69671,COR07-PAM16||Intron 27:69671,GLIS2||3' Proximal Enhancer: 15067,PAM16||Intron 1 :4082, PBMC:HC; 16:4506231, DNAJA3||Exon l l :Exon 12:30426,NMRAL1 ||3' Proximal Enhancer: 18665, PBMC:OA_SLE_HC; 16:4560300, C16orf5||3' Proximal Enhancer:28171 |3' Proximal Enhancer:28516,HMOX2||Exon 6: 14442|Exon 6:35582|Exon 6:Exon 7:33960, PBMC:HC; 16:46854830, C16orf87||Intron 2: 10244, PBMC:notRA; 16:4730465, MGRNl ||Intron l l :Intron 12:55641, PBMC:HC; 16:48530097, PBMC:notRA; 16:48592694, N4BPl ||Intron 2:51426, PBMCnotRA; 16:49564370, ZNF423||Intron 6:296548, PBMC:HC; 16:49732224, ZNF423||Intron 4: 128694, PBMC:notRA; 16:49732376, ZNF423||Intron 4: 128542, PBMC:notRA; 16:49732567, ZNF423||Intron 4: 128351, PBMC:notRA; 16:49732623, ZNF423||Intron 4: 128295, PBMCnotRA; 16:49890720, Tcel OA; 16:50100815, HEATR3||Intron 2:935, PBMC:SLE; 16:54155639, FTO||3' Proximal Enhancer:417765, PBMC:notRA; 16:54225800, PBMC:notRA; 16:55686715, SLC6A2||Distal Promoter:-2826|Distal Promoter:-3636|Distal Promoter:-3840, PBMC:notRA; 16:55868370, CESl ||Proximal Promoter:-1295, PBMC:OA; 16:56330268, PBMC:OA_SLE_HC; 16:57019755, CETP||3' Proximal Enhancer:23921, Tcel SLE; 16:57022486, CETP||3' Proximal Enhancer:26652, BcelhSLE; 16:57023022, CETP||3' Proximal Enhancer:27188, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC; 16:57023191, CETP||3' Proximal Enhancer:27357, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:HC; 16:57447502, CCL17||Intron 1 :8824, Mono:HC; 16:57562740, CCDC102A||Exon 2:7737, PBMC:HC,PBMC:OA_SLE_HC,Wholeblood:notRA; 16:57562841, CCDC102A||Exon 2:7636, PBMC:HC,PBMC:OA_SLE_HC; 16:57563395, CCDC102A||Intron 1 :7082, Wholeblood:notRA; 16:58035805, C16orf57||Intron l :529,ZNF319||Proximal Promoter: -2043, Mono:OA; 16:58769104, GOT2||Proximal Promoter:-858, PBMC:HC; 16:58783857, PBMC:notRA; 16:62984521, PBMC:notRA; 16:66413050, CDH5|| Intron 1 : 12526, PBMCnotRA; 16:66458043, BEANl ||Distal Promoter: -3156, Mono:OA; 16:66511944, BEANl ||Intron 3:Intron 4:50745, Wholeblood:notRA; 16:67210632, EXOC3Ll ||3' Proximal Enhancer: 13475,HSF4||3' Proximal Enhancer: 13345,KIAA0895L||Exon 7:7251,NOL3||3' Proximal Enhancer:2868|3' Proximal Enhancer:2877|3' Proximal Enhancer: 6228, PBMC:notRA; 16:67233983, E2F4||3' Proximal Enhancer:7916,ELM03||Intron 4:956,EXOC3Ll ||5' Proximal Enhancer:-9876,LRRC29||3' Proximal Enhancer:26738|3' Proximal Enhancer:26918,MIR328||3' Proximal Enhancer:2315, Bcel SLE; 16:67461683, HSDl lB2||Distal Promoter:-3352, PBMC:HC; 16:68034002, DPEP2|| Proximal Promoter:-638, PBMC:HC; 16:68321858, SLC7A6|| Intron 4:Intron 5:23440, PBMC:notRA; 16:6913336, RBFOXl ||Intron l :89527|Intron 3:844205, Bcel HC; 16:69350052, SNTB2||3' Proximal Enhancer: 129003,VPS4A||Intron 2:4766, Mono:HC; 16:70196247, PDPR||3' Proximal Enhancer:48719, PBMC:OA_SLE_HC; 16:70587308, BcelhHC; 16:70624354, IL34||Intron 1 : 10557, Wholeblood:notRA; 16:71011407, HYDIN||Intron 30:253162, Bcel SLE; 16:71260651, HYDIN||Intron l :3918|Intron l :3941 |Intron 1 :3974, PBMC:OA_SLE_HC; 16:71759364, AP1G1 ||3' Proximal Enhancer: 83612, PBMC:notRA; 16:72459516, PBMC:HC; 16:72644371, Mono:SLE; 16:73088677, ZFHX3||5' Proximal Enhancer: -6403 |Intron 1 :3857, Mono:OA; 16:743998, FBXL16||Exon 6: 11827,JMJD8||5' Proximal Enhancer: -9559,WDR24||Distal Promoter:-3598, PBMC:notRA; 16:75036318, ZNRFl ||Intron 1 :3404, PBMC:HC; 16:75145843, LDHD||Exon 11 :4827,ZNRF1 ||3' Proximal Enhancer: 112929, Mono:SLE; 16:75150744, LDHD|| Proximal Promoter:-74,ZNRFl ||3' Proximal Enhancen l 17830, PBMC:SLE; 16:75150784, LDHD|| Proximal Promoter:-114,ZNRFl ||3' Proximal Enhancer: 117870, T cell: SLE; 16:75150799, LDHD||Proximal Promoter:- 129,ZNRF1 ||3' Proximal Enhancen l 17885, Tcel SLE; 16:75322715, CFDP1 ||3' Proximal Enhancer: 144672, PBMC:HC; 16:75505953, CHST6||3' Proximal Enhancer:22973,TMEM170A||5' Proximal Enhancer:-7369, BcelhOA; 16:75575906, CHST5||5' Proximal Enhancer: -6838,TMEM231 ||Intron 4: 14230|Intron 5: 14264, PBMC:OA; 16:77998415, VATlL||Intron 7: 175933, Wholeblood:notRA; 16:785033, CCDC78||5' Proximal Enhancer:- 8560,HAGHL||3' Proximal Enhancer: 7768,NARFL||Intron 4:5964, PBMC:notRA; 16:7855274, PBMC:OA_SLE_HC; 16:7855622, PBMCnotRA; 16:788184, HAGHL||3' Proximal Enhancer: 10919,NARFL| |Intron 2:2813, PBMC:HC; 16:79306292, PBMC:HC,Tcell:HC; 16:80231787, PBMC:notRA,Wholeblood:notRA; 16:81272080, BCM01 ||Proximal Promoter:-215, Mono:SLE; 16:82033681, SDR42El ||Exon 3: 11412, PBMCnotRA; 16:832683, CHTF18||5' Proximal Enhancer: - 5938,RPUSD1 ||3' Proximal Enhancer:5700, Mono:OA; 16:83980015, OSGINl ||5' Proximal Enhancer: - 6811, PBMC:OA_SLE_HC; 16:84003607, NECAB2|| Intron l : 1371,OSGINl ||3' Proximal Enhancer: 16781, PBMC:notRA; 16:84076900, SLC38A8||Proximal Promoter:-l 138, PBMC:OA_SLE_HC; 16:84552874, PBMC:SLE; 16:84690554, KLHL36||Exon 3:8424, PBMC:HC; 16:84693148, KLHL36||Intron 3: 11018, PBMC:HC,PBMC:OA_SLE_HC; 16:84760429, USP10||Intron 1 :26875, PBMC:SLE; 16:85120012, KIAA0513||Intron 10:58603, PBMC:OA; 16:85268860, PBMC:SLE,Tcell:OA_SLE_HC; 16:85394259, PBMC:notRA; 16:854325, CHTF18||3' Proximal Enhancer: 15704,GNG13||Distal Promoter: - 3592,PRR25||Proximal Promoter:- 1117, PBMC:SLE; 16:85449316, PBMC:notRA; 16:85470674, Mono:HC; 16:85531414, PBMCnotRA; 16:85542816, Bcell:OA_SLE_HC; 16:85577847, PBMC:HC; 16:85601612, PBMC:notRA; 16:85776108, C16orf74|| Intron l :8581,MIR1910||Proximal Promoter:-802, PBMC:notRA; 16:85981310, Mono:HC; 16:85989730, Mono:HC; 16:86112141, PBMC:OA_SLE_HC; 16:86231823, PBMC:notRA; 16:86274683, PBMC:notRA; 16:86370962, LOC732275||Intron 4:8323, PBMC:notRA; 16:86371248, LOC732275||Intron 3:8037, PBMCnotRA; 16:86400581, PBMC:OA_SLE_HC; 16:86457593, PBMC:OA_SLE_HC,PBMC:notRA; 16:86548323, FOXFl ||3' Proximal Enhancer:4191,LOC400550||5' Proximal Enhancer: -5857, PBMCnotRA; 16:86601361, FOXC2||Exon 1 :505, PBMC:notRA; 16:86795490, PBMC:notRA; 16:86840467, PBMC:HC; 16:86840653, PBMC:HC,PBMC:OA_SLE_HC; 16:86899685, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC; 16:8715306, METTL22|| Proximal Promoter:-220, PBMC:notRA; 16:87248612, PBMC:notRA; 16:87251692, PBMCnotRA; 16:87323420, Mono:OA_SLE_HC; 16:87398040, FBX031 ||Intron l : 19354|Intron 2:27668, Wholeblood:notRA; 16:87450089, ZCCHC14||Intron 8:75371, Bcell:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 16:87521410, ZCCHC14||Intron 1 :4050, PBMC:HC; 16:87735724, JPH3||3' Proximal Enhancer:99226,KLHDC4||3' Proximal Enhancer:63874, Bcel HC; 16:87736832, JPH3||3' Proximal Enhancer: 100334,KLHDC4||3' Proximal Enhancer:62766, Mono:OA_SLE_HC; 16:87736889, JPH3||3' Proximal Enhancer: 100391,KLHDC4||3' Proximal Enhancer:62709,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 16:88134848, TcelhHC; 16:88268339, PBMC:notRA; 16:88268771, Bcell:SLE; 16:88547533, ZFPMl ||Intron 1 :27520, PBMC:HC; 16:88594506, ZFPMl ||Exon 6:74493, Bcell:HC; 16:88757816, MGC23284||3' Proximal Enhancer:28036,RNF166||3' Proximal Enhancer: 12209|3' Proximal Enhancer: 1498413' Proximal Enhancer: 15013,SNAI3||Distal Promoter:-4934,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC,Tcell:OA_SLE_HC; 16:88770966, CTU2||Proximal Promoter:-1924,RNF166||Intron l : 1834|Intron l : 1863|Proximal Promoter: -941, PBMC:HC; 16:88804051, PBMC:notRA; 16:88858277, Bcell:SLE,PBMC:HC; 16:88995416, CBFA2T3||Intron 1 : 121921 Intron 1 :48088, PBMC:SLE; 16:89033692, CBFA2T3||Intron 1 :9812, Bcell:SLE,Tcell:SLE; 16:89033785, CBFA2T3||Intron 1 :9719, Tcell:OA_SLE_HC; 16:89048433, CBFA2T3||Distal Promoter:-4929, BcelhHC; 16:89118838, PBMC:notRA; 16:89162196, ACSF3||Intron 1 : 1980, BcelhHC; 16:89163625, ACSF3||Intron 1 :3409, PBMC:notRA; 16:89180587, ACSF3||Intron 3:Intron 4:Intron 5:20371, PBMC:HC,PBMC:notRA; 16:89300123, ZNF778||3' Proximal Enhancer: 16013, PBMC:HC; 16:8943436, CARHSP1 ||3' Proximal Enhancer: 18812| 3' Proximal Enhancer: 19427,PMM2||3' Proximal Enhancer:51767, PBMC:HC; 16:89550474, PBMC:SLE; 16:89678764, DPEP1 ||5' Proximal Enhancer:-8235|Proximal Promoter:-951, PBMC:notRA; 16:89740564, C16orf55||3' Proximal Enhancer: 16355, PBMC:notRA; 16:89909677, SPIRE2||Intron 1 : 14771, PBMC:HC; 16:90050102, AFG3LlP||Intron 5: 11115, BcelhSLE; 16:9326393, MIR548X|| Proximal Promoter:-2380, PBMC:notRA; 17: 1040653, PBMC:OA_SLE_HC,PBMC:notRA; 17: 10634954, TMEM220||Proximal Promoter:-1308, PBMC:notRA; 17: 1133546, PBMC:HC,PBMC:OA_SLE_HC; 17: 1133706, PBMC:HC; 17: 11503508, DNAH9||Intron 1 : 1761, PBMC:notRA; 17: 12425767, Mono:HC,PBMC:HC,Tcell:HC; 17: 12562530, MYOCD||5' Proximal Enhancer: -6676, PBMC:notRA; 17: 14206774, HS3ST3Bl ||Intron l :2269,MGC12916||Proximal Promoter:-282, PBMC:HC; 17: 14207530, HS3ST3Bl ||Intron l :3025,MGC12916||Proximal Promoter:474, PBMC:HC; 17: 14738114, PBMC:OA_SLE_HC; 17: 1494566, SLC43A2||Exon 8:37564, PBMC:notRA,Wholeblood:notRA; 17: 15164809, MIR4731 ||5' Proximal Enhancer:-9796,PMP22||Intron l : 1080|Intron l :3835|Proximal Promoter: -716,
Bcell:SLE,Tcell:OA_SLE_HC; 17: 1549284, PRPF8||3' Proximal Enhancer:38892,RILP||3' Proximal Enhancer:4108,SCARFl ||Proximal Promoter: -243, PBMC:HC; 17: 1551941, PRPF8||3' Proximal Enhancer:36235,RILP||Intron 4: 1451,SCARFl ||Distal Promoter:-2900, PBMC:SLE; 17: 15683060, MEIS3P1 ||5' Proximal Enhancer:-7103, PBMC:notRA; 17: 16257223, CENPV||Proximal Promoter: -411, Wholeblood:notRA; 17: 16397992, FAM211A||Distal Promoter: -2512,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 17: 16488023, Tcell:HC,Tcell:OA_SLE_HC,Tcell:SLE; 17: 16593517, CCDC144A||Proximal Promoter:- 121, PBMC:notRA; 17: 16757305, PBMC:notRA; 17: 171187, LOC100506388||5' Proximal Enhancer: -9808,RPH3AL||Exon 3:Exon 4:31446, PBMC:notRA; 17: 17566891, PBMC:OA; 17: 179611, LOC100506388||Proximal Promoter:-1384,RPH3AL||Intron l :Intron 2:23022, PBMC:HC; 17: 18023971, MY015A||Exon 2: 11952, PBMC:notRA; 17: 18266135, SHMTl ||Intron 1 :721, PBMC:SLE; 17: 18305305, PBMC:OA_SLE_HC; 17: 18529285, CCDC144B||Proximal Promoter:- 355,TBC1D28||3' Proximal Enhancer: 18455, PBMCnotRA; 17: 19141619, EPN2||Intron 1 :930, Mono:OA; 17: 19287978, MAPK7||3' Proximal Enhancer:6205|3' Proximal Enhancer:6945,MFAP4||Exon 6:2554, BcelhSLE; 17: 19631485, ALDH3A1 ||3' Proximal Enhancer: 17287| 3' Proximal Enhancer: 17440|3' Proximal Enhancer:20261, PBMC:HC; 17: 19990302, SPECCl ||Intron l :77654|Proximal Promoter:-32, Tcel OA; 17:20128997, SPECCl ||Intron 2:69691 |Intron 4: 138663|Intron 4:216349, PBMC:OA_SLE_HC; 17:20445757, PBMC:OA_SLE_HC,PBMC:SLE; 17:20491042, CDRT15L2||3' Proximal Enhancer: 8006, PBMC:notRA; 17:21226746, MAP2K3||3' Proximal Enhancer:35399|3' Proximal Enhancer:38779, PBMC:HC; 17:21227099, MAP2K3||3' Proximal Enhancer:35752|3' Proximal Enhancer:39132, Tcel OA; 17:21828178, FAM27L||3' Proximal Enhancer:2809, PBMC:notRA; 17:22023880, MTRNR2L1 ||Exon 1 : 1444, PBMC:notRA; 17:22203008, Wholeblood:notRA; 17:25416204, Wholeblood:notRA; 17:263193, C17orf 7||Exon 2:3076, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 17:26899428, ALDOC||3' Proximal Enhancer:4523,PIGS||Proximal Promoter:-541,SPAG5||3' Proximal Enhancer:26628, PBMC:SLE; 17:27050360, NEK8||5' Proximal Enhancer:-5471,RAB34||5' Proximal Enhancer:-5074|5' Proximal Enhancer:-5109|5' Proximal Enhancer: -5452,RPL23A||Intron 3:3361, SNORD42A||Proximal Promoter: - 86,SNORD42B||3' Proximal Enhancer:2793,SNORD4A||3' Proximal Enhancer:761,SNORD4B||Proximal Promoter:-338,TLCDl ||3' Proximal Enhancer:2870|3' Proximal Enhancer:3589, Bcel HC; 17:27135257, C17orf63||Intron l :Intron 2:34584, Mono:SLE; 17:2843149, RAP 1GAP2|| Intron 3: 143418, Mono:HC; 17:2843257, RAP 1GAP2|| Intron 3: 143526, Mono:HC; 17:29148918, CRLF3||Intron 1 :2860, PBMC:notRA; 17:29283870, ADAP2||Intron 10:35117, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC; 17:29285543, ADAP2||Exon 11 :36790, Tcell:OA_SLE_HC,Tcell:SLE; 17:29297380, DPRXP4||Distal Promoter: -4972,RNF 135||Proximal Promoter:-575, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 17:29297391, DPRXP4||Distal Promoter: -4961,RNF 135||Proximal Promoter: -564,
PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 17:29297414, DPRXP4||Distal Promoter: -
4938,RNF 135| |Proximal Promoter:-541, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC: SLE; 17:29297437, DPRXP4||Distal Promoter:-4915,RNF 135||Proximal Promoter:-518,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 17:29297458, DPRXP4||Distal Promoter: - 4894,RNF135||Proximal Promoter:-497, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 17:29297478, DPRXP4||Distal Promoter:-4874,RNF135||Proximal Promoter: -477, PBMC:OA_SLE_HC,PBMC:SLE; 17:29636863, EVI2A||3' Proximal Enhancer: 11904,EVI2B||Intron 1 :4267, Bcel OA; 17:29672644, PBMC:notRA; 17:30850485, MY01D||Intron 21 :353417, PBMC:SLE; 17:31268322, TMEM98||Exon 7:Exon 8: 13395, PBMC:notRA; 17:31662900, ACCNl ||Intron 1 :820925, PBMC:notRA; 17:33426885, RAD51D||Exon 10:Exon 7:Exon 8:Exon 9:20003,RAD51L3-RFFL||Intron 5:21656, PBMC:HC; 17:33842301, PBMC:OA_SLE_HC; 17:33864734, Mono:SLE; 17:33927921, AP2Bl ||Intron 3: 13640, PBMC:OA_SLE_HC; 17:34079665, C17orf50||5' Proximal Enhancer:-8250,GAS2L2||Proximal Promoter:232,RASL10B||3' Proximal Enhancer:20987, PBMC:SLE; 17:34079987, C17orf50||5' Proximal Enhancer:-7928,GAS2L2||Proximal Promoter: -90,RASL10B||3' Proximal Enhancer:21309, Mono:SLE; 17:34079998, C17orf50||5' Proximal Enhancer:-7917,GAS2L2||Proximal Promoter:- 101,RASL10B||3' Proximal Enhancer:21320, PBMC:OA_SLE_HC,PBMC:SLE; 17:34599556, TBC1D3C||5' Proximal Enhancer:-7524, PBMC:OA_SLE_HC,PBMC:SLE; 17:34845115, MY019||3' Proximal Enhancer:46190,ZNHIT3||Intron 2:2643, PBMC:notRA; 17:34891843, GGNBP2||5' Proximal Enhancer: - 8893,MY019||Proximal Promoter:-538,PIGW||Proximal Promoter:441, Bcell:OA_SLE_HC; 17:35300448, AATF||5' Proximal Enhancer:-5726,LHXl ||Exon 5:5677, PBMC:OA,PBMC:OA_SLE_HC,PBMC:SLE; 17:35490983, ACACA||Intron 43:Intron 44: 165709|Intron 45:225076|Intron 45:Intron 49:275919, Mono:SLE; 17:36735584, SRCINl ||Intron 1 :26599, BcelhOA; 17:3704482, C17orf85||3' Proximal Enhancer:45058|3' Proximal Enhancer:45063, PBMC:HC; 17:37360836, CACNB1 ||5' Proximal Enhancer: - 6880,RPL19||Exon 6:4301,STAC2||3' Proximal Enhancer:21204, PBMC:notRA; 17:37608096, CDK12||5' Proximal Enhancer: -9642,MEDl ||Proximal Promoter: -569, PBMC:OA_SLE_HC,PBMC:notRA; 17:37767494, NEUROD2|| Distal Promoter:-3319, Mono:OA; 17:38476024, RARA||Intron l : 10602|Intron 1 : 1552, PBMC:notRA; 17:38493822, RARA|| Distal Promoter:-4448|Intron 2: 19350|Intron 2:28400, Mono:HC; 17:38632764, TNS4||Exon 13:25090, PBMC:SLE; 17:3863976, ATP2A3||Intron 1 :3782, BcelhSLE; 17:38696507, PBMC:HC; 17:38979140, KRT10||Proximal Promoter:-277,TMEM99||Intron l :3704|Intron l :3767|Intron 1 :3797, PBMC:SLE; 17:39093054, KRT23||Exon 2:782, PBMC:HC; 17:39151857, KRT40||5' Proximal Enhancer:-8470,KRTAP3-2||3' Proximal Enhancer:4281,KRTAP3- 3||Proximal Promoter: -1472, Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 17:39261525, KRTAP4-8||5' Proximal Enhancer: -7150,KRTAP4-9||Proximal Promoter:- 115, PBMC:notRA; 17:39279735, KRTAP4- 11 ||5' Proximal Enhancer: -5129,KRTAP4-12||Exon 1 :684, PBMC:SLE; 17:39296715, KRTAP4-5||3' Proximal Enhancer:9339,KRTAP4-6||Proximal Promoter:24, PBMC:notRA; 17:39472114, KRTAP16-1 ||5' Proximal Enhancer: -6609,KRTAP17- l ||Proximal Promoter: -167, BcelhHC; 17:39739912, KRT14||Exon 5:3235, PBMC:notRA; 17:40169518, DNAJC7||Proximal Promoter:-335|Proximal
Promoter: 197,NKIRAS2||Distal Promoter: -2568|Proximal Promoter:-75,ZNF385C||3' Proximal Enhancer:20526, PBMC:OA_SLE_HC,PBMC:notRA; 17:40169520, DNAJC7||Proximal Promoter: - 337|Proximal Promoter: 195,NKIRAS2||Distal Promoter:-2566|Proximal Promoter: -73,ZNF385C||3' Proximal Enhancer:20524, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 17:40174494, DNAJC7||5' Proximal Enhancer:-5311 |Distal Promoter:-4779,NKIRAS2||Exon 3:4901 |Exon 3:Intron 3:2408,ZNF385C||3' Proximal Enhancer: 15550, PBMC:notRA; 17:40177415, DNAJC7||5' Proximal Enhancer:-7700|5' Proximal Enhancer:-8232,NKIRAS2||Exon 4:7822|Exon 4:Exon 5:5329,ZNF385C||3' Proximal Enhancer: 12629, PBMC:OA; 17:40226702, PBMC:HC; 17:40262500, DHX58||Intron 5:2251,KAT2A||3' Proximal Enhancer: 10882, Tcel SLE; 17:403288, VPS53||3' Proximal Enhancer:214808, Bcel SLE; 17:4079306, ANKFYl ||Intron 19:87968, PBMC:HC; 17:40981088, BECNl ||Distal Promoter:-4778,PSME3||Distal Promoter: -4334, PBMC:notRA; 17:41133928, AARSDl ||Proximal Promoter:- 1383 |Proximal Promoter:-1908,RUNDCl ||Intron 1 : 1347, PBMC:OA; 17:41278573, BRCAl ||Proximal Promoter:-1073|Proximal Promoter:- 1105| Proximal Promoter: - 1233|Proximal Promoter:-2441,NBR2||Intron 1 :974, PBMC:notRA; 17:41278652, BRCAl ||Distal Promoter:-2520|Proximal Promoter:- 1152|Proximal Promoter:- 1184|Proximal Promoter:- 1312,NBR2||Intron 1 : 1053, PBMC:notRA; 17:41564846, DHX8||Intron 1 :3513, PBMC:notRA; 17:41723125, MEOXl ||Intron l : 15806|Intron 2: 16137, Bcel SLE; 17:42020838, PPY||Proximal Promoter:-1005,PYY||3' Proximal Enhancer:60999, Tcel OA; 17:42032747, PYY||Intron 3:49090, PBMC:notRA; 17:42075116, NAGS||5' Proximal Enhancer:-6915,PYY||Intron 1 :6721, PBMC:notRA; 17:42441302, F AMI 71A2|| Proximal Promoter:-67,ITGA2B||3' Proximal Enhancer:25571, PBMC:notRA; 17:43023947, KIF18B||Intron 1 : 1135, PBMC:notRA; 17:43218792, ACBD4||Intron 1 l :8826|Intron 8:Intron 9:5779,HEXIM1 ||5' Proximal Enhancer:-5891,PLCD3||5' Proximal Enhancer:-8901, PBMC:HC; 17:43507875, ARHGAP27||Distal Promoter: -4863|Intron 3:2407,PLEKHM1 ||3' Proximal Enhancer:60271, PBMC:notRA; 17:43700761, CRHRl ||Intron 2:3052,MGC57346||Intron 2:2781 |Intron 2:3050, Bcell:OA_SLE_HC; 17:44087784, Tcell:OA_SLE_HC; 17:44337874, PBMC:notRA; 17:4448324, MYBBPlA||Exon 17: 10357,SPNS2||3' Proximal Enhancer:46196, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 17:445321, VPS53||Intron 16:Intron 17: 172775, PBMC:notRA; 17:4487099, SMTNL2|| Proximal Promoter:- 176|Proximal Promoter:-734, Mono:OA_SLE_HC,Mono:SLE; 17:4487117, SMTNL2|| Proximal Promoter:-158|Proximal Promoter: -716, Mono:OA_SLE_HC; 17:4487125, SMTNL2||Proximal Promoter:- 150|Proximal Promoter:-708, Mono:OA_SLE_HC; 17:45401733, C17orf57||Proximal Promoter:407, PBMC:OA_SLE_HC; 17:45729462, KPNBl ||Intron 2:2188, PBMC:HC,PBMC:OA_SLE_HC; 17:45933306, SP6||Proximal Promoter: -66, PBMC:HC; 17:46059110, CDK5RAP3||Exon 14: 10682, PBMC:notRA; 17:46618614, HOXB2||3' Proximal Enhancer:3779,HOXB3||3' Proximal Enhancer:33196,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 17:46619555, HOXB2||3' Proximal
Enhancer:2838,HOXB3||3' Proximal Enhancer:32255, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 17:46622536, HOXB2||Proximal Promoter:-143,HOXB3||3' Proximal Enhancer:29274, PBMC:HC; 17:46622607, HOXB2||Proximal Promoter: -214,HOXB3||3' Proximal Enhancer:29203, PBMC:HC; 17:46622715, HOXB2||Proximal Promoter:-322,HOXB3||3' Proximal Enhancer:29095, Mono:OA; 17:46667725, HOXB5||3' Proximal Enhancer:3378,HOXB6||3' Proximal Enhancer: 14609,LOC404266||5' Proximal Enhancer:-5594|Proximal Promoter:-l 16|Proximal Promoter:-1928|Proximal Promoter:- 1956|Proximal Promoter: -97, PBMC:HC; 17:46669455, HOXB5||Exon 2: 1648,HOXB6||3' Proximal Enhancer: 12879,LOC404266||Distal Promoter:-3864|Intron l : 1614|Intron l : 1633|Proximal Promoter: - 198|Proximal Promoter:-226, PBMC:HC; 17:46808309, HOXB13||Proximal Promoter: -2198,HOXB13- AS1 ||3' Proximal Enhancer:7768,MIR3185||5' Proximal Enhancer:-6472,PRAC||5' Proximal Enhancer: - 8427, Mono:OA_SLE_HC; 17:46952555, PBMC:notRA; 17:47091339, IGF2BPl ||Intron 2: 16566, Tcell:HC; 17:47091978, IGF2BPl ||Intron 2: 17205, Mono:HC; 17:47092178, IGF2BPl ||Intron 2: 17405, Tcell:HC; 17:4804104, C17orfl07||Exon 3: 1157,CHRNE||Exon 8:2265,MINK1 ||3' Proximal Enhancer:67470, PBMC:notRA; 17:4804374, C17orfl07||Exon 3: 1427,CHRNE||Exon 7: 1995,MINK1 ||3' Proximal Enhancer:67740, PBMC:notRA; 17:48502312, ACSF2||Proximal Promoter: -1206, PBMC:HC; 17:48585216, MYCBPAP||Proximal Promoter:-528, PBMC:notRA; 17:48585270, MYCBPAP||Proximal Promoter: -474, PBMCnotRA; 17:48637445, CACNAlG||Proximal Promoter:-1003,LOC253962||Intron 1 :2024,SPATA20||3' Proximal Enhancer: 12884, PBMC:OA_SLE_HC; 17:48857353, TcelhHC; 17:48861062, PBMC:HC; 17:48981371, Tcell:OA_SLE_HC; 17:52977213, TOMlLl ||Proximal Promoter: - 838, PBMC:notRA; 17:53684393, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 17:54858770, PBMC:OA_SLE_HC; 17:54860136, C17orf67||3' Proximal Enhancer:33114, PBMC:notRA; 17:54987827, Bcell:SLE,Mono:SLE,PBMC:SLE; 17:55484600, MSI2||Intron 5: 150227|Intron 6: 150670, PBMC:OA_SLE_HC,PBMC:SLE; 17:55502491, MSI2||Intron 5: 168118|Intron 6: 168561, PBMC:HC; 17:55685941, MSI2||Intron 7:351568|Intron 8:352011, PBMC:HC; 17:55962703, CUEDCl ||Exon 2: 18047, PBMC:notRA; 17:56355362, LPO||3' Proximal Enhancer:39576,MPO||Exon 7:2934, PBMC:HC; 17:56767431, RAD51C||Distal Promoter:-2531,TEX14||Intron 1 : 1985, PBMC:notRA; 17:58500186, C17orf64||Proximal Promoter:322, PBMC:notRA; 17:59668895, NACA2|| Proximal Promoter:-332, PBMC:notRA; 17:60347626, TBClD3P2||Intron 7:5390, Bcell: OA SLE HC ; 17:60500856, EFCAB3||3' Proximal Enhancer:42943|3' Proximal Enhancer:53278,METTL2A||Proximal Promoter: -389, Bcell:OA_SLE_HC,Bcell:SLE; 17:6160770, Mono:OA_SLE_HC,PBMC:notRA; 17:61613061, KCNH6||Exon 6: 12367, BcelhHC; 17:61926700, SMARCD2||5' Proximal Enhancer:-6349,TCAM1P||5' Proximal Enhancer: -7675, PBMC:HC; 17:62009628, CD79B||Proximal Promoter:76,SCN4A||3' Proximal Enhancer:40650, PBMC:HC; 17:62772909, LOC146880||3' Proximal Enhancer:4713|Intron 3:5208,PLEKHM1P||3' Proximal Enhancer: 60393, Mono:OA; 17:63549924, AXIN2||Intron 2:7816, PBMC:notRA; 17:64456857, PRKCA||Intron 2: 157932, PBMC:HC; 17:6495080, KIAA0753||Intron 16:49167, PBMC:HC; 17:65822392, BPTF||Exon 1 :613, PBMC:notRA; 17:66201167, LOC440461 ||3' Proximal Enhancer:6367, PBMC:notRA; 17:6656315, XAF l ||Distal Promoter: -2840, PBMC:OA_SLE_HC; 17:6658898, XAF l ||Proximal Promoter: -257, Bcell:OA_SLE_HC,PBMC:SLE; 17:6659070, XAFl ||Proximal Promoter:-85, Bcell:OA_SLE_HC,PBMC:SLE,Tcell:SLE; 17:6659164, XAFl ||Proximal Promoters, Bcell:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 17:66592243, FAM20A||Intron 1 :4852, PBMC:HC; 17:68133597, KCNJ16||3' Proximal Enhancer:32603|3' Proximal Enhancer:62172, PBMC:SLE; 17:686357, GLOD4|| Proximal Promoter:-786,RNMTLl ||Exon 2:845, Wholeblood:notRA; 17:69199815, PBMC:notRA; 17:6921295, ALOX12||3' Proximal Enhancer:21912,BCL6B||5' Proximal Enhancer: - 5073,C17orf49||3' Proximal Enhancer:3240,LOC100506713||5' Proximal Enhancer: - 5642,MIR195||Proximal Promoter:-275,MIR497||Proximal Promoter:46,MIR497HG||Intron
1 : 1678,RNASEK||3' Proximal Enhancer:5560,RNASEK-C17ORF49||3' Proximal Enhancer:5560, PBMC:SLE; 17:6983991, CLEC10A||Proximal Promoter:-391, Bcel HC; 17:70609699, LINC00511 ||Intron 3:26912, Mono:OA_SLE_HC; 17:71756141, LINC00469||Intron 3:68535, Wholeblood:notRA; 17:7254909, ACAP1 ||3' Proximal Enhancer: 15062,KCTDl l ||Proximal Promoter: -298,TMEM95||Distal Promoter: -3587, PBMC:SLE; 17:7255046, ACAP1 ||3' Proximal Enhancer: 15199,KCTDl l ||Proximal Promoter:-161,TMEM95||Distal Promoter:-3450, PBMC:SLE; 17:7255624, ACAP1||3' Proximal Enhancer: 15777,KCTDl l ||Proximal Promoter:417,TMEM95||Distal Promoter: -2872,
PBMC:OA_SLE_HC,PBMC:SLE; 17:7255736, ACAP1 ||3' Proximal Enhancer: 15889,KCTDl l ||Exon l :529,TMEM95||Distal Promoter:-2760, PBMC:SLE; 17:72667005, RAB37||Proximal Promoter: -250, PBMC:HC,PBMC:OA_SLE_HC; 17:72754589, MIR3615||3' Proximal Enhancer:9838,SLC9A3Rl ||Intron 1 :9827, Mono:OA; 17:72948349, C17ori28||Intron 17:20551,OTOP3||3' Proximal Enhancer: 16453, PBMC:notRA; 17:72957135, C17ori28||Intron 6: 11765, PBMC:notRA; 17:73004677, CDR2L||3' Proximal Enhancer:20951,ICTl ||Distal Promoter:-4102, PBMC:HC; 17:73032613, ATP5H||3' Proximal Enhancer: 10461, PBMC:OA_SLE_HC; 17:73780571, H3F3B||Distal Promoter:-4711,MIR4738||Proximal Promoter: 117,UNK||Proximal Promoter:-348, BcelhOA; 17:73824396, UNC13D||Intron 31 : 16402,UNK||3' Proximal Enhancer: 43477, BcelhSLE; 17:73993843, CDK3||Distal Promoter: -3143,EVPL||3' Proximal Enhancer:29664,TENl ||Intron 3: 18546,TENl-CDK3||Intron 3: 18546, PBMC:HC; 17:74266324, FAMlOOBpxon 3:5039,QRICH2||3' Proximal Enhancer:37437,
PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 17:74266574, FAM100B||Exon 3:5289,QRICH2||3' Proximal Enhancer:37187, Tcell:OA_SLE_HC,Tcell:SLE; 17:74524611, CYGB||Exon 4:9171,PRCD||Intron 1 :944, BcelhOA; 17:74585455, ST6GALNAC2||Distal Promoter: -3310, PBMC:HC; 17:74639928, ST6GALNACl ||Proximal Promoter:-34, Mono:HC; 17:7475079, CD68||5' Proximal Enhancer:-7725|5' Proximal Enhancer:-7726,EIF4Al ||Proximal Promoter: -944, SENP3||Exon l l :9771,SENP3-EIF4Al ||Intron 1 l :9771,SNORA48||Distal Promoter: -295 l,SNORA67||5' Proximal Enhancer:-6193,SNORD10||5' Proximal Enhancer:-5049, PBMC:OA_SLE_HC; 17:7477935, CD68||Distal Promoter: -4869|Distal Promoter:-4870,EIF4Al ||Exon 3: 1912,MPDU1 ||5' Proximal Enhancer: - 9029,SENP3||3' Proximal Enhancer: 12627,SENP3-EIF4Al ||Exon 14: 12627,SNORA48||Proximal Promoter: -95,SNORA67||Distal Promoter:-3337,SNORD10||Proximal Promoter: -2193, PBMC:HC; 17:74878420, MGAT5B||Intron 2:9692|Intron 3: 13623, PBMC:OA_SLE_HC,PBMC:notRA; 17:74978687, PBMC:HC; 17:75084281, LINC00338||Proximal Promoter:-443,SCARNA16||Proximal Promoter: - 1107,SEC14Ll ||Proximal Promoter: -443 |Proximal Promoter: -953,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 17:75316233, SEPT9||Exon l :637|Intron 2:32261 |Intron 2:38742, PBMC:HC; 17:75371476, SEPT9||Intron l :2205|Intron l :55880|Intron 2:87504|Intron 2:93985|Proximal Promoter:-688, PBMC:SLE; 17:753974, NXN||Intron l : 129024|Intron 1 : 13377, PBMC:notRA; 17:75405842, PBMC:OA_SLE_HC; 17:75431407, PBMC:SLE; 17:75446431, SEPT9||Proximal Promoter:- 181, PBMC:HC; 17:75446450, SEPT9||Proximal Promoter:- 162, PBMC:HC; 17:75490748, SEPT9||Intron 8: 19424|Intron 8:44136, PBMC:notRA; 17:75884327, FLJ45079||Distal Promoter: -4158, PBMC:OA_SLE_HC; 17:75956190, Mono:OA; 17:76121276, TMC6||Exon 6:3585|Exon 6:7212,TMC8||5' Proximal Enhancer:-5582, PBMC:SLE; 17:76151124, C17ori99||Intron 2:8691, PBMC:HC; 17:76222194, BIRC5||3' Proximal Enhancer: 11918,TMEM235||5' Proximal Enhancer:-5196, BcelhOA SLE HC; 17:76250053, Tcel HC; 17:76254129, PBMC:HC,PBMC:OA_SLE_HC; 17:76335184, Bcell:OA_SLE_HC; 17:76795278, USP36||Intron 18:41691, PBMC:SLE; 17:76801712, USP36||Intron 15:35257, PBMC:HC,Tcell:HC; 17:76801775, USP36||Intron 15:35194, Tcel HC; 17:76850256, TIMP2||Exon 5:71216, PBMC:HC; 17:76871734, TIMP2|| Intron 1 :49738, Mono:OA; 17:76948389, TcelhOA; 17:76965407, LGALS3BP||3' Proximal Enhancer: 10654, Mono:SLE; 17:76967695, LGALS3BP||Exon 6:8366, Mono:SLE,PBMC:SLE; 17:76975944, LGALS3BP||Proximal Promoter: 117, Bcell:SLE,Mono:SLE,PBMC:SLE; 17:76976010, LGAL S3 BP || Proximal Promoter:51, Mono:SLE,PBMC:SLE; 17:76976057, LGALS3BP||Proximal Promoter^, Mono:OA_SLE_HC; 17:76976091, LGALS3BP||Proximal Promoter: -30,
Bcell:SLE,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:SLE; 17:76976245, LGAL S3 BP || Proximal Promoter:- 184, Mono:SLE,PBMC:SLE,Tcell:SLE; 17:76976267, LGALS3BP||Proximal Promoter:-206, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:SLE; 17:76976352, LGALS3BP||Proximal Promoter:-291, Bcell:OA_SLE_HC,PBMC:SLE; 17:76976357, LGALS3BP||Proximal Promoter:-296,
Bcell:OA_SLE_HC,Mono:SLE,PBMC:SLE; 17:77042315, ClQTNFl ||Intron l :Intron 2:22065|Intron 2: 11844, Mono:HC,Mono:OA_SLE_HC,Mono:SLE; 17:773023, NXN||5' Proximal Enhancer:-5672|Intron 1 : 109975, BcelhHC; 17:77478813, RBFOX3||Proximal Promoter: -250, BcelhSLE; 17:77679767, MIR4739||3' Proximal Enhancer: 1291, PBMC:HC; 17:77685623, MIR4739||Distal Promoter:-4565, PBMC:notRA; 17:77810509, CBX4||Intron 3:2704, PBMC:HC; 17:77916733, TBClD16||Intron 10:92914, PBMC:notRA; 17:77916768, TBClD16||Intron 10:92879, PBMC:notRA; 17:77982477, TBClD16||Intron 3:27170, Bcell:OA_SLE_HC; 17:78021508, CCDC40||Intron 4: 11078, PBMC:OA_SLE_HC; 17:78073854, CCDC40||3' Proximal EnhancenExon 20:63424,GAA||Proximal Promoter:- 1500, Bcell:OA_SLE_HC; 17:78079668, CCDC40||3' Proximal Enhancer:69238,GAA||Exon 3:Exon 4:4314, PBMC:notRA; 17:78156236, CARD14||5' Proximal Enhancer:-5362|Intron 2:3956, PBMC:OA; 17:78194151, SGSH||Proximal Promoter:48,SLC26Al l ||Proximal Promoter: -48, PBMC:notRA; 17:78533842, RPTOR||Intron 1 : 15218, PBMC:HC; 17:78549358, RPTOR||Intron 1 :30734, PBMC : SLE,PBMC :notRA; 17:78623601, RPTOR||Intron 3: 104977, PBMC:notRA; 17:78700928, RPTOR||Intron 4: 182304, PBMC:OA_SLE_HC; 17:78701084, RPTOR||Intron 4: 182460, PBMC:OA_SLE_HC; 17:78701257, RPTOR||Intron 4: 182633, PBMC:OA_SLE_HC; 17:78720226, RPTOR||Intron 5:201602, Tcell:OA_SLE_HC; 17:78754318, RPTOR||Intron 6:235694, Tcell:OA_SLE_HC; 17:78821604, RPTOR||Intron 11 :302980, PBMC:HC; 17:78851503, RPTOR||Intron 13:332879, PBMC:HC; 17:78853966, RPTOR||Intron 13:335342, PBMC:HC; 17:7892150, PBMCnotRA; 17:78962984, CHMP6||Distal Promoter: -2656, PBMC:HC,PBMC:OA_SLE_HC; 17:78963221, CHMP6||Proximal Promoter:-2419, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 17:79128918, PBMC:HC; 17:79129051, PBMC:HC; 17:79372973, BAHCCl ||Proximal Promoter:-566,MIR4740||3' Proximal Enhancer: 1605, PBMC:OA; 17:79374327, BAHCCl ||Intron l :788,MIR4740||Proximal Promoter:251, PBMC:SLE; 17:79374741, BAHCCl ||Intron l : 1202,MIR4740||Proximal Promoter: -163, Mono:OA_SLE_HC,PBMC:SLE; 17:79393463, PBMC:HC; 17:79581711, NPLOC4|| Intron 3:22427, PBMC:HC; 17:79615824, PDE6G||3' Proximal Enhancer:7783,TSPAN10||3' Proximal Enhancer:6476, PBMC:HC; 17:7965013, BcelhHC; 17:80084751, CCDC57||Intron 16:85938, PBMC:HC; 17:80275542, CD7||Proximal Promoter:-62,SECTMl ||3' Proximal Enhancer: 16379, PBMC:HC; 17:80285515, SECTMl ||Intron 1 :6406, Bcel OA; 17:80290169, SECTMl ||Intron 1 : 1752, PBMC:OA; 17:80346912, C17orfl01 ||3' Proximal Enhancer:29601, PBMC:HC; 17:80535367, FOXK2||Intron 4:57774, PBMC:HC; 17:80545272, FOXK2||Intron 8:67679, PBMC:HC; 17:80545322, FOXK2||Intron 8:67729, PBMC:HC; 17:8066669, TMEM107||3' Proximal Enhancer: 13045,VAMP2||Proximal Promoter: -376, PBMC:HC,PBMC:OA_SLE_HC; 17:80673958, FN3KRP|| Proximal Promoter:-623, Bcel OA; 17:80816851, PBMC:HC; 17:80845107, Tcel OA; 17:80849463, PBMC:notRA; 17:80860250, PBMC:notRA; 17:80870529, PBMC:notRA; 17:80909836, B3GNTLl ||Intron 11 :99850, PBMC:notRA; 17:80928410, B3GNTLl ||Intron 6:81276, PBMC:notRA; 17:80981575, B3GNTLl ||Intron 4:28111, Mono:SLE; 17:8481454, MYH10||Intron 4:52625, Mono:HC; 17:8661909, SPDYE4||Proximal Promoter:- 32, PBMC:notRA; 17:8762014, PIK3R6|| Intron 1 :8980, PBMC:HC; 17:8777762, PIK3R5||3' Proximal Enhancer:38072|3' Proximal Enhancer:91267,PIK3R6||5' Proximal Enhancer:-6768, PBMC:HC,PBMC:OA_SLE_HC; 17:925669, ABR||Intron 15:86655|Intron 16: 157462|Intron 16: 164947,MIR3183||Proximal Promoter: 130, PBMC:HC; 17:935884, PBMC:notRA; 17:945834, PBMC:HC; 17:9806745, GAS7||3' Proximal Enhancer: 122878|3' Proximal Enhancer: 133319|3' Proximal Enhancer:295123|3' Proximal Enhancer:56021,RCVRN||Intron 1 : 1939, PBMC:HC; 18: 11147385, PIEZ02||Intron 1 : 1376, PBMC:SLE; 18: 11147785, PIEZ02||Intron 1 :976, PBMC:SLE; 18: 11948, PBMC:notRA; 18: 12041672, Mono:HC; 18: 12308339, TUBB6||Proximal Promoter:83, Bcel OA; 18: 13914358, MC2R|| Intron 1 : 1177, Mono:OA_SLE_HC; 18: 14178949, ANKRD20A5P||Proximal Promoter:-146, TcelhHC; 18: 14748128, ANKRD30B || Proximal Promoter:-l 10, PBMCnotRA; 18:20714399, CABLES l ||Proximal Promoter:-128|Proximal Promoter:-1327, PBMC:HC; 18:21572656, TTC39C||Proximal Promoter:-80, PBMC:HC; 18:21572748, TTC39C||Proximal Promoter: 12, PBMC:HC; 18:21656374, TTC39C||Intron 4:61991 |Intron 4:83638, Mono:SLE,PBMC:HC,PBMC:OA_SLE_HC; 18:22007271, IMPACT||Intron 1 :663, Mono:OA_SLE_HC; 18:22039857, HRH4|| Proximal Promoter:- 735,IMPACT||3' Proximal Enhancer:33249, PBMC:HC; 18:29170928, TTR||Proximal Promoter:-801, PBMC:SLE; 18:29263741, B4GALT6||Intron 1 :945, Bcell:OA_SLE_HC,Bcell:SLE; 18:29304818, Mono:SLE; 18:29307959, Mono:SLE; 18:30092971, WBPl lPl ||Exon 1 : 1346, PBMCnotRA; 18:3011965, PBMC:SLE; 18:3495888, DLGAP1 ||3' Proximal Enhancer:349470|3' Proximal Enhancer:378365|3' Proximal Enhancer:378879|3' Proximal Enhancer:959378, PBMC:SLE; 18:43305784, SLC14Al ||Intron 2: 1693|Proximal Promoter:- 1133, PBMC:OA_SLE_HC; 18:4453856, PBMC:OA; 18:45458021, SMAD2||Proximal Promoter: -1095 |Proximal Promoter:-506|Proximal Promoter:-509, PBMC:notRA; 18:45660777, ZBTB7C||Intron 1 :2903, PBMC:notRA; 18:47794623, CCDCl l ||Proximal Promoter: - 1758,MBD1 ||3' Proximal Enhancer: 11764|3' Proximal Enhancer: 13514|3' Proximal Enhancer: Intron 14:Intron 16: 13521, PBMC:HC,PBMC:OA_SLE_HC; 18:48083223, MAPK4||Distal Promoter: -3260, PBMC:notRA; 18:48088362, MAPK4|| Intron 1 : 1879, PBMC:notRA; 18:55097461, ONECUT2||5' Proximal Enhancer: -5455, Tcel OA; 18:55887865, NEDD4L||Intron l :25244|Intron 2: 173408|Intron 2: 176256|Intron 2:71301 |Proximal Promoter:-888, PBMC:OA_SLE_HC; 18:56343105, MALTl ||Intron 1 :4488, PBMC:SLE; 18:56887320, GRP||Proximal Promoter:-79, Bcel OA; 18:60985380, BCL2||Exon 2: 1233,KDSR||3' Proximal Enhancer:49126, PBMC:HC; 18:60988017, BCL2||Proximal Promoter:- 1404,KDSR||3' Proximal Enhancer:46489, PBMC:SLE,PBMC:notRA; 18:61557735, SERPINB2|| Intron l :Intron 2:2797, PBMC:HC; 18:6414976, PBMC:HC; 18:6414978, PBMC:HC; 18:67070324, DOK6||Intron 1 :2041, PBMC:notRA; 18:67624393, CD226||Proximal Promoter:-161, Bcell:OA_SLE_HC,Mono:HC,Mono:OA_SLE_HC; 18:68097929, PBMC:notRA; 18:71811234, FBXO!5||Intron l:3765|Intron l :3866,TIMM21||Distal Promoter: -4511, Mono:OA_SLE_HC,PBMC:notRA; 18:72167187, CNDP2||Exon 2:3688|Proximal Promoter:365, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 18:72167213, CNDP2||Exon 2:3714|Proximal Promoter:391, PBMC:OA_SLE_HC; 18:72916012, TSHZ1 ||5' Proximal Enhancer:-6718,ZADH2||Intron 1 :5269, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 18:72917101, TSHZ1||5' Proximal Enhancer:-5629,ZADH2||Intron 1 :4180, PBMC:OA_SLE_HC; 18:72917163, TSHZ1 ||5' Proximal Enhancer:-5567,ZADH2||Intron 1 :4118, PBMC:OA_SLE_HC; 18:74114708, ZNF516||Intron 3:92438, PBMC:HC; 18:74534576, LOC100131655||Proximal Promoter:-325,ZNF236||Proximal Promoter:- 1539, Wholeblood:notRA; 18:74768360, MBP||Intron 3:76414, PBMC:OA_SLE_HC,PBMC:SLE; 18:74824413, MBP||Intron 1 :20361, PBMC:HC; 18:74845829, MBP||Proximal Promoter:-1055, PBMC:HC; 18:76002290, PBMC:notRA; 18:76473146, Mono:OA; 18:77134251, ATP9B||Intron 28:304855, PBMC:HC; 18:77196320, NFATCl ||Intron 2:Intron 3 :40549| Intron 3:35995, Tcell:OA_SLE_HC; 18:77215491, NFATCl ||Intron 5:Intron 6:59720|Intron 6:55166, PBMC:HC; 18:77236278, NFATC1 ||3' Proximal Enhancer: Intron 7:Intron 8:80507|Intron 8:75953, PBMC:HC,PBMC:OA_SLE_HC; 18:77278806, NFATCl ||Intron 8:Intron 9: 123035|Intron 9: 118481, PBMC:notRA; 18:77283493, NFATCl ||Intron 8:Intron 9: 127722|Intron 9: 123168, PBMC:notRA; 18:77440800, CTDPl ||Intron l : 1000|Proximal Promoter: -629, PBMC:OA; 18:77678514, PQLCl ||Intron 3:Intron 4:Intron 5:33139, PBMC:notRA; 18:77746937, TXNL4A|| Intron 1 : 1595, PBMC:OA; 18:77749232, TXNL4A||Proximal Promoter: -700, PBMC:OA; 18:77836355, PBMC:notRA; 18:908290, ADCYAPl ||Exon 3:2994|Exon 4:3347, Tcel OA; 18:9105577, NDUFV2||Intron 1 :2950, PBMC:HC; 19: 10197856, ANGPTL6||3' Proximal Enhancer: 15569,C19orf66||Intron 2: 1051, Bcell:OA_SLE_HC,Mono:SLE; 19: 10206625, ANGPTL6||Intron 2:6800,C19orf66||3' Proximal Enhancer:9820,
PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC; 19: 10206746, ANGPTL611 Exon 2 : 6679,C 19orf66113 ' Proximal Enhancer:9941, PBMC:OA_SLE_HC,PBMC:notRA; 19: 10223710, EIF3G||3' Proximal Enhancer:6889,P2RYl l ||Intron 1 : 1514,PPAN||3' Proximal Enhancer:6812,PPAN-P2RYl l ||Intron 12:6812,SNORD105||3' Proximal Enhancer:5384,SNORD105B||3' Proximal Enhancer:3286, PBMC:HC; 19: 10415557, FDX1L||3' Proximal Enhancen l 1134,ICAM5||3' Proximal Enhancer: 14903,ZGLPl ||Exon 4:4676, PBMC:OA_SLE_HC; 19: 10691954, APlM2||Exon 6:6037, PBMC:notRA; 19: 10735548, SLC44A2||Intron l :22428|Proximal Promoter: -622, PBMC:HC; 19: 10750786, SLC44A2||Intron 20: 14616|Intron 20:37666, Wholeblood:notRA; 19: 11406993, TSPAN16||Proximal Promoter: 170, PBMC:HC; 19: 11517079, RGL3||Intron 7: 12939, PBMC:OA_SLE_HC; 19: 11517152, RGL3||Exon 7: 12866, PBMC:OA_SLE_HC,PBMC:SLE; 19: 1155030, SBN02||Intron 1 : 19252, PBMC:HC; 19: 1155184, SBN02||Intron 1 : 19098, Tcel HC; 19: 11804727, ZNF833P||3' Proximal Enhancer: 19915, PBMC:HC; 19: 11852538, ZNF823||Distal Promoter:-2778, PBMC:HC; 19: 12150028, ZNF433||Distal Promoter: -3503,ZNF878||3' Proximal Enhancer: 13754, PBMC:notRA; 19: 12175935, ZNF844||Proximal Promoter:390, PBMC:HC; 19: 12207214, ZNF788||Intron 1 :4137, PBMC:notRA; 19: 12547760, ZNF443||Intron 1 :4166, PBMC:OA_SLE_HC; 19: 12876846, BEST2||3' Proximal Enhancer: 13440,HOOK2||Intron 15:9588, PBMC:OA_SLE_HC; 19: 12877000, BEST2||3' Proximal Enhancer: 13594,HOOK2||Exon 15:9434, PBMC:OA_SLE_HC; 19: 12986352, DNASE2||Exon 6:5983,KLF1 ||3' Proximal Enhancer: 11665,MASTl ||3' Proximal Enhancer:37094, PBMC:notRA; 19: 13198960, NFIX||Intron 8:92377, PBMC:notRA; 19: 1387894, GAMT||3' Proximal Enhancer: 13658,MUMl ||3' Proximal Enhancer:31572|3' Proximal Enhancer:32919,NDUFS7||Intron 2:4012, PBMC:notRA; 19: 13941075, LOC284454||3' Proximal Enhancer:6028,MIR23A||3' Proximal Enhancer:6398,MIR24-2||3' Proximal Enhancer:6098,MIR27A||3' Proximal Enhancer:6256,ZSWIM4||Exon 13:34802, BcelhOA; 19: 1403530, DAZAPl ||Distal Promoter: -4053,GAMT||Proximal Promoter: - 1978,NDUFS7||3' Proximal Enhancer: 19648, PBMCnotRA; 19: 14142201, IL27RA||Proximal Promoter:- 60,RLN3||3' Proximal Enhancer:3185, PBMC:HC; 19: 1438388, DAZAP1 ||3' Proximal Enhancer:30805,RPS15||Proximal Promoter:26, PBMC:notRA; 19: 14492003, CD97||Proximal Promoter:48, PBMC:notRA; 19: 1485944, C19orl25||5' Proximal Enhancer:-6716,PCSK4||Intron 8:4463,REEP6||5' Proximal Enhancer:-5220, Tcell:OA_SLE_HC; 19: 15162971, CASP14||Intron 1 :2681, BcelhOA; 19: 15590532, PGLYRP2|| Proximal Promoter:-217, BcelhSLE; 19: 16178253, TPM4||5' Proximal Enhancer:-8881 |Proximal Promoter:-63, Bcel OA; 19: 16435660, KLF2||Proximal Promoter: 10, PBMC:notRA; 19: 16437789, KLF2||Exon 3:2139, PBMC:HC; 19: 16655751, CHERP||Proximal Promoter: - 2488,SLC35E1 ||3' Proximal Enhancer:27442, Bcell:OA_SLE_HC; 19: 17015427, CPAMD8||Intron 30: 122198, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 19: 17377697, BABAM 11 |Proximal Promoter:-534,USHBPl ||Proximal Promoter: -2153,
PBMC:HC,PBMC:notRA; 19: 17404960, ABHD8||Intron 4:9322,ANKLE1 ||3' Proximal Enhancer: 12507, PBMC:OA; 19: 17599784, SLC27Al ||Intron 5: 18485, PBMCnotRA; 19: 17600122, SLC27Al ||Intron 6: 18823, PBMC:notRA; 19: 17621073, PGLS||Proximal Promoter:-1358,SLC27Al ||3' Proximal Enhancer:39774, PBMC:notRA; 19: 1768630, ONECUT3||Intron 1 : 14969, PBMC:notRA; 19: 17721489, UNC13A||Intron 40:77519, PBMC:notRA; 19: 18260330, MAST3||Exon 27:51728,PIK3R2||Distal Promoter: -3685, PBMCSLE; 19:18260350, MAST3||Exon 27:51748,PIK3R2||Distal Promoter:-3665, PBMC:SLE; 19:18280601, IFI30||Distal Promoter:-3977,PIK3R2||Exon 16: 16586, TcelhHC; 19: 18331177, PDE4C||Intron 5:Intron 6:6108|Intron 6:4126|Intron 7:27833, PBMCSLE; 19:18336352, PDE4C||Intron l:933|Intron 2:22658|Proximal Promoter:- 1049, Mono:OA_SLE_HC; 19:18344322, PDE4C||5' Proximal Enhancer:-7037|5' Proximal Enhancer:-9019|Intron 1:14688, Mono:HC,Tcell:HC; 19:18575406, ELL||Intron 4:57531, PBMC:HC; 19:18793853, CRTCl||Proximal Promoter: -571, PBMC:OA; 19:18959208, UPFl||Intron 3: 16465, PBMC:notRA; 19: 19976613, ZNF253||Proximal Promoter:- 100, Wholeblood:notRA; 19:20165122, PBMC:notRA; 19:20585206, MIR1270-1||5' Proximal Enhancer:- 5884,MIR1270-2||5' Proximal Enhancer:-5884,ZNF826P||Intron 2:22565, PBMC:notRA; 19:2091406, AP3D1||3' Proximal Enhancer:60150,IZUMO4||5' Proximal Enhancer:-5461,MOB3A||Intron 1:4863, PBMC:HC; 19:21105303, ZNF85||Proximal Promoter:-755, PBMC:notRA; 19:21324782, ZNF431||Proximal Promoter:-57, PBMC:notRA; 19:21860753, PBMC:notRA; 19:21860821, PBMC:notRA; 19:21861136, PBMC:notRA; 19:21950409, Tcell:OA; 19:22123728, Mono:OA_SLE_HC; 19:22123885, Mono:OA_SLE_HC; 19:23454693, PBMCnotRA; 19:24184523, PBMC:notRA; 19:2431171, LMNB2||Intron 1 l:25787,TIMM13||Distal Promoter:-3296,TMPRSS9||3' Proximal Enhancer:41388, PBMC:HC; 19:2489637, PBMC:notRA; 19:2491825, PBMC:OA; 19:2579745, GNG7||Intron 2:123001, Bcell:OA_SLE_HC; 19:2607903, GNG7||Intron 2:94843, Tcell:HC; 19:29218732, Wholeblood:notRA; 19:30018733, LOC284395||Proximal Promoter:-2074,VSTM2B||Intron 2: 1243, Tcell:HC; 19:3159786, GNA15||Intron 6:23596, Mono:OA; 19:3191030, NCLN||Intron 1:5156, PBMC:notRA; 19:33165484, ANKRD27||Intron l:618,RGS9BP||Proximal Promoter:-828, Mono:OA; 19:33210662, NUDT19||3' Proximal Enhancer:27796,TDRD12||Proximal Promoter:-16, Bcell:OA; 19:33574995, GPATCHl||Intron 1:3210, PBMC:notRA; 19:33726655, SLC7A10||5' Proximal Enhancer: - 9899, Bcell:OA_SLE_HC; 19:3373819, NFIC||Intron l:14259|Intron 1:7255, PBMC:OA_SLE_HC; 19:3398907, NFIC||Intron 2:32343|Intron 2:39347, PBMC:OA_SLE_HC; 19:34621907, PBMC:OA_SLE_HC; 19:35228732, ZNF181||Intron 1:3253, PBMC:notRA; 19:35249217, ZNF599||Exon 4: 14917, Bcell:HC; 19:35399253, PBMC:notRA; 19:35615444, FXYD3||3' Proximal Enhancer:8713,LGI4||Exon 9: 10734, PBMC:OA_SLE_HC; 19:35630305, FXYDl||Intron l:574|Proximal Promoter:-86,FXYD7||Distal Promoter:-3848,LGI4||Distal Promoter: -4127, PBMC:HC; 19:35630355, FXYDl||Intron 1: 6241 Proximal Promoter: -36,FXYD7||Distal Promoter:-3798,LGI4||Distal Promoter: -4177, PBMC:HC; 19:36248877, C19orf55||Proximal Promoter:-166,HSPB6||Proximal Promoter: -947,LIN37||3' Proximal Enhancer:9616, PBMC:notRA; 19:36264029, ARHGAP33||Proximal Promoter: - 2387,C19orf55||3' Proximal Enhancer: 14986, PBMC:HC; 19:36439299, LRFN3||3' Proximal Enhancer: 11278, PBMC:OA_SLE_HC; 19:36607078, POLR2I||Proximal Promoter:-872,TBCB||Exon 2: 1191, PBMC:OA; 19:36643572, CAPNS1||3' Proximal Enhancer: 12655,COX7Al||Proximal Promoter: 199, PBMC:OA_SLE_HC; 19:36759220, PBMC:notRA; 19:36800845,
LOC100134317||Proximal Promoter:-1399,LOC100506930||3' Proximal Enhancer:21775, PBMC:notRA; 19:3688176, PIP5KlC||Intron 1:12301, Mono:OA; 19:37154552, ZNF461||Intron 2:3187, PBMC:notRA; 19:37461278, ZNF568||Intron 5:Intron 6:54048, Mono:OA; 19:37794573, PBMC:notRA; 19:37825307, HKRl||Proximal Promoter:-272, PBMC:SLE; 19:37825309, HKRl||Proximal Promoter: -270, PBMC:SLE; 19:37825320, HKRl||Proximal Promoter: -259, PBMC:OA_SLE_HC,PBMC:SLE; 19:37825388, HKRl||Proximal Promoter:- 191, PBMC:OA_SLE_HC,PBMC:SLE; 19:37825406, HKRl||Proximal Promoter: -173, PBMC:OA_SLE_HC,PBMC:SLE; 19:37825446, HKRl||Proximal Promoter:- 133, PBMC:SLE; 19:37825679, HKRl||Proximal Promoten lOO, PBMC:SLE; 19:37826008, HKR1|| Proximal Promoter:429, PBMC:OA_SLE_HC,PBMC:SLE; 19:38229377, ZNF573||Exon 4:Exon 5:Exon 6:Exon 8:40853, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 19:3831293, ZFR2||Intron 5:37734, Mono:OA; 19:3870806, ATCAY||5' Proximal Enhancer: -981 l,ZFR2||Proximal Promoter: -1779, PBMC:HC,Tcell:HC; 19:3879858, ATCAY||Proximal Promoter: -759, PBMC:HC; 19:389308, PBMC:notRA; 19:39260954, LGALS7||3' Proximal Enhancer:3203, PBMC:HC; 19:39523395, FBX027||Proximal Promoter:-197, PBMC:OA_SLE_HC; 19:39892799, MED29||3' Proximal Enhancer:10837,MIR4530||3' Proximal Enhancer:7519,ZFP36||Distal Promoter: -4687, PBMC:HC; 19:39899376, MED29||3' Proximal Enhancer:17414,MIR4530||3' Proximal Enhancer:942,PLEKHG2||Distal Promoter: -4373,ZFP36||Exon 2: 1890, PBMC:HC; 19:39998199, DLL3||Exon 7:8643, SELV||5' Proximal Enhancer:-7553, Wholeblood:notRA; 19:39998270, DLL3||Intron 7:8714,SELV||5' Proximal Enhancer: -7482, Wholeblood:notRA; 19:39998290, DLL3||Intron 7:8734,SELV||5' Proximal Enhancer: -7462, Wholeblood:notRA; 19:40093111, LGALS13||Proximal Promoter:-57,
PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 19:40129920, LOC100129935||Exon 1:596, PBMC:notRA; 19:40229766, CLC||Proximal Promoter: -1097, Tcell:HC,Tcell:OA_SLE_HC; 19:40314927, DYRK1B||3' Proximal Enhancer:9914, PBMC:OA; 19:40315401, DYRK1B||3' Proximal Enhancer:9440,FBL||3' Proximal Enhancer:21653, PBMC:notRA; 19:4033718, PIAS4||Intron 9:25970, PBMC:HC,PBMC:OA_SLE_HC; 19:40708324, MAP3K10||Intron 2: 10674, PBMC:notRA; 19:40723857, CNTD2||3' Proximal Enhancer:8740,MAP3K10||3' Proximal Enhancer:26207,TTC9B||Proximal Promoter:449, Mono:OA; 19:40729386, AKT2||3' Proximal Enhancer:61916,CNTD2||Exon 4:3211,MAP3K10||3' Proximal Enhancer:31736,TTC9B||5' Proximal Enhancer:-5080, PBMC:HC; 19:40919485, PRX||Proximal Promoter:-214,SERTADl||3' Proximal Enhancer: 12447, PBMC:HC; 19:40950431, BLVRB||3' Proximal Enhancer:21294,SERTAD3||Proximal Promoter:-149|Proximal Promoter: -1926, PBMC:OA_SLE_HC,PBMC:SLE; 19:41172324, NUMBL||Exon 10:24232, PBMC:notRA; 19:41222599, ADCK4||Proximal Promoter:-1588|Proximal Promoter: 19 l,ITPKC||Proximal Promoter: -408, PBMC:notRA; 19:41283090, MIA||Intron 3:1809|Intron 4:2009,MIA-RAB4B||Intron 3:1649,RAB4B||Proximal Promoter:-1033,RAB4B-EGLN2||Proximal Promoter:-1033, BcelhOA; 19:41307778, EGLN2||Intron 2:2445|Intron 2:2731,MIA-RAB4B||3' Proximal Enhancer:26337,RAB4B||3' Proximal Enhancer:23655,RAB4B-EGLN2||Intron 8:23655, Mono:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 19:41317837, EGLN2||3' Proximal Enhancer: 12504|3' Proximal Enhancer: 12790,RAB4B-EGLN2||3' Proximal Enhancer:33714, Mono:OA; 19:41593202, CYP2A13||Proximal Promoter:- 1165, Bcell:OA_SLE_HC; 19:41620211, CYP2Fl||Proximal Promoter:- 141, PBMC:notRA; 19:41640676, CYP2F1||3' Proximal Enhancer:20324, PBMC:notRA; 19:41767669, AXL||Exon 19:Exon 20:42562,FINRNPULl||Proximal Promoter:-2450|Proximal Promoter: -721, PBMC:OA; 19:41868887, B9D2||Intron 2: 1191,TGFB1||5' Proximal Enhancer: -9056,TMEM91||Proximal Promoter:-983, Mono:OA; 19:41934715, ATP5SL||3' Proximal Enhancer: 10766|3' Proximal Enhancer: 11128,B3GNT8||Proximal Promoter:-80,BCKDHA||3' Proximal Enhancer: 31022, PBMC:HC; 19:42637805, LOC100505622||Intron 2:1025,MIR4323||Proximal Promoter:-140,POU2F2||Proximal Promoter:- 1180, PBMC:notRA; 19:4303957, FSDl||Proximal Promoter:-633,TMIGD2||Proximal Promoter: -1529, PBMC:HC; 19:43421584, PSG6||Proximal Promoter:405|Proximal Promoter:459,PSG7||3' Proximal Enhancer: 19746, PBMC:notRA; 19:4361555, MPND||3' Proximal Enhancer: 18032,SH3GLl||Exon 10:38860|Exon 10:Exon 9:39010, Mono:OA,PBMC:notRA; 19:43710277, LOC284344||3' Proximal Enhancer:42521,PSG4||Proximal Promoter: -487, PBMC:SLE; 19:44200812, PBMC:OA_SLE_HC,PBMC:notRA; 19:44763334, ZNF233||Proximal Promoter:-698|Proximal Promoter:-732, PBMC:HC,PBMC:notRA; 19:45741288, EXOC3L2||Distal Promoter: -3819, PBMC:notRA; 19:459731, ODF3L2||3' Proximal Enhancer:15252,SHC2||Intron 1: 1265, PBMC:HC,PBMC:OA_SLE_HC; 19:46318748, RSPH6A|| Proximal Promoter: -143, SYMPK||Exon 27:47800, PBMC:OA; 19:46544802, IGFL4||Proximal Promoter: -528, PBMC:OA; 19:46807272, HIF3A||Exon 2:5640|Exon 2:6970|Proximal Promoter:417, PBMC:OA_SLE_HC; 19:48252623, EHD2||3' Proximal Enhancer:36023,GLTSCR2||Intron 2:383 l,SNORD23||5' Proximal Enhancer:-6486, PBMC:HC; 19:48497828, BSPHl||Proximal Promoter:- 2401,ELSPBPl||Proximal Promoter: -79, PBMC:notRA; 19:48527773, CABP5||3' Proximal Enhancer: 19538,ELSPBPl||Intron 6:29866, Mono: SLE,PBMC:OA_SLE_HC,PBMC: SLE; 19:48565104, PLA2G4C||Intron 14:49005, PBMC:OA_SLE_HC,PBMC:SLE; 19:48565189, PLA2G4C||Intron 14:48920, PBMC:OA_SLE_HC; 19:48614177, LIG1||3' Proximal Enhancer:59383,PLA2G4C||Proximal Promoter:- 68, PBMC:SLE,Tcell:OA_SLE_HC; 19:48644271, LIGl||Intron 11:29289, PBMCnotRA; 19:48698419, PBMC:OA,PBMC:OA_SLE_HC; 19:49000743, LMTK3||Exon 12: 15703, PBMC:OA_SLE_HC; 19:49202858, FUT2||Intron 1:3631, PBMC:OA_SLE_HC; 19:49342101, HSD17B14||Proximal Promoter:- 2167,PLEKHA4||Intron 15:Intron 18:29783, PBMC:OA_SLE_HC; 19:49636594, PPFIA3||Exon 9:13932, PBMC:OA_SLE_HC; 19:49669281, TRPM4|| Intron 2:8266, Mono:OA,PBMC:OA_SLE_HC; 19:49689673, TRPM4|| Intron 12:28658, PBMC:notRA; 19:49838478, CD37||Proximal Promoter:- 198,TEAD2||3' Proximal Enhancer:27236, PBMC:notRA; 19:49891494, CCDC155||Proximal Promoter:20, PBMC:HC; 19:49891574, CCDC155||Proximal PromotenlOO, PBMC:HC; 19:49894178, CCDC155||Exon 2:2704, TcelhOA SLE HC; 19:50249584, TSKS||Intron 6:16931, PBMC:HC,PBMC:OA_SLE_HC; 19:50267221, AP2Al||Distal Promoter:-2958,TSKS||Proximal Promoter: -706, Mono:OA; 19:5074616, KDM4B||Intron 7:105493, PBMC:HC; 19:50848024, NAPSB||Proximal Promoter:-19, PBMC:HC,PBMC:notRA; 19:51018946, ASPDH||Proximal Promoter:-1804|Proximal Promoter: - 999,JOSD2||Distal Promoter: -4601,LRRC4B||3' Proximal Enhancer:52356, PBMC:notRA; 19:51141361, SYT3||Intron 2: 1731|Proximal Promoter:-59, PBMC:HC; 19:51376639, KLK2|| Proximal Promoter: - 49,KLKP1||3' Proximal Enhancer:23015, Mono:OA_SLE_HC; 19:51380877, KLK2||Intron 3:Intron 4:4189,KLKP1||3' Proximal Enhancer: 18777, Bcell:SLE,PBMC:SLE,Tcell:SLE; 19:51411782, KLK4||Intron 3:2212, Wholeblood:notRA; 19:51600935, CTUl||Exon 3:10712, PBMC:OA; 19:51774592, C19orf75||3' Proximal Enhancer: 13629, Mono:HC,Mono:OA_SLE_HC; 19:51774666, C19orf75||3' Proximal Enhancer: 13703, Mono:HC,Mono:OA_SLE_HC; 19:51815373, IGLON5||Proximal Promoter:272, PBMC:SLE; 19:51830634, IGLON5|| Intron 6: 15533,VSIG10L||3' Proximal Enhancer: 14744, PBMC:OA_SLE_HC; 19:51891210, LIM2|| Proximal Promoter:0,LOC147646||3' Proximal Enhancer:2618, PBMC:HC; 19:523300, CDC34||5' Proximal Enhancer:-8432,TPGS1||3' Proximal Enhancer: 15804, PBMC:notRA; 19:52391250, ZNF577||Proximal Promoter: -2 l|Proximal Promoter: - 61,ZNF649||3' Proximal Enhancer: 17055, PBMC:OA,Tcell:OA_SLE_HC; 19:52391257, ZNF577||Proximal Promoter: -28|Proximal Promoter:-68,ZNF649||3' Proximal Enhancer: 17048, PBMC:HC,PBMC:OA_SLE_HC; 19:52391304, ZNF577||Proximal Promoter:- 115|Proximal Promoter: - 75,ZNF649||3' Proximal Enhancer: 17001, PBMC:OA_SLE_HC; 19:52407630, ZNF649||Intron 1 :675, PBMC:notRA; 19:52514445, ZNF614||3' Proximal Enhancer: 17235,ZNF615||Distal Promoter: -2962, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 19:52646265, ZNF616||Distal Promoter: - 3074, PBMCnotRA; 19:52675321, ZNF836||Proximal Promoter:-425, PBMC:OA_SLE_HC; 19:52838671, ZNF480||3' Proximal Enhancer:38246,ZNF610||Proximal Promoter:-826, PBMC:notRA; 19:5286594, PTPRS||Intron 1 :54220, PBMCnotRA; 19:52956674, ZNF578||Proximal Promoter: -154, PBMC:OA; 19:52956821, ZNF578||Proximal Promoter:-7, PBMC:OA; 19:52957051, ZNF578||Proximal Promoter:223, PBMC:OA; 19:53030605, ZNF808||Proximal Promoter:-303, PBMC:notRA; 19:53038972, ZNF808||Intron 2:8064, Bcell:SLE,PBMC:SLE; 19:53039145, ZNF808||Intron 2:8237, BcelhSLE; 19:53039444, ZNF808||Intron 2:8536, PBMC:SLE,Tcell:SLE; 19:53107200, ZNF137P||3' Proximal Enhancer:7264,ZNF83||3' Proximal Enhancer:34444|3' Proximal Enhancer:86686, Mono:SLE; 19:53192577, ZNF83||Intron 1 : 1309, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,PBMC:SLE; 19:53324732, ZNF28||Proximal Promoter: 190, PBMC:notRA; 19:5335159, PTPRS||Intron 1 :5655, PBMC:notRA; 19:53361164, ZNF468||Proximal Promoter: -262, Wholeblood:notRA; 19:53361448, ZNF468||Proximal Promoter:-546, PBMC:notRA; 19:53466020, ZNF702P||3' Proximal Enhancer:30764,ZNF816||Proximal Promoter: 144,ZNF816-ZNF321P||Proximal Promoter: 144,
PBMC:notRA; 19:54041308, ZNF331 ||Intron 2: 17132|Proximal Promoter:-231 |Proximal Promoter: - 24|Proximal Promoter:-733, PBMC:notRA; 19:54041329, ZNF331 ||Intron 2: 17153|Proximal Promoter: - 210|Proximal Promoter: -3 |Proximal Promoter: -712, PBMC:notRA; 19:54106789, LOC284379||Proximal Promoter: -38, PBMC:notRA; 19:54177144, MIR1323||3' Proximal Enhancer: 1923,MIR498||Proximal Promoter: -306,MIR512-1 ||3' Proximal Enhancer:4728|3' Proximal Enhancer:7212,MIR512-2||3' Proximal Enhancer:4734|3' Proximal Enhancer: 7218,MIR515-11|5' Proximal Enhancer:-5112,MIR515-2||5' Proximal Enhancer:-5112,MIR519E||5' Proximal Enhancer:-6049,MIR520E||Proximal Promoter:-1820,MIR520F||5' Proximal Enhancer:-8268, PBMC:HC; 19:54191706, MIR1283-l ||Proximal Promoter: -28,MIR515-1 ||3' Proximal Enhancer:3444|3' Proximal Enhancer:9450,MIR515-2||3' Proximal Enhancer: 3444|3' Proximal Enhancer:9450,MIR519B||5' Proximal Enhancer:-6760,MIR519C||3' Proximal Enhancer: 1984,MIR519E||3' Proximal Enhancer: 8513, MIR520A||Proximal Promoter:-2428,MIR520F||3' Proximal
Enhancer:6294,MIR523||5' Proximal Enhancer: -9932,MIR525||5' Proximal Enhancer: -9080,MIR526B||5' Proximal Enhancer:-5940, PBMC:notRA; 19:54239701, MIR516Bl ||Proximal Promoter: - 397,MIR517C||Distal Promoter:-4865,MIR518Al ||3' Proximal Enhancer:5442,MIR518A2||Distal Promoter:-2885,MIR518D||3' Proximal Enhancer: 1571,MIR518E||3' Proximal Enhancer:6610,MIR520H||5' Proximal Enhancer:-6064,MIR526A2||3' Proximal Enhancer:9526, PBMC:notRA; 19:54567123, TARM1 ||3' Proximal Enhancer: 1751 l,VSTMl ||Proximal Promoter:84, PBMC:notRA; 19:54567279, TARM1 ||3' Proximal Enhancer: 17355,VSTMl ||Proximal Promoter:-72, PBMC:notRA; 19:54606153, NDUFA3||Proximal Promoter:-6,OSCAR||Proximal Promoter:-2005,TFPT||3' Proximal Enhancer: 12902, PBMC:notRA; 19:54741710, LILRA6||Exon 8:5014, PBMC:HC; 19:54976501, CDC42EP5||Exon 3:7921,LENG8||3' Proximal Enhancer: 16437,LENG9||Proximal Promoter:- 1607, Tcel OA; 19:55660620, C19orf51 ||3' Proximal Enhancer: 17398,TNNI3||3' Proximal Enhancer:8480,TNNTl ||Proximal Promoter: - 14, PBMC:HC; 19:55660625, C19orf51 ||3' Proximal Enhancer: 17393,TNNI3||3' Proximal Enhancer:8475,TNNTl ||Proximal Promoter:-19, PBMC:HC; 19:55667446, C19orf51 ||3' Proximal Enhancer: 10572,TNNI3||Intron 4: 1654,TNNT1 ||5' Proximal Enhancer:-6840, Bcel OA; 19:55668612, C19orf51 ||3' Proximal Enhancer:9406,TNNI3||Proximal Promoter:488,TNNTl ||5' Proximal Enhancer: - 8006, PBMC:HC; 19:55669091, C19orf51 ||3' Proximal Enhancer: 8927,T NI3||Proximal Promoter:9,TNNTl ||5' Proximal Enhancer:-8485, PBMC:HC; 19:55684640, C19orf51 ||5' Proximal Enhancer:-6622,PTPRH||3' Proximal Enhancer:36234,SYT5||Exon 9:7080,
PBMC:OA_SLE_HC,PBMC:SLE; 19:55688114, PTPRH||3' Proximal Enhancer:32760,SYT5||Intron 3:3606, PBMC:SLE; 19:55692526, PTPRH||3' Proximal Enhancer:28348,SYT5||Proximal Promoter:-806, PBMC:notRA; 19:5587239, SAFB2||Exon 21 :35699,
PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 19:55887799, IL11 ||5' Proximal Enhancer: - 5985,RPL28||5' Proximal Enhancer:-9500,TMEM190||Proximal Promoter: -404,TMEM238||3' Proximal Enhancer:7828, Tcell:HC,Tcell:OA_SLE_HC; 19:55995271, NAT14||Proximal Promoter:- 1285,SSC5D||Distal Promoter: -4598,ZNF628||Exon 3:7573, PBMC:OA_SLE_HC,PBMC:SLE; 19:55998490, NAT14||Exon 3: 1934,SSC5D||Proximal Promoter:-1379,ZNF628||3' Proximal Enhancer: 10792, PBMC:OA; 19:56000201, NAT14||3' Proximal Enhancer:3645,SSC5D||Proximal Promoter:332,ZNF628||3' Proximal Enhancer: 12503, PBMC:SLE; 19:56000944, NAT14||3' Proximal Enhancer:4388,SSC5D||Exon 3: 1075,ZNF628||3' Proximal Enhancer: 13246, PBMC:SLE; 19:56061334, SGK110||Distal Promoter: -4425, PBMC:HC; 19:56156430, CCDC106||Distal Promoter:-2523,U2AF2||5' Proximal Enhancer:-8985,ZNF580||3' Proximal Enhancer:2968|3' Proximal Enhancer:3013|3' Proximal Enhancer:4039,ZNF581||Exon 2: 1445, PBMC:HC; 19:5692159, HSD11B1L||3' Proximal Enhancer: 11085|3' Proximal Enhancer:l 1108|3' Proximal Enhancer:11113|3' Proximal Enhancer:11125,LONPl||Exon 18:28017,RPL36||3' Proximal Enhancer: 1814|3' Proximal Enhancer: 1888, BcelhHC; 19:57019373, ZNF471||Proximal Promoter: 162, PBMC:OA; 19:57079146, ZNF470||Proximal Promoter:257, PBMC:HC; 19:57337469, PBMC:OA; 19:57349709, MIMTl||Distal Promoter: -2560, Bcell:OA_SLE_HC; 19:57350004, MIMTl||Proximal Promoter: -2265, Bcell:OA_SLE_HC; 19:57352465, MIMTl||Proximal Promoter:196, Bcell:OA_SLE_HC; 19:575412, BSG||Intron l:2876|Intron 1:4088, BcelhOA SLE HC; 19:57610699, PBMC:OA; 19:57682795, DUXA||Distal Promoter:-3939, PBMC:HC; 19:57765336, ZNF805||Exon 3:Exon 4:13284, PBMC:notRA; 19:579501, BSG||Exon 2:Exon 3:6965|Intron 1:8177, PBMC:notRA; 19:58220657, ZNF154||Proximal Promoter:-78, Tcell:OA_SLE_HC; 19:58220818, ZNF154||Proximal Promoter: -239, Bcel SLE; 19:58223693, ZNF154||Distal Promoter:-3114,ZNF671||3' Proximal Enhancer: 15302, Mono:SLE; 19:58399865, ZNF814||Intron 1:577, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 19:58400095, ZNF814||Proximal Promoter:347, T cell: SLE; 19:58545542, ZSCANl||Proximal Promoter: 109, PBMC:OA; 19:58549241, ZSCANl||Exon 3:3808, PBMC:SLE; 19:58578578, ZNF135||3' Proximal EnhancenExon 4:Exon 5:7972, PBMC:notRA; 19:58728610, ZNF274||3' Proximal Enhancer:34215, Bcel SLE; 19:58951672, ZNF132||Proximal Promoter:-83, PBMC:OA_SLE_HC; 19:597635, HCN2||Intron 1:7743, Wholeblood:notRA; 19:6039991, RFX2||Exon 5:70673, BcelhHC; 19:626119, HCN2||3' Proximal Enhancer:36227,POLRMT||Intron 3:7449, PBMC:notRA; 19:7098587, PBMC:notRA; 19:725168, PALM|| Intron 1:16216, PBMCnotRA; 19:7766960, FCER2||Distal Promoter: -2595 |Proximal Promoter: 72, Mono:HC; 19:7767089, FCER2||Distal Promoter: -2724|Proximal Promoter:-57, Mono:HC; 19:8212234, FBN3|| Proximal Promoter: 151, PBMC:OA; 19:8212675, FBN3||Proximal Promoter: -290, PBMC:HC; 19:8275083, CERS4||Intron 1:867, PBMC:notRA; 19:8398214, KANK3||Intron 6:9932, PBMC:OA; 19:846354, ELANE||5' Proximal Enhancer:-5936,PRTN3||Exon 4:5370, Mono:HC; 19:847943, ELANE||Distal Promoter:- 4347,PRTN3||Exon 5:6959, Bcell:OA,Mono:HC; 19:861071, CFD||Intron 3:1407,ELANE||3' Proximal Enhancer:8781,MED16||3' Proximal Enhancer:32147, PBMC:OA_SLE_HC; 19:888814, MED16||Intron 4:4404,R3HDM4||3' Proximal Enhancer:24411, PBMC:notRA; 19:940967, ARID3A||Intron 3:14931, Bcel OA; 19:9473696, ZNF177||Proximal Promoter: l,ZNF559-ZNF177||Intron l:38326|Intron 5:38795, BcelhOA; 19:9789027, ZNF562||Distal Promoter:-3251, PBMC:notRA; 19:996720, GRIN3B||Distal Promoter: -3716,WDR18||3' Proximal Enhancer: 12393, Bcell:OA_SLE_HC; 1: 10044519, NMNATl||Exon 5:41034, PBMC:notRA; 1:100944010, CDC14A||Intron 10:125988, PBMC:OA_SLE_HC; 1: 101003688, GPR88||Proximal Promoter:-39, PBMC:HC; 1: 101258727, BcelhHC; 1:101313199, PBMC:HC; 1: 101509557, Bcell:SLE,Mono:SLE; 1: 104111877, AMY2B||Intron 2: 14556,LOC648740||Proximal Promoter: -148, PBMC:notRA; 1: 1046164, C loril 591| Intron 1:5572, PBMCnotRA; 1:10695686, CASZ1||3' Proximal Enhancer: 161021,ΡΕΧ 141| 3' Proximal Enhancer: 160684, PBMC:HC; 1:109289066, FNDC7||3' Proximal Enhancer:3351 l,STXBP3||Proximal Promoter:-218, Bcel OA; 1:109422184, GPSM2||Intron 1:2582, Bcel OA; 1: 109705170, KIAA1324||Intron 2:48586, Tcel HC; 1:109735314, KIAA1324||Exon 14:78730, Mono:OA_SLE_HC; 1: 110009509, SYPL2|| Proximal Promoter:410, PBMC:OA; 1:110035670, ATXN7L2||3' Proximal Enhancer:9110,CYB561Dl||Proximal Promoter:-1030|Proximal Promoter: -987, PBMC:OA; 1:110167590, AMPD2||Intron l:4315|Intron l:5132|Proximal Promoter:-458, PBMC:notRA; 1: 11018764, Clorfl27||Intron 6:23330, PBMC:OA_SLE_HC; 1:110282525, GSTM3||Exon 3:Intron 2: 1135, PBMC:HC; 1: 110306507, EPS8L3||Proximal Promoter: 137, PBMC:HC; 1:11042161, Cloril27||Proximal Promoter: -67, Mono:OA; 1: 110438827, Mono:HC; 1:111743537, DE ND2D||Proximal Promoter: -256, PBMC:HC; 1:111744108, DE D2D||Proximal Promoter:-827, PBMC:HC; 1:1118157, TTLL10||Intron 10:8872|Intron 6:3081, PBMC:notRA; 1: 112026152, ADORA3||Exon 6:20591|Exon 6:80445,Clorfl62||3' Proximal Enhancer:9549, Tcel HC; 1:113393322, PBMC:notRA; 1: 114429965, AP4B1||3' Proximal Enhancer: 17560|3' Proximal Enhancer:17776,BCL2L15||Proximal Promoter:204,LOC100287722||Intron 3:30709, Mono:OA; 1: 114430031, AP4B1||3' Proximal Enhancer: 17494|3' Proximal Enhancer: 17710,BCL2L15||Proximal Promoter: 138,LOC100287722||Intron 3:30775, PBMC:HC; 1: 114449926, AP4Bl||Proximal Promoter:- 2185|Proximal Promoter:-2401,DCLRElB||Intron 2:2012, PBMC:notRA; 1:114495894, HIPKl||Intron 2:2128|Intron 3:23899|Proximal Promoter:-604, Mono:HC; 1:114521853, ΗΙΡΚ1||3' Proximal Enhancer:25355|3' Proximal Enhancer:28087|3' Proximal Enhancer:49858,OLFML3||Proximal Promoter:- 176, Mono:HC; 1: 114631962, SYT6||Exon 8:63100|Exon 8:64510, PBMCnotRA; 1:115324285, SIKEl||Proximal Promoter:-977, PBMC:notRA; 1:11534690, PTCHD2||Distal Promoter: -4604, PBMC:OA; 1: 1158325, B3GALT6||5' Proximal Enhancer: -9303,SDF4||Intron 4:9122,TNFRSF4||5' Proximal Enhancer: - 8777, PBMC:OA_SLE_HC; 1:11593927, PTCHD2||Intron 17:54633, TcelhOA; 1:116256618, CASQ2||Intron 8:54808, PBMC:SLE; 1:1164537, B3GALT6||Distal Promoter:-3091,SDF4||Intron 1:2910, PBMC:notRA; 1:117207245, IGSF3||Intron 2:3069,MIR320B1||5' Proximal Enhancer: -7125, PBMC:notRA; 1:117487269, PTGFRN|| Intron 2:34581, PBMC:notRA; 1:11760856, C loril 871| Intron 1:9076,MAD2L2||5' Proximal Enhancer: -9178, PBMC:HC,PBMC:OA_SLE_HC; 1:1178245, B3GALT6||3' Proximal Enhancer:10617,FAM132A||Exon 7:3857, PBMC:notRA; 1: 11795897, AGTRAP||Proximal Promoter: -244, PBMC:HC; 1:118427435, GDAP2||Intron 10:44867, PBMC:notRA; 1: 11898576, CLCN6||3' Proximal Enhancer: Intron 21:32370,NPPA||3' Proximal Enhancer:9264,NPPA-ASl||Proximal Promoter: -1799, PBMC:OA; 1:119571871, WARS2||3' Proximal Enhancer: 111424, PBMC:notRA; 1: 120165303, ZNF697||Exon 3:25087, PBMC:HC,PBMC:OA_SLE_HC; 1:120217696, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 1:121260494, EMBPl||Proximal Promoter:-415, PBMC:HC; 1: 12538341, VPS13D||Intron 66:Intron 67:248229, PBMC:SLE; 1:12538541, VPS13D||Intron 66:Intron 67:248429, PBMC:OA_SLE_HC; 1:12618574, DHRS3||3' Proximal Enhancer:59246, PBMC:OA; 1:1265354, CPSF3L||5' Proximal Enhancer:-5308,DVL1||3' Proximal Enhancer:19138,GLTPDl||3' Proximal Enhancer:5212,TASlR3||Proximal Promoter:- 1371, PBMC:HC; 1:12774904, AADACL31 |Proximal Promoter:- 1213, PBMC:HC; 1:1310123, AURKAIPl||Exon 2:695|Proximal Promoter:439|Proximal Promoter:457, PBMC:notRA; 1: 13111908, PRAMEF51 |Intron 2:5843, PBMC:OA_SLE_HC,PBMC:SLE; 1:1392347, ATAD3C||Intron 7:7279, PBMC:notRA; 1:14124575, Bcel OA; 1:144615272, NBPF9|| Proximal Promoter: 314,PFNlP2||Distal Promoter:-2545, PBMC:notRA; 1: 144852047, PDE4DIP||Exon 44:142975|Exon 44: 142986|Exon 46:187945, Bcel HC; 1: 144859929, PDE4DIP||Exon 38:135093|Exon 38: 135104|Exon 40:180063, Mono:OA_SLE_HC; 1: 145441552, TXNIPpxon 8:3091, PBMC:HC; 1: 146515238, LOC728989||Proximal Promoter:-639, Wholeblood:notRA; 1:146522492, LOC728989||5' Proximal Enhancer:-7893, PBMC:notRA; 1: 146649770, FM05||3' Proximal Enhancer:47460,PDIA3P||Proximal Promoter:341,PRKAB2||5' Proximal Enhancer: - 5641, PBMC:HC; 1:146649842, FM05||3' Proximal Enhancer:47388,PDIA3P||Proximal Promoter:413,PRKAB2||5' Proximal Enhancer:-5713, PBMC:HC,PBMC:OA_SLE_HC; 1: 146649851, FM05||3' Proximal Enhancer:47379,PDIA3P||Proximal Promoter:422,PRKAB2||5' Proximal Enhancer: - 5722, PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1: 147737016, Bcell: OA SLE HC ; 1: 147782116, PBMC:notRA; 1: 147782452, PBMC:notRA; 1:148854778, BcelhOA; 1: 14927851, KAZN||Intron 1:2639, PBMC:HC,PBMC:OA_SLE_HC; 1:150554875, MCLl||Distal Promoter: -2661, PBMC:notRA; 1: 151030968, Clorf56||3' Proximal Enhancer: 10710,CDC42SEl||Intron l: 1157,MLLTl l||Proximal Promoter:- 1182, PBMC:OA; 1: 15104223, KAZN||Intron 1:179011, BcelhHC; 1: 151132257, LYSMDl||Exon 3:6113|Exon 3:6167,SCNM1||5' Proximal Enhancer:-6240,TNFAIP8L2||3' Proximal Enhancer:3153,TNFAIP8L2-SCNMl||Intron 1:3153, Mono:HC; 1: 151805241, C2CD4D||3' Proximal Enhancer:7792,LOC100132111||5' Proximal Enhancer:-5703,RORC||5' Proximal Enhancer: - 6688|Proximal Promoter: -893, Mono:OA_SLE_HC; 1:152009253, S100Al l||Proximal Promoter:258, BcelhOA; 1: 152011357, S100Al l||Proximal Promoter:- 1846, PBMC:notRA; 1:152161521, PBMC:notRA; 1: 152161683, PBMC:notRA; 1: 15242180, KAZN||5' Proximal Enhancer:- 84441 Intron 1:316968, PBMC:OA; 1:153068231, SPRR2E||Proximal Promoter:-1230, PBMC:notRA; 1:153353168, S100A12||5' Proximal Enhancer:-5093,S100A8||3' Proximal Enhancer: 10496, PBMC:OA_SLE_HC,PBMC:notRA; 1:153662339, NPRl||Exon 19:11176, PBMC:notRA; 1: 153920347, CRTC2||Exon 14:10785,DE ND4B||Proximal Promoter:- 1193, PBMC:notRA; 1:154292240, AQP10||Proximal Promoter:-1351,ATP8B2||5' Proximal Enhancer: -5795|5' Proximal Enhancer:-8035, PBMC:notRA; 1: 154577895, ADAR||Intron 1:2256 l|Intron l:2829|Intron 1:881,
Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 1:154582007, ADAR||Distal Promoter:-3231|Intron l: 18449|Proximal Promoter:-1283, PBMC:HC,PBMC:OA_SLE_HC; 1: 154582156, ADAR||Distal Promoter: -3380|Intron l: 18300|Proximal Promoter: -1432, PBMC:HC,PBMC:OA_SLE_HC; 1: 154839813, KC N3||5' Proximal Enhancer: -7475 |Intron 1:2941, PBMC:HC; 1: 154839909, KCNN3||5' Proximal Enhancer:-7571|Intron 1:2845, PBMC:HC,PBMC:OA_SLE_HC; 1: 155109378, DPM3||3' Proximal Enhancer:3505|3' Proximal Enhancer:3618,EFNAl||3' Proximal Enhancer:9030,SLC50Al||Exon 3:Intron 2:1091, PBMCSLE; 1: 155910523, ARHGEF2||3' Proximal Enhancer:37443|3' Proximal Enhancer:37813,RXFP4||Proximal Promoter:-956, Mono:OA_SLE_HC; 1: 155950963, ARHGEF2||Distal Promoter: -2627|Distal Promoter:-2997, PBMC:notRA; 1:156466088, MEF2D||Intron 1:4441, Mono:HC; 1: 156509844, IQGAP3|| Intron 23:32552, Bcell:OA_SLE_HC,Bcell:SLE; 1: 156546256, IQGAP3||Distal Promoter: -3860,TTC24||Distal Promoter:-3262, Tcell:OA_SLE_HC; 1:156836717, INSRR||5' Proximal Enhancer:-8005,NTRKl||Exon 4:6047|Exon 5:51176, Tcel OA; 1:156928845, BcelhHC; 1:157209680, PBMC:notRA; 1:157802305, CD5L||Intron 5:9329, T cell: SLE; 1:158147849, CDlD||Proximal Promoter:- 1887, PBMCnotRA; 1:158435277, OR10Kl||Proximal Promoter:-74, PBMCnotRA; 1:15865, WASH7P||Exon 9:13505, Tcell: OA SLE HC ; 1:158725300, OR6K6||Exon 1:695, PBMC:notRA; 1: 158800024, MNDA||Proximal Promoter:-l 143, PBMC:OA; 1:158900384, PYHINl||Proximal Promoter: - 952, PBMC:notRA; 1:158984321, IFI16||Intron 1:4640, PBMC:OA_SLE_HC; 1: 15931098, PBMC:notRA; 1: 159888603, IGSF9||3' Proximal Enhancer:26783,TAGLN2||Exon 5:6681, PBMC:notRA; 1: 159891638, IGSF9||3' Proximal Enhancer:23748,TAGLN2||Intron 1:3646, PBMC:SLE,Tcell:OA_SLE_HC; 1: 159892206, IGSF9||3' Proximal Enhancer:23180,TAGLN2||Intron 1:3078, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 1:160429714, BcelhOA SLE HC; 1:1606292, CDKllB||Intron 5:Intron 6:Intron 7:49483, SLC35E2B||Intron 4:17951, Bcell:OA_SLE_HC; 1:161229214, PCP4Ll||Intron 1:698, PBMC:notRA; 1:161476548, FCGR2A||Intron 3:1344, Mono:OA; 1:161498450, FCGR2A||3' Proximal Enhancer:23246,HSPA6||3' Proximal Enhancer:4415, PBMC:HC; 1:161576629, FCGR2C||3' Proximal Enhancer:25501,HSPA7||Exon 1:781, Wholeblood:notRA; 1:161675579, FCRLA||Proximal Promoter:- 1182, PBMC:OA_SLE_HC; 1:161700167, FCRLB||3' Proximal Enhancer:7711, PBMC:OA_SLE_HC; 1:162381781, SH2DlB||Proximal Promoter:147, PBMC:SLE; 1:162532502, UAPl||Intron 1:1207, PBMC:HC; 1:1631100, CDK11A||3' Proximal Enhancer:24691,CDKllB||Intron 5:Intron 6:Intron 7:24675,MMP23A||Proximal Promoter:- 277,SLC35E2B||5' Proximal Enhancer:-6857, PBMC:notRA; 1:163437170, PBMC:OA_SLE_HC; 1:16349079, CLCNKA||Intron l:594,HSPB7||Distal Promoter: -3794, PBMC:OA_SLE_HC; 1:165205506, LMXlA||Intron 4:119972|Intron 4:120446, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 1:16553267, RSG1||3' Proximal Enhancer: 10392, PBMC:notRA; 1:1655867, CDK11A|| Proximal Promoter:- 76,SLC35E2||3' Proximal Enhancer:21571,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:OA_SLE_HC; 1:165859714, UCK2||Intron 2:62983, PBMC:HC; 1:166917267, ILDR2||Intron 3:27294, Bcell:OA_SLE_HC; 1:167421706, CD247||Intron 1:66141, PBMC:SLE; 1:167442612, CD247||Intron 1:45235, PBMC:HC; 1:167485873, CD247||Intron 1:1974, PBMC:HC; 1:167486978, CD247||Intron 1:869, PBMC:HC,Tcell:HC; 1:168271061, TBX19||Intron 5:20784, PBMC:notRA; 1:168888044, PBMC:notRA; 1:169079632, ATPlBl||Intron 1:3686, Tcell:HC; 1:169433715, SLC19A2||Exon 6:21493, Bcell:SLE,Mono:SLE; 1:16947253, CROCCP2||Intron 5:10148,NBPF1||5' Proximal Enhancer: -7271, PBMC:SLE; 1:1696692, NADK||5' Proximal Enhancer:-661 l|Exon 2:13217|Exon 2:13605|Exon 2:14816, PBMC:HC; 1:17019474, ESPNP||Intron 10:27178, Wholeblood:notRA; 1:17027919, ESPNP||Intron 6:18733, PBMC:HC; 1:17183227, MIR3675||3' Proximal Enhancer:2289, PBMC:notRA; 1:171916040, DNM3||Intron 2:105420, PBMC:notRA; 1:17193979, MIR3675||5' Proximal Enhancer:-8463, PBMC:HC; 1:17199104, PBMC:notRA; 1:17240070, CROCC||5' Proximal Enhancer:-8374, PBMC:notRA; 1:17244851, CROCC||Distal Promoter:-3593, PBMC:OA; 1:172608644, PBMC:HC; 1:172628020, FASLG||Proximal Promoter: -164, PBMC:HC; 1:172628263, FASLG||Proximal Promoter:79, PBMC:HC; 1:17265567, CROCC||Exon 12:17123, PBMC:notRA; 1:17394374, PADI2||Exon 16:51574, Wholeblood:notRA; 1:175042297, T N||Intron 1:5304, PBMC:HC; 1:175162347, KIAA0040||Proximal Promoter:- 118|Proximal Promoter:-398, Bcel OA; 1:175162550, KIAA0040||Proximal Promoter: -32 l|Proximal Promoter: -601, BcelhOA; 1:176177166, PBMC:HC; 1:176318588, PBMC:notRA; 1:176912031, ASTNl||Intron 14:221993, PBMC:notRA; 1:176999916, ASTNl||Intron 4:134108,MIR488||Proximal Promoter:-1335, PBMC:notRA; 1:178025627, PBMC:OA; 1:17900032, ARHGEF10L||5' Proximal Enhancer:-7015|Intron 1:33703, Mono:OA_SLE_HC; 1:179757065, FAM163A||Intron 1:44768, Bcell:OA_SLE_HC; 1:180198309, LHX4|| Proximal Promoter:- 1123, Bcel OA; 1:181056912, IER5||Proximal Promoter:-725, Mono:OA; 1:181143336, PBMC:notRA; 1:181290986, PBMC:notRA; 1:182002021, PBMC:HC,PBMC:OA_SLE_HC; 1:182353640, GLUL||Exon 7:6899|Exon 7:Exon 8:7701, PBMC:notRA; 1:182556113, RNASEL|| Intron 1:2281, PBMC:notRA; 1:182557217, RNASEL|| Intron 1:1177, PBMCnotRA; 1:182810711, DHX9||Intron 1:2273, PBMC:HC; 1:184504284, Clorf21||Intron 3:148135, Mono:HC; 1:184836205, FAM129A||Intron 5:107477, PBMC:OA_SLE_HC; 1:18589627, IGSF21||Intron 2:155388, PBMC:HC; 1:18684587, IGSF21||Intron 4:250348, PBMC:notRA; 1:18704828, IGSF21||Exon 10:270589, PBMC:notRA; 1:18809531, KLHDC7A||Exon 1:2108, PBMC:notRA; 1:189194949, PBMC:notRA; 1:192095846, Tcell:OA_SLE_HC; 1:19277202, IFF02||Intron 1:5624, PBMC:SLE; 1:193075640, GLRX2|| Proximal Promoter:- 1032|Proximal Promoter:-396|Proximal Promoter:-453, PBMC:notRA; 1:193722865, BcelhHC; 1:19394757, UBR4||3' Proximal Enhancer: 141989, PBMC:HC,PBMC:OA_SLE_HC; 1:19401069, UBR4||Exon 106:135677, PBMC:HC; 1:19451037, UBR4||Exon 65:85709, PBMC:OA_SLE_HC; 1:19506481, UBR4||Intron 17:30265, Mono:OA_SLE_HC; 1:1951466, GABRD||Intron 1:699, Mono:OA_SLE_HC; 1:19600909, AKR7A3||3' Proximal Enhancer: 1437 l,AKR7L||Proximal Promoter:-341, Mono:OA; 1:196866512, CFHR4||Intron 1:9369, PBMC:OA_SLE_HC; 1:19687988, CAPZB||Intron 4:123213|Intron 4:124078, PBMC:notRA; 1:19717337, CAPZB||Intron 2:93864|Intron 2:94729, PBMC:HC; 1:198174503, NEK7||Intron 1:48396, PBMC:HC; 1:19975329, Clorfl51-NBLl||Intron l:Intron 2:51859,NBLl||Intron l:3070|Intron l:3464|Intron l:4523|Intron l:5122|Intron 1:5607, PBMC:HC,PBMC:OA_SLE_HC; 1:19985666, Clorfl51-NBLl||3' Proximal Enhancer:62196,HTR6||5' Proximal Enhancer:-6113,NBL1||3' Proximal Enhancer:13407|3' Proximal Enhancer:13801|3' Proximal Enhancer: 14860|3' Proximal Enhancer:15459|3' Proximal Enhancer: 15944, Mono:OA_SLE_HC; 1:19990783, Clorfl51-NBLl||3' Proximal
Enhancer:67313,HTR6||Proximal Promoter:-996,NBLl||3' Proximal Enhancer: 18524|3' Proximal Enhancer: 18918|3' Proximal Enhancer: 19977|3' Proximal Enhancer:20576|3' Proximal Enhancer:21061, PBMC:SLE; 1:19992504, Clorfl51-NBLl||3' Proximal Enhancer:69034,HTR6||Exon 1:725,NBL1||3' Proximal Enhancer:20245|3' Proximal Enhancer:20639|3' Proximal Enhancer:21698|3' Proximal Enhancer:22297|3' Proximal Enhancer:22782, PBMC:OA; 1:19992564, Clorfl51-NBLl||3' Proximal Enhancer:69094,HTR6||Exon 1:785,NBL1||3' Proximal Enhancer:20305|3' Proximal Enhancer:20699|3' Proximal Enhancer:21758|3' Proximal Enhancer:22357|3' Proximal Enhancer:22842, PBMC:OA; 1:20015027, HTR6||3' Proximal Enhancer:23248,TMC04||Intron 15:111383, PBMC:SLE; 1:201618030, NAVl||Exon 1:581, PBMC:SLE; 1:201618209, NAVl||Exon 1:760, PBMC:SLE; 1:201618654, NAVl||Intron 1:1205, PBMC:SLE; 1:201618901, NAVl||Intron 1:1452, PBMCSLE; 1:201619622, NAVl||Intron 1:2173, PBMC:OA_SLE_HC; 1:202090980, GPR37Ll||Proximal Promoter:- 1048, Bcell:HC; 1:202123442, ARL8A||5' Proximal Enhancer:-9576,PTPN7||Exon 5:5677|Exon 5:Exon 6:7274, PBMC:HC; 1:202172778, LGR6|| Intron 1:966 l|Proximal Promoter:-126, PBMC:OA_SLE_HC; 1:202172848, LGR6||Intron 1 :9731 |Proximal Promoter:-56, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 1:202172867, LGR6||Intron 1: 97501 Proximal Promoter:-37, PBMC:OA_SLE_HC; 1:202172912, LGR6||Intron l:9795|Proximal Promoter^, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 1:202205348, LGR6||Intron 4:22066|Intron 4:32444|Intron 4:42231, Mono:OA_SLE_HC; 1:202828149, LOC148709||Distal Promoter:- 2732, PBMC:HC; 1:203156097, CHI3Ll||Proximal Promoter:- 175, PBMCnotRA; 1:203764710, ZBED6||Proximal Promoter:-1940,ZC3H1 lA||Proximal Promoter:-40, PBMC:notRA; 1:204275926, PLEKH A611 Intron 1:53118, Mono:OA; 1:205341079, LEMD1||3' Proximal
Enhancer:50135,LOC284576||Proximal Promoter:-1300, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 1:205539221, MFSD4||Intron 1:1110, Bcell:OA_SLE_HC; 1:205819406, PM20Dl||Proximal Promoter:- 130, PBMC:OA_SLE_HC; 1:205819463, PM20Dl||Proximal Promoter:- 187, PBMC:OA_SLE_HC; 1:205819609, PM20Dl||Proximal Promoter:-333, PBMC:OA_SLE_HC; 1:206131535, FAM72A||5' Proximal Enhancer:-7375, PBMC:notRA; 1:206506826, SRGAP2||5' Proximal Enhancer: -9373, PBMC:notRA; 1:20693333, LOC339505||Intron 10:61954, PBMC:OA; 1:206941464, IL10||Exon 5:4375, Mono:HC; 1:206946166, IL10||Proximal Promoter:-327, PBMC:HC; 1:206946187, IL10||Proximal Promoter: -348, PBMC:HC; 1:207120407, PIGR||Proximal Promoter:-596, Mono:HC; 1:207277466, C4BPA||Proximal Promoter:-140,C4BPB||3' Proximal Enhancer: 14839|3' Proximal Enhancer: 1488313' Proximal Enhancer: 15255, PBMC:HC; 1:207455715, PBMC:OA_SLE_HC; 1:207672696, CRl||Intron 1:3224,CR2||3' Proximal Enhancer:45052, PBMC:OA; 1:208081541, CD34||Intron 1:3142, PBMC:HC; 1:20929640, CDA||Intron 1:14197, PBMC:HC; 1:20958590, PINKl||Proximal Promoter:-1357, Bcell:OA_SLE_HC; 1:209801351, LAMB3||Intron 10:23328|Intron 11:24323 |Intron ll:24469,MIR4260||Distal Promoter:-4496, Bcell:OA_SLE_HC; 1:209822928, PBMC:HC; 1:20985249, DDOST||Intron 2:2788,KIF17||3' Proximal Enhancer:59068,PINKl||3' Proximal Enhancer:25302, Mono:HC; 1:210000883, DIEXF|| Proximal Promoter:-428, Mono:HC,Mono:OA_SLE_HC,Mono:SLE; 1:210001066, DIEXF|| Proximal Promoter:-245, Mono:OA_SLE_HC,PBMC:HC; 1:210001082, DIEXF||Proximal Promoter:-229, Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 1:212845129, PBMC:OA; 1:21376633, EIF4G3||Intron 2:61243|Intron 4:126748|Intron 6:124618, Bcell:OA_SLE_HC,Mono:HC; 1:214006138, LOC100505832||Intron 3:133470, BcelhHC; 1:214435182, PBMC:notRA; 1:214461479, SMYD2||Intron 1:6915, Wholeblood:notRA; 1:2146288, Tcell:OA_SLE_HC; 1:2161886, SKI||Intron 1:1753, Mono:SLE; 1:2164542, SKI||Intron 1:4409, Tcell:HC,Tcell:OA_SLE_HC; 1:2164602, SKI||Intron 1:4469, PBMC:HC,Tcell:HC,Tcell:OA_SLE_HC; 1:2165579, SKI||Intron 1:5446, TcelhOA SLE HC; 1:21670736, Bcell:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 1:21763975, NBPF3||Distal Promoter: - 2655, PBMC:HC; 1:21866491, ALPL||Intron 1:30634, Wholeblood:notRA; 1:2191658, SKI||Intron 1:31525, Mono:HC; 1:219634786, PBMC:OA_SLE_HC; 1:219786527, PBMC:notRA; 1:221047545, HLX||5' Proximal Enhancer:-5197, PBMC:HC; 1:22327982, CELA3A||Proximal Promoter: -166, Bcell:OA_SLE_HC; 1:223315886, TLR5||Intron 1:738, TcelhSLE; 1:224030614, TP53BP2||Intron 1:3060, PBMC:HC; 1:224806373, CNIH3||Intron 1:2195, Mono:HC; 1:225998870, EPHXl||Intron 1:1074, PBMC:OA_SLE_HC; 1:226036279, EPHX1||3' Proximal Enhancer:23278|3' Proximal Enhancer:38483,TMEM63A||Intron 22:34141, Mono:HC,PBMC:HC; 1:226107899, PYCR2||Exon 7:4066, Bcell:OA_SLE_HC; 1:226297528, PBMC:notRA; 1:226411070, LIN9||3' Proximal Enhancer:86128,MIXLl||Proximal Promoter:-312, PBMC:OA; 1:226823363, ITPKB||Intron 7:103513, PBMC:notRA; 1:226833134, ITPKB||Intron 4:93742, Bcel OA; 1:227125826, ADCK3||Proximal Promoter: -2111, PBMC:HC; 1:227133801, ADCK3||Intron 1:5864, PBMC:OA; 1:227177885, ADCK3||3' Proximal Enhancer:49948,CDC42BPA||Exon 35:Exon 36:327941, PBMC:notRA; 1:227726508, Mono:OA_SLE_HC; 1:228291682, ARF1||3' Proximal Enhancer:20832|3' Proximal Enhancer:21322,ClorG5||Proximal Promoter:-660,MIR3620||3' Proximal Enhancer:6719,MRPL55||3' Proximal Enhancer:5331, PBMC:HC,PBMC:OA_SLE_HC; 1:228395756, OBSCN||Proximal Promoter: - 104, PBMC:OA_SLE_HC; 1:228560439, OBSCNpxon 94:164579, Wholeblood:notRA; 1:228564601, OBSCN||Intron 100:168741, PBMC:HC,PBMC:OA_SLE_HC; 1:228660732, PBMC:notRA; 1:228756711, PBMC:OA_SLE_HC; 1:228756714, PBMC:OA_SLE_HC; 1:229294380, PBMC:HC; 1:229477078, Clorf 6||Intron 2:1610, Tcel SLE; 1:229477268, Clorf96|| Intron 2:1420, PBMC:SLE; 1:230311676, GALNT2||Intron 1:108721, PBMC:OA_SLE_HC; 1:23034799, EPHB2||Distal Promoter:-2531, PBMC:HC; 1:231155948, FAM89A||Intron l:20047,MIR1182||Proximal Promoter: -278, Mono:OA_SLE_HC; 1:231163673, FAM89A||Intron 1:12322,MIR1182||5' Proximal Enhancer:-8003, Tcell:OA_SLE_HC; 1:23206348, Bcell:OA_SLE_HC; 1:233004866, PBMC:HC; 1:2335348, PEX10||3' Proximal Enhancer:8662,RERl||Exon 7:12135, Bcell:OA; 1:233765281, KCNKl||Intron 1:15532,MIR4427||3' Proximal Enhancer:5384, Tcell:OA; 1:234040045, SLC35F3||Proximal Promoter: - 633, PBMC:HC; 1:23474871, LUZPl||Intron 1:20480, PBMC:OA_SLE_HC,PBMC:notRA; 1:234880737, PBMC:notRA; 1:235105872, PBMC:HC,Tcell:HC; 1:235292369, RBM34||3' Proximal Enhancer:32202,SNORA14B||Proximal Promoter:-l 117,TOMM20||Proximal Promoter:- 113,
PBMC:OA_SLE_HC; 1:236083208, PBMC:notRA; 1:236849389, ACTN2||Proximal Promoter:-380, PBMC:HC; 1:23763279, ASAP3||Intron 14:Intron 15:47471, PBMC:HC,Tcell:HC; 1:238649445, LOC339535||Proximal Promoter: -128, Mono:OA_SLE_HC; 1:23953778, MDS2||Proximal Promoter:-45, PBMC:notRA; 1:239550303, PBMC:OA; 1:239552128, PBMC:HC; 1:240161061, RPS7P5||5' Proximal Enhancer:-9762, PBMC:OA_SLE_HC; 1:242002464, EX01||5' Proximal Enhancer:-9028|5' Proximal Enhancer:-9568, Mono:OA_SLE_HC; 1:244747323, Clorfl01||Intron 10:Intron 13:122651, PBMCnotRA; 1:245653016, KIF26B||Intron 4:334730, Mono:OA_SLE_HC; 1:24645380, GRHL3||Distal Promoter: - 4149|Proximal Promoter:-431|Proximal Promoter:-675, PBMC:notRA; 1:246860007, PBMC:OA_SLE_HC; 1:246958421, LOC149134||3' Proximal Enhancer:5503, PBMC:OA_SLE_HC; 1:247580074, NLRP3||Intron l:617|Proximal Promoter: -1276, PBMC:HC; 1:247581417, NLRP3||Exon 2:Intron l:1960|Proximal Promoter:67, PBMC:HC; 1:247616523, NLRP3||3' Proximal Enhancer:35173|3' Proximal Enhancer:37066,OR2Bl l||Proximal Promoter:-1239, Mono:OA_SLE_HC,PBMC:notRA; 1:247616686, NLRP3||3' Proximal Enhancer:35336|3' Proximal Enhancer:37229,OR2Bl l||Proximal Promoter: -1402, Mono:OA_SLE_HC,PBMC:notRA; 1:247694041, LOC148824||Proximal Promoter:65,OR2C3||Exon 2:3100, Mono:OA_SLE_HC; 1:247694061, LOC148824||Proximal Promoter:45,OR2C3||Exon 2:3080, Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 1:247694271, LOC148824||Proximal Promoter:-165,OR2C3||Exon 2:2870, PBMC:HC,PBMC:OA_SLE_HC; 1:247694275, LOC148824||Proximal Promoter:-169,OR2C3||Exon 2:2866,
PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC; 1:248059252, OR2W3||Proximal Promoter:364, PBMC:notRA; 1:248100345, OR2L13||Proximal Promoter: -147, PBMC:OA_SLE_HC; 1:248100407, OR2L13||Proximal Promoter:-85, PBMC:OA_SLE_HC; 1:24861872, RCAN3||Exon 2:Exon 3:Exon 4:21069|Exon 4:Exon 5:32486|Exon 4:Exon 5:33032|Exon 5:27789, PBMC:HC; 1:248683682, OR2G6||Proximal Promoter:-1265, PBMC:notRA; 1:24921758, Clorfl30||Intron 1:39192, PBMC:notRA; 1:25040257, PBMC:OA; 1:25251730, RUNX3||Intron 2:5040|Intron 3:39771, PBMC:HC; 1:25254149, RUNX3||Exon 2:2621|Exon 3:37352, Bcell:OA_SLE_HC; 1:25257505, RUNX3||Intron l:33996|Proximal Promoter:-735, PBMC:SLE; 1:25257547, RUNX3||Intron l:33954|Proximal Promoter: -777, PBMC:SLE; 1:25290947, RUNX3||Intron 1:554, Tcell:OA_SLE_HC; 1:25291041, RU X3|| Proximal Promoter:460, Tcell:OA_SLE_HC; 1:25291385, RUNX3|| Proximal Promoter:116, PBMC:HC; 1:25291989, RUNX3||Proximal Promoter: -488, Bcell:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC; 1:25292072, RUNX3||Proximal Promoter: -571, Tcell:OA_SLE_HC; 1:25292215, RU X3||Proximal Promoter:-714, PBMC:OA,PBMC:OA_SLE_HC; 1:26002535, MANIC l||Intron 1:58577, PBMC:HC; 1:26101755, MANlCl||Intron 8:157797, PBMC:SLE; 1:26527909, CATSPER4||Exon 9:10791, PBMC:notRA; 1:26547234, Bcell:OA_SLE_HC; 1:26880547, MIR19761| Proximal Promoter:-485,RPS6KAl||Intron 6:8205|Intron 7:24299, PBMC:notRA; 1:27143747, ZDHHC18||5' Proximal Enhancer: -9453, PBMC:notRA; 1:27248983, NR0B2||5' Proximal Enhancer:-8416,NUDC||Intron 1:760, PBMC:OA; 1:27627058, WDTCl||Intron 12:66052, PBMC:HC; 1:27683912, MAP3K6||Exon 23:9425,SYTL1||3' Proximal Enhancer: 15430, Bcell:SLE,PBMC:SLE; 1:27846843, BcelhOA; 1:27954026, FGR||Intron 1:770 l|Proximal Promoter: -1275 |Proximal Promoter:-920,
Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 1:27964774, FGR| I Distal Promoter: -3047, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 1:27977270, PBMC:SLE; 1:28237361, RPA2||Intron 2:3875, Mono:OA; 1:2839935, PBMC:OA; 1:28417750, EYA3||Distal Promoter:-2602,LOC653566||3' Proximal Enhancer:5319, PBMC:notRA; 1:2876347, Bcel OA; 1:2876546, PBMC:OA; 1:2885085, PBMC:OA_SLE_HC; 1:28994850, GMEBl||Proximal Promoter:-389, Tcel OA; 1:29045698, GMEB1||3' Proximal Enhancer:50459, Tcell:OA_SLE_HC; 1:29225533, EPB41||Intron 1:11931, Bcell:OA_SLE_HC; 1:2981840, FLJ42875||Intron l:2449,PRDM16||Distal Promoter:-3901, Wholeblood:notRA; 1:2984445, FLJ42875||Proximal Promoter:-156,PRDM16||Proximal Promoter: -1296, PBMC:OA_SLE_HC; 1:3080196, Tcell: OA SLE HC ; 1:3105151, PBMC:OA_SLE_HC; 1:3105189, PBMC:OA_SLE_HC; 1:31217240, LAPTM5||Intron 1:13443,MIR4420||5' Proximal Enhancer:-5161, PBMC:HC; 1:3123695, PBMC:SLE; 1:3134756, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:31465032, PRO0611||3' Proximal Enhancer:4121, Mono:OA_SLE_HC; 1:31711088, NKAINl||Intron 1:1646, PBMC:SLE; 1:31717101, NKAINl||Distal Promoter:-4367, Tcell:OA; 1:3213486, PBMC:notRA; 1:32444348, PBMC:notRA; 1:32716557, FAM167B||3' Proximal Enhancer:3740,LCK||Proximal Promoter: - 282,MTMR9LP||5' Proximal Enhancer: -9246, PBMC:HC; 1:32717002, FAM167B||3' Proximal Enhancer:4185,LCK||Proximal Promoter: 163,MTMR9LP||5' Proximal Enhancer:-9691, PBMC:HC; 1:32739049, LCK||Intron l:22210|Proximal Promoter: -662, PBMC:HC; 1:3332705, Tcell:OA; 1:33367401, HPCA||3' Proximal Enhancer: 15304,TMEM54||Proximal Promoter: -448, Wholeblood:notRA; 1:33842402, PBMC:OA; 1:3514921, PBMC:HC; 1:35676489, Bcell:OA_SLE_HC,Bcell:SLE; 1:35836009, ZMYM4||Exon 7:101442, PBMC:HC; 1:35875651, ZMYM4||Intron 26:141084, PBMC:notRA; 1:36038701, NCDN||3' Proximal Enhancer: 15309,TFAP2E||Proximal Promoter: -269, Wholeblood:notRA; 1:36038708, NCDN||3' Proximal Enhancer: 15316,TFAP2E||Proximal Promoter: -262, Wholeblood:notRA; 1:36177329, Clorl216||3' Proximal Enhancer:7461, PBMC:notRA; 1:36832173, STK40||Intron 2:19312, Bcell:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC; 1:36839270, STK40||Intron 1: 12215, Wholeblood:notRA; 1:36914349, MRPS15||3' Proximal Enhancer: 15691,OSCPl||Intron 1:1737, PBMC:HC; 1:37973652, MEAF6||Intron 4:6712, PBMC:OA; 1:37984690, MEAF6||Distal Promoter: -4326, Tcel HC; 1:3822352, Clorfl74||5' Proximal Enhancer:-5495,LOC100133612||Intron 2:5385, Mono:HC,Mono:OA_SLE_HC; 1:4008051, LOC728716||Intron 2:7380, PBMC:OA_SLE_HC; 1:4087676, PBMC:notRA; 1:41131970, RIMS3||Proximal Promoter: -646, Mono:OA; 1:41350292, PBMC:HC; 1:42224680, HIVEP3||Intron 1: 159698, PBMC:notRA; 1:42272694, HIVEP3||Intron 1:111684, PBMC:HC; 1:42380309, HIVEP3||Intron l:4069|Intron l:4187|Intron 2: 121287, TcelhHC; 1:42846987, RIMKLA||Intron 1:520, PBMC:HC; 1:43389028, SLC2A1||3' Proximal Enhancer:35819, PBMC:notRA; 1:43406792, SLC2Al||Intron 2:18055, PBMC:HC; 1:43472972, PBMC:OA; 1:43811019, MPL||Intron 6:7545, Mono:HC; 1:44114355, KDM4A||Proximal Promoter: -1441, PBMC:notRA; 1:44402422, ARTN||Exon 4:Exon 5:3431,ST3GAL3||3' Proximal Enhancer:229205, BcelhSLE; 1:4481995, LOC284661||Intron 3:9885, PBMC:HC,PBMC:notRA; 1:44998151, RNF220||Intron 2:127192, BcelhHC; 1:46646224, POMGNTl||3' Proximal Enhancer: 17897|3' Proximal Enhancer:39753,TSPANl||Exon 2:5476, Bcell:OA_SLE_HC; 1:46668822, Cloril90||Proximal Promoter: -183, POMGNTl||Distal Promoter: - 4701|Intron 1:17155, Bcel OA; 1:46766431, LRRC41||Intron l:2607,UQCRH||Distal Promoter: -2948, PBMC:HC; 1:47051752, MKNKl||Intron 2: 18214, PBMC:HC; 1:4714008, AJAPl||Proximal Promoter:- 1096, PBMC:OA; 1:4718212, AJAPl||Intron 1:3108, TcelhHC; 1:4725584, AJAPl||Intron 1: 10480, PBMC:notRA; 1:47329048, CYP4Z2P||Intron 8:37099, PBMC:notRA; 1:47799638, CMPKl||Proximal Promoter:170, PBMC:notRA; 1:48002630, Bcell:OA_SLE_HC,Bcell:SLE; 1:48508839, Bcel HC; 1:4856487, PBMC:notRA; 1:50883013, DMRTA2||3' Proximal Enhancer:6106, PBMC:OA; 1:52485971, TXNDC12||Exon 7:35076, PBMC:notRA; 1:5295746, Tcel HC; 1:53067637, GPX7|| Proximal Promoter: - 405, PBMC:SLE; 1:53067717, GPX7|| Proximal Promoter: -325, PBMC:OA_SLE_HC; 1:53392650, ECHDC2||5' Proximal Enhancer:-5204,SCP2||Proximal Promoter:-250, Mono:SLE; 1:53600889, SLClA7||Intron 1:7400, PBMC:notRA; 1:53878650, PBMC:OA_SLE_HC; 1:53966412, GLIS1||3' Proximal Enhancer:233465, PBMC:OA; 1:54562121, PBMC:HC; 1:54619655, CDCP2||Proximal Promoter:-212, Bcell:OA_SLE_HC,Bcell:SLE; 1:54666250, CYB5RL||Proximal Promoter: - 504,MRPL37||Proximal Promoter:411, PBMC:notRA; 1:54797076, SSBP3||Intron 4:74903 |Intron 4:75016, Bcell:OA_SLE_HC; 1:55012989, ACOTl l||Proximal Promoter:-817, PBMC:HC; 1:55089959, ACOTl l||Intron 15:76153,FAM151A||Proximal Promoter:-759, Tcel HC; 1:55265830, Clorfl77||5' Proximal Enhancer:-5905,TTC22||Intron 1:1111, PBMC:notRA; 1:55504848, PCSK9||Proximal Promoter: - 300, Wholeblood:notRA; 1:55506512, PCSK9||Intron 1:1364, PBMC:OA_SLE_HC; 1:55678649, LOC100507634||Proximal Promoter:-2431,USP24||Intron 1:2390, PBMC:OA_SLE_HC; 1:56453730, Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 1:56463319, Wholeblood:notRA; 1:565170, PBMC:notRA; 1:566570, PBMC:notRA; 1:567312, PBMCnotRA; 1:56901693, TcelhOA; 1:569427, Tcel HC; 1:58898672, PBMC:HC,PBMC:OA_SLE_HC; 1:58898793, PBMC:HC; 1:59008471, OMAl||Intron 1:3975, PBMC:OA_SLE_HC; 1:59043173, TACSTD2||Proximal Promoter:-7, PBMC:HC,PBMC:OA_SLE_HC; 1:59043199, TACSTD2|| Proximal Promoter: -33,
PBMC:HC,PBMC:OA_SLE_HC; 1:59043208, TACSTD2||Proximal Promoter: -42, PBMC:OA_SLE_HC; 1:59043255, TACSTD2|| Proximal Promoter:-89, PBMC:HC,PBMC:OA_SLE_HC; 1:59043280, TACSTD2||Proximal Promoter:-l 14, PBMC:HC,PBMC:OA_SLE_HC; 1:5920438, MIR4689||3' Proximal Enhancer:2363,NPHP4||3' Proximal Enhancer: 132095, Bcell:OA,Mono:OA,Tcell:OA; 1:60171660, FGGY||Intron 12:39591 l|Intron 14:Intron 15:409036, PBMC:HC; 1:60280096, HOOKl||Proximal Promoter: -436, Mono:OA; 1:6085995, KCNAB2||5' Proximal Enhancer:-8352|Intron l:33638|Proximal Promoter:-77, PBMC:HC; 1:6086018, KCNAB2||5' Proximal Enhancer:-8329|Intron l:33661|Proximal Promoter: -54, PBMC:HC; 1:61435148, PBMC:notRA; 1:62107542, PBMC:notRA; 1:62499140, INADL||Intron 29:290992, PBMCnotRA; 1:6266753, RNF207||Exon 2:565,RPL22||5' Proximal Enhancer: - 7074, PBMC:OA; 1:6268858, RNF207||Intron 3:2670,RPL22||5' Proximal Enhancer:-9179, BcelhOA; 1:6355008, ACOT7||Exon 7:63996|Exon 7:65756|Exon 7:90875|Exon 7:98818, PBMC:SLE; 1:6390053, ACOT7||Intron 4:28951| Intron 4:3071 l|Intron 4:55830|Intron 4:63773, Mono:OA_SLE_HC; 1:64014634, DLEU2L||Proximal Promoter:-16,EFCAB7||Intron 7:25622, PBMC:notRA; 1:64014643, DLEU2L||Proximal Promoter:-7,EFCAB7||Intron 7:25631, PBMC:notRA; 1:64627024, RORl||Intron 8:387335, BcelhOA; 1:6486842, ESPN||Intron 1: 1995,HES2||5' Proximal Enhancer:-6863,MIR4252||3' Proximal Enhancer:3114, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:65096537, PBMC:SLE; 1:65889855, DNAJC6||3' Proximal Enhancer: 159426,LEPR||Intron l:3521,LEPROT||Intron l:3725|Intron 2:3457, PBMC:OA; 1:6649337, KLHL21||3' Proximal Enhancer:13592,TASlRl||3' Proximal Enhancer:34000,ZBTB48||Exon 11:9275, PBMC:HC; 1:67798929, IL12RB2||Intron 7:25883, PBMC:HC; 1:68516101, DIRAS3||Proximal
Promoter:359,LOC100289178||Intron 2:218131, PBMC:notRA; 1:68966466, DEPDCl||Distal Promoter: - 3667, PBMCnotRA; 1:70687415, SRSFl l||Exon 2: 16051, PBMC:notRA; 1:70821806, ANKRD13C||Proximal Promoter:- 1389,HHLA3||Intron 1:1314, PBMC:HC; 1:7113389, CAMTAl || Intron 3:268006, PBMC:OA; 1:7181893, CAMTAl || Intron 4:336510, BcelhHC; 1:7432614, CAMTAl || Intron 5:587231, PBMC:HC,PBMC:OA_SLE_HC; 1:75199100, CRYZ|| Proximal Promoter:-8,TYW3||Proximal Promoter:239|Proximal Promoter:261|Proximal Promoter:265, TcelhOA; 1:76251636, RABGGTBI |Proximal Promoter:-249,SNORD45A||Proximal Promoter:-1937,SNORD45B||Distal Promoter: -3525,SNORD45C||Proximal Promoter:- 1120, PBMC:notRA; 1:77230619,
Mono:OA_SLE_HC,PBMC:HC; 1:77230704, Mono:OA_SLE_HC; 1:77230837, Mono:OA_SLE_HC; 1:77746028, AK5||Proximal Promoter:-1633|Proximal Promoter:-2258, PBMC:SLE; 1:78440671, FUBPl||Intron 1:4106, PBMC:notRA; 1:78452127, FUBP1||5' Proximal Enhancer:-7350, PBMC:HC; 1:78703580, MGC27382||Intron 1:8298, PBMC:SLE; 1:78751952, MGC27382||Intron 3:56670, PBMC:OA; 1:79085162, IFI44L||Proximal Promoter: -925,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 1:79085250, IFI44L||Proximal Promoter:- 837, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 1:79085586, IFI44L||Proximal Promoter:-501,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:79085713, IFI44L||Proximal Promoter:- 374, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:79085765, IFI44L|| Proximal Promoter:-322, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:79088769, IFI44L||Intron 1:2682, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC;
1:79118191, IFI44||Intron 2:2715,IFI44L||3' Proximal Enhancer:32104,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:8000314, TNFRSF9||Intron 2:2911, PBMC:notRA; 1:8005108, TNFRSF9||Proximal Promoter: -1883, PBMC:HC; 1:805338, FAM41C||Intron 2:6844, Wholeblood:notRA; 1:8120055, PBMC:OA_SLE_HC,PBMC:SLE; 1:81878937, PBMC:notRA; 1:85405081, MCOLN2||Intron 9:57715, PBMC:HC; 1:85461303, MCOLN2||Intron 1:1493, Mono:HC; 1:8577534, RERE||Intron 7:Intron 8:300165, PBMC:notRA; 1:869368, SAMDl l||Intron 4:8248, Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 1:8712546, RERE||Intron 2:Intron 3:165153, PBMC:notRA; 1:87617142, PBMC:HC; 1:89406505, CCBL2||Intron 12:Intron 13:52138, Mono:SLE; 1:89448407, CCBL2||Intron l:Intron 2:10236,RBMXLl||Exon 2:Exon 3:10236, PBMC:notRA; 1:90160031, LRRC8C||Intron 2:61388, PBMC:OA_SLE_HC; 1:9069875, SLC2A7|| Intron 9: 16529, Bcell:HC; 1:91182731, BARHL2|| Proximal Promoter:63, PBMC:OA; 1:911995, Clorfl70||Exon 4:5478,PLEKHN1||3' Proximal Enhancer: 10119, PBMC:OA_SLE_HC; 1:912055, C lorfl 701| Intron 3:5418,PLEKHN1||3' Proximal Enhancer: 10179, PBMC:OA_SLE_HC,Tcell:HC; 1:91488275, ZNF644||Proximal Promoter:-1210|Proximal Promoter:-463, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 1:91870389, HFMl||Proximal Promoter:37, BcelhOA; 1:91873278, HFMl||Distal Promoter:-2852, PBMC:notRA; 1:92012408, Wholeblood:notRA; 1:92099858, HSP90B3P||Proximal Promoter: -709, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 1:92101219, HSP90B3P||Intron 1:652, PBMC:SLE; 1:92417998, BRDT||Intron l:Intron 2:3071 |Proximal Promoter:290, PBMC:OA_SLE_HC; 1:93293756, FAM69A||3' Proximal Enhancer: 133323,RPL5||Distal Promoter:-3837,SNORD21||5' Proximal Enhancer: - 9089, PBMC:notRA; 1:94167631, PBMC:HC; 1:94559714, ABCA4||Intron 6:26991, PBMC:HC; 1:94703098, ARHGAP29||Proximal Promoter:209, PBMC:notRA; 1:949392, AGRN||5' Proximal Enhancer:-6110,ISG15||Exon 2:546, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,Tcell:SLE; 1:949449, AGRN||5' Proximal Enhancer:-6053,ISG15||Exon 2:603,
Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,PBMC:notRA; 1:949634, AGRN||5' Proximal Enhancer: - 5868,ISG15||Exon 2:788, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,Tcell:SLE; 1:949850, AGRN||5' Proximal Enhancer:-5652,ISG15||Exon 2:1004, Mono:SLE,PBMC:OA_SLE_HC; 1:949893, AGRN||5' Proximal Enhancer:-5609,ISG15||Exon 2:1047, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC; 1:95088560, TcelhHC; 1:95285888, SLC44A3||Proximal Promoter:-12|Proximal Promoter: -211, Mono:OA_SLE_HC; 1:957119, AGRN||Intron 1: 1617,ISG15||3' Proximal Enhancer: 8273, PBMC:HC; 1:958274, AGRN||Intron 2:2772,ISG15||3' Proximal Enhancer:9428, PBMC:SLE; 1:958351, AGRN||Intron 2:2849,ISG15||3' Proximal Enhancer: 9505, PBMC:SLE,Tcell:HC; 1:962651, AGRN||Intron 2:7149, Mono:SLE,PBMC:SLE; 1:970294, AGRN||Intron 2: 14792, Wholeblood:notRA; 1:9730401, Mono:HC; 20:139576, DEFB127||Exon 2: 1391, PBMC:notRA; 20:17660838, RRBPl||Intron 1:2090, PBMCnotRA; 20: 17680544, BANF2||Intron l:6225|Proximal Promoter:-48, PBMC:OA_SLE_HC; 20: 18113979, CSRP2BP||5' Proximal Enhancer: - 8888,PET117||Distal Promoter:-4519, TcelhOA; 20:18121410, CSRP2BP||Distal Promoter: -4332|Proximal Promoter:-1457,PET117||Intron 1:2912, PBMC:notRA; 20:21679843, PAX1||5' Proximal Enhancer:-6453, PBMC:notRA; 20:2308707, TGM3|| Intron 8:32095, BcelhHC; 20:23550632, CST9L||Proximal Promoter:- 1246, PBMC:notRA; 20:23586547, CST9||Proximal Promoter:63, PBMC:notRA; 20:23617145, CST3||Intron 1:1429, PBMC:notRA; 20:2442475, SNORD119||3' Proximal Enhancer:1218,SNRPB||Exon 7:Intron 6:9024, PBMC:notRA; 20:24969842, C20orG||Intron 1:3583, PBMC:HC; 20:259898, C20ori 6||Exon 5:11521, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 20:259925, C20ori 6||Exon 5: 11494, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 20:2634697, IDH3B||3' Proximal Enhancer:10146,MIR1292||3' Proximal Enhancer: 1275,NOP56||Intron 3: 1520,SNORA51||Proximal Promoter:-1015,SNORD110||Proximal Promoter:-160,SNORD56||Distal Promoter: -2572,SNORD57||Distal Promoter: -2887,SNORD86||Proximal Promoter:-2045, PBMC:HC,PBMC:OA_SLE_HC; 20:2780114, CPXMl||Intron 1: 1178, Mono:OA_SLE_HC; 20:2820927, FAM113A||Proximal
Promoter:405,VPS16||Proximal Promoter: -445, TcelhOA; 20:2852292, PTPRA||Intron 5:7452|Proximal Promoter:-1849,VPS16||3' Proximal Enhancer:30920, Tcell:OA; 20:29535150, PBMC:OA_SLE_HC; 20:29611652, FRGlB||Proximal Promoter:-226, PBMC:OA_SLE_HC; 20:29611903, FRGlB||Proximal Promoter:25, PBMC:OA_SLE_HC; 20:29611924, FRGlB||Proximal Promoter:46, PBMC:OA_SLE_HC; 20:30063129, DEFB1241| Proximal Promoter:-2313,REMl||Proximal Promoter:25, BcelhOA; 20:30073399, LINC00028||Proximal Promoter:- 181, REM 1||3' Proximal Enhancer: 10295, PBMC:OA_SLE_HC; 20:30074041, LINC00028||Proximal Promoter:461,REMl||3' Proximal Enhancer: 10937, PBMC:OA_SLE_HC,PBMC:SLE; 20:30190720, IDl||Proximal Promoter: -2365,MIR3193||Distal Promoter:-4268, BcelhHC; 20:30229335, COX4I2||Intron 3:3645, PBMC:HC; 20:30433673, FOXSl||Proximal Promoter: -253, Mono:HC,PBMC:OA; 20:30437560, FOXSl||Distal Promoter: -4140, PBMC:OA_SLE_HC,PBMC:SLE; 20:30437731, FOXSl||Distal Promoter: -4311,
PBMC:OA_SLE_HC,PBMC:SLE; 20:3065343, AVP||Proximal Promoter:27, BcelhSLE; 20:3065403, AVP||Proximal Promoter: -33, Mono:SLE; 20:3065423, AVP||Proximal Promoter:-53, Bcel SLE; 20:3145178, FASTKD5||Distal Promoter:-4646,ProSAPiPl||Exon 3:4029,UBOX5||Distal Promoter: -4638, PBMC:OA_SLE_HC,PBMC:SLE; 20:3145356, FASTKD5||Distal Promoter: -4824,ProSAPiPl||Exon 3:3851,UBOX5||Distal Promoter:-4816, PBMC:OA_SLE_HC,PBMC:SLE; 20:3145359, FASTKD5||Distal Promoter: -4827,ProSAPiPl||Exon 3:3848,UBOX5||Distal Promoter: -4819, PBMC:OA_SLE_HC; 20:3145597, FASTKD5||5' Proximal Enhancer:-5065,ProSAPiPl||Exon 3:3610,UBOX5||5' Proximal Enhancer:-5057, PBMC:SLE; 20:3149495, FASTKD5||5' Proximal Enhancer:-8963,ProSAPiPl||Proximal Promoter: -288,UBOX5||5' Proximal Enhancer: -8955, Mono:OA; 20:31669392, BPIFB3||3' Proximal Enhancer:26163,BPIFB4||Proximal Promoter:75, PBMC:HC; 20:34253242, CPNEl||Proximal Promoter: - 364|Proximal Promoter:-383,NFSl||3' Proximal Enhancer:34045,RBM12||Proximal Promoter: -364, Wholeblood:notRA; 20:35273933, NDRG3||3' Proximal Enhancer: 100608,SLA2||Intron 1:686, PBMC:HC; 20:35578437, SAMHDl||Intron 1: 1809, Tcel HC; 20:36230537, Mono:OA; 20:37062621, LOC3887961 |Intron 2:1341|Intron 2:1397,SNORA71A||5' Proximal Enhancer:-6535,SNORA71B||5' Proximal Enhancer:-8643,SNORA71C||Distal Promoter: -4174, SNORA71D||Proximal Promoter:21, BcelhHC; 20:37100986, RALGAPB|| Proximal Promoter: -499, Wholeblood:notRA; 20:42142847, L3MBTLl||Intron 3:6528|Proximal Promoter:-228, Mono:OA; 20:42142947, L3MBTLl||Intron 3:6628|Proximal Promoter:-128, Wholeblood:notRA; 20:42143174, L3MBTLl||Intron 3:6855|Proximal Promoter:99, PBMC:notRA; 20:42143502, L3MBTLl||Intron 4:7183|Proximal Promoter:427, PBMC:notRA; 20:42548586, TOX2||Intron l:3805|Intron 1:5095, PBMC:notRA; 20:42744457, JPH2||Exon 4:71761, Mono:HC; 20:43512143, YWHAB||Proximal Promoter: -2200, Tcel HC; 20:43743967, WFDC12||3' Proximal Enhancer:9139,WFDC5||Proximal Promoter: -154, PBMC:OA_SLE_HC; 20:43882990, SLPI||Proximal Promoter:216, Mono:OA; 20:44007674, SYS1||3' Proximal Enhancer:15935|3' Proximal Enhancer: 17098,SYSl-DBNDD2||Intron
3:15866,TP53TG5||Proximal Promoter:-717, PBMC:SLE; 20:44657115, SLC12A5||Intron l:6787|Proximal Promoter:-705, PBMC:HC; 20:45081360, Bcell:OA_SLE_HC; 20:45093514, MKRN7P||Proximal Promoter:417, PBMC:notRA; 20:45313215, SLC13A3||Proximal Promoter:-91,TP53RK||Exon 2:5061, Mono:OA; 20:45947025, LOC100131496||Proximal Promoter:-220,ZMYND8||Intron 2:38449, PBMC:HC; 20:46988236, LINC00494||Proximal Promoter:-417, PBMC:notRA; 20:47001970, LINC00494||3' Proximal Enhancer: 13317, TcelhOA; 20:47896769, SNORD12||Proximal Promoter:-450,SNORD12B||Proximal Promoter:-80,SNORD12C||3' Proximal Enhancer: 1288,ZNFXl||Proximal Promoter: -2013,ZNFX1- ASl||Intron 2: 1591|Intron 2:2055, Bcell:OA_SLE_HC; 20:47897207, SNORD12||Proximal Promoter:- 12,SNORD12B||Proximal Promoter:358,SNORD12C||3' Proximal Enhancer: 1726,ZNFXl||Proximal Promoter: -2451,ZNFXl-ASl||Intron 2:Intron 3:2493|Intron 3:2029, Bcell:OA_SLE_HC; 20:47897260, SNORD12||Proximal Promoter:41,SNORD12B||Proximal Promoter:411,SNORD12C||3' Proximal Enhancer:1779,ZNFXl||Distal Promoter: -2504,ZNFXl-ASl||Intron 2:Intron 3:2546|Intron 3:2082, Bcell:OA_SLE_HC; 20:48770800, TMEM189||Proximal Promoter:-465,TMEM189-UBE2Vl||Proximal Promoter: -465, TcelhSLE; 20:49640589, KCNGl||Proximal Promoter: -914, PBMC:OA_SLE_HC; 20:4983091, SLC23A2||Intron l:7848|Proximal Promoter: -946, PBMC:OA_SLE_HC; 20:50108912, PBMC:HC; 20:50110833, PBMC:SLE; 20:50214496, ATP9A||Exon 28:170412, BcelhHC; 20:50701266, ZFP64||Exon 9:107258, PBMC:notRA; 20:54922827,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 20:55043239, C20orf43||Proximal Promoter: -407,CASS4||3' Proximal Enhancer:55926|3' Proximal Enhancer:56072, PBMC:notRA; 20:55043299, C20orf43||Proximal Promoter:-347,CASS4||3' Proximal Enhancer:55986|3' Proximal Enhancer:56132, PBMC:notRA; 20:55199493, TFAP2C||Distal Promoter: -4864, Wholeblood:notRA; 20:56179171, ZBP1||3' Proximal Enhancer: Exon 7:Exon 8:16461, PBMC:notRA; 20:57414407, GNAS||Proximal Promoter: -387,GNAS-ASl||Intron 4:11551, Bcell:OA; 20:57426626, GNAS||Intron l:11832|Proximal Promoter:-1409,GNAS-ASl||Proximal Promoter:-668, PBMC:OA_SLE_HC; 20:57426759, GNAS||Intron 1:11965|Proximal Promoter: -1276,GNAS-ASl||Proximal Promoter: -801, PBMC:HC; 20:57426931, GNAS||Intron l:12137|Proximal Promoter:- 1104,GNAS-ASl||Proximal Promoter: -973, BcelhOA; 20:57426935, GNAS||Intron l:12141|Proximal Promoter:- 1100,GNAS- ASl||Proximal Promoter:-977, PBMC:HC,Tcell:HC; 20:57427103, GNAS||Intron l: 12309|Proximal Promoter: -932,GNAS-ASl||Proximal Promoter:-l 145, PBMC:HC; 20:57427472, GNAS||Intron l: 12678|Proximal Promoter:-563,GNAS-ASl||Proximal Promoter:- 1514, TcelhHC; 20:57427642, GNAS||Intron l:12848|Proximal Promoter:-393,GNAS-ASl||Proximal Promoter:-1684, TcelhHC; 20:57427650, GNAS||Intron l:12856|Proximal Promoter:-385,GNAS-ASl||Proximal Promoter: -1692, PBMC:notRA; 20:57463530, GNAS||Distal Promoter:-2895|Intron l:35495|Intron l:48736|Proximal Promoter: -649, PBMC:notRA; 20:57463653, GNAS||Distal Promoter:-2772|Intron l:35618|Intron l:48859|Proximal Promoter:-526, PBMC:notRA; 20:57463711, GNAS||Distal Promoter:-2714|Intron l:35676|Intron l:48917|Proximal Promoter: -468, PBMC:notRA; 20:57463725, GNAS||Distal Promoter: - 2700|Intron l:35690|Intron 1:4893 l|Proximal Promoter:-454, PBMCnotRA; 20:57463903, GNAS||Distal Promoter: -2522|Intron l:35868|Intron 1 : 491091 Proximal Promoter:-276, PBMC:notRA; 20:57608945, ATP5E||Proximal Promoter:-1523,SLM02||Exon 6:8956,SLM02-ATP5E||Intron 4:Intron 6:8956,TUBB1||3' Proximal Enhancer: 14637, PBMC:notRA; 20:5928064, MCM8||Distal Promoter: - 3233,TRMT6||Intron 1:3109, PBMC:notRA; 20:6034446, LRRN4|| Proximal Promoter:248, PBMC : SLE,PBMC :notRA; 20:60472065, CDH4||Intron 7:297249|Intron 7:397589|Intron 8:644584, BcelhHC; 20:60932415, PBMC:HC; 20:60958108, CABLES2||3' Proximal Enhancer:24231,RPS21||Distal Promoter: -4012, PBMC:notRA; 20:61047376, GATA5||Intron 3:3650, PBMC:notRA; 20:61052060, GATA5||Proximal Promoter:- 1034, PBMC:notRA; 20:61160996, C20orfl66||Intron 2:13337,MIR1-1||3' Proximal Enhancer:9484,MIR133A2||Proximal Promoter:-l 122, Wholeblood:notRA; 20:61590751, SLC17A9||Intron 3:6753, PBMC:OA_SLE_HC; 20:61590823, SLC17A9||Intron 3:6825, PBMC:OA_SLE_HC; 20:61977814, CHRNA4||Exon 6: 14881, Bcel HC; 20:62053198, KCNQ2||Intron 10:Intron 11:50795, PBMC:notRA; 20:62179030, C20orfl95||5' Proximal Enhancer:-5342,SRMS||Proximal Promoter: -173, PBMC:OA_SLE_HC,PBMC:SLE; 20:62179233, C20orfl95||5' Proximal Enhancer: - 5139,SRMS||Proximal Promoter: -376, Mono:SLE,PBMC:OA_SLE_HC; 20:62191507, C20orfl95||3' Proximal Enhancer:7135,PRIC285||Intron 12:7600|Intron 18: 14085, PBMC:SLE; 20:62198469, PRIC285||Exon l:638|Exon 7:7123, PBMC:OA_SLE_HC,PBMC:SLE; 20:62198872, PRIC285||Exon 7:6720|Proximal Promoter:235, PBMC:OA_SLE_HC; 20:62199034, PRIC285||Intron 6:6558|Proximal Promoter: 73, Mono:SLE,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 20:62199156, PRIC285||Intron 6:6436|Proximal Promoter:-49, Tcell:OA_SLE_HC; 20:62199181, PRIC2851| Intron 6:641 l|Proximal Promoter:-74, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 20:62199190, PRIC285||Intron 6:6402|Proximal Promoter:-83, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 20:62200091, PRIC285||Exon 6:5501|Proximal Promoter: -984, Mono:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 20:62200199, PRIC285||Exon 6:5393 |Proximal Promoter: -1092,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 20:62200285, PRIC285||Exon 6:5307|Proximal Promoter:- 1178, PBMC:OA_SLE_HC,Tcell:SLE; 20:62200603, PRIC285||Exon 5:4989|Proximal Promoter: -1496, PBMC:SLE; 20:62204908, PRIC285||5' Proximal Enhancer: -580 l|Intron 1:684, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC,Tcell:SLE; 20:62367888, LIMEl||Proximal Promoter:-89,SLC2A4RG||Distal Promoter:-3322,ZBTB46||3' Proximal Enhancer:68968,ZGPAT||3' Proximal Enhancer:28509|3' Proximal Enhancer:29095, PBMC:HC; 20:62368256, LIMEl||Proximal Promoter:279,SLC2A4RG||Distal Promoter: -2954,ZBTB46||3' Proximal Enhancer:68600,ZGPAT||3' Proximal Enhancer:28877|3' Proximal Enhancer:29463, PBMC:HC; 20:62405407, ZBTB46||Intron 3:31449, PBMC:notRA; 20:62434140, ZBTB46||Intron 1:2716, PBMC:HC; 20:62660605, LINC00176||5' Proximal Enhancer:-5091,PRPF6||Intron 18:48175, PBMC:HC; 20:741723, C20orf54||Exon 5:7505, PBMC:OA_SLE_HC; 21:15436260, Mono:OA; 21:17566381, LINC00478||Intron 3:123540|Proximal Promoter: -317, PBMC:HC; 21:26734161, PBMC:notRA; 21:28335945, ADAMTS5||Intron 1:3494,MIR4759||3' Proximal Enhancer:9666, PBMC:OA_SLE_HC; 21:28516138, PBMC:notRA; 21:30392289, RWDD2B||Proximal Promoter: -604,USP16||Distal Promoter: -4648, PBMC:notRA; 21:33673209, MRAP|| Intron 3:9086, PBMC:notRA; 21:33948561, TCP10L||Exon 5:9284, PBMC:OA_SLE_HC; 21:34396986, OLIG2|| Proximal Promoter:-1229, Wholeblood:notRA; 21:34405997, OLIG2||3' Proximal Enhancer:7782, PBMC:HC; 21:34773372, IFNGR2|| Proximal Promoter: -1829, Bcell:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC; 21:36089405, CLIC6||Exon 6:47718,LINC00160||5' Proximal Enhancer:-6699, Mono:OA_SLE_HC,Mono:SLE; 21:36398056, PBMC:HC; 21:36410464, RUNXl-ITl||Exon 1:1259, PBMC:SLE; 21:37437565, CBRl||Distal Promoter: -4719,LOC100133286||3' Proximal Enhancer:61373,SETD4||Distal Promoter:-4746|Distal Promoter: -4749|Distal Promoter: -4954, PBMC:HC,Tcell:HC; 21:37442777, CBRl||Proximal Promoter:493,LOC100133286||Exon 4:56161, PBMC:HC; 21:37504755, CBR3||Distal Promoter: -2507,LOC100506428||3' Proximal EnhancenExon 3:Exon 4:23851, PBMC:notRA; 21:37667921, DOPEY2||3' Proximal Enhancer: 131083, PBMC:notRA; 21:37761363, CHAFlB||Intron 3:3675, PBMC:OA_SLE_HC; 21:37915091, CLDN14||Intron l:33776|Proximal Promoter:-193, PBMC:notRA; 21:38349937, HLCS||Intron l:12608|Intron 1:3327, PBMC:notRA; 21:38445968, PIGP||Proximal Promoter:-510|Proximal Promoter:-865,TTC3||5' Proximal Enhancer:-9278|Proximal Promoter:398, Mono:OA_SLE_HC; 21:39644332, KCNJ15||Intron 1: 15463 |Intron 2:15669|Proximal Promoter:-96, PBMC:notRA; 21:39644354, KCNJ15||Intron l:15485|Intron 2:15691|Proximal Promoter:-74, PBMC:notRA; 21:40033634, ERG||Proximal Promoter:- 1043|Proximal Promoter:- 16|Proximal Promoter:70, PBMC:OA; 21:40816464, LCA5L||Proximal Promoter:-336,SH3BGR||5' Proximal Enhancer: -7315 |Proximal Promoter:-1332, Mono:OA_SLE_HC; 21:42219211, PBMC:HC; 21:42789922, MX1||5' Proximal Enhancer:-8055|5' Proximal Enhancer:- 8180|Distal Promoter: -2597,MX2||3' Proximal Enhancer:55973, PBMC:notRA; 21:42791867, MX1||5' Proximal Enhancer:-6110|5' Proximal Enhancer: -6235 |Proximal Promoter:-652, Mono:OA_SLE_HC; 21:42792609, MX1||5' Proximal Enhancer:-5368|5' Proximal Enhancer: -5493 |Proximal Promoter:90, PBMC:OA_SLE_HC,Tcell:SLE; 21:42792703, MX1||5' Proximal Enhancer:-5274|5' Proximal Enhancer:- 5399|Proximal Promoter: 184, Tcel SLE; 21:42797588, MXl||Intron 3:5069|Proximal Promoter: - 389|Proximal Promoter:-514, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC;
21:42797847, MXl||Intron 3:5328|Proximal Promoter:-130|Proximal Promoter: -255, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC; 21:42798747, MXl||Intron l:645|Intron l:770|Intron 3:6228, PBMC:SLE; 21:42799141, MXl||Exon 2:1164|Exon 4:6622|Intron 1:1039, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC;
21:43547872, PBMC:OA_SLE_HC; 21:43560719, PBMC:OA_SLE_HC; 21:43989949, SLC37Al||Intron 18:70208, PBMC:OA_SLE_HC; 21:44101491, PDE9A||Intron 1:27630, PBMC:HC; 21:44110482, PDE9A||Intron l:Intron 2:Intron 3:36621, PBMC:notRA; 21:44396204, PKNOXl||Intron 1:1562, PBMC:HC,PBMC:OA_SLE_HC; 21:44830477, SIK1||3' Proximal Enhancer: 16525, Mono:HC; 21:44985357, HSF2BP||Intron 8:94017, PBMC:notRA; 21:45576085, PBMC:HC; 21:46074616, KRTAP10-11||3' Proximal Enhancer:8286,KRTAP12-3||Distal Promoter:-3232,KRTAP12-4||Proximal Promoter: -40, Wholeblood:notRA; 21:46378438, FAM207A||Intron 2:18484, PBMC:notRA; 21:46385572, FAM207A||Intron 3:25618, PBMC:SLE; 21:46686908, POFUT2||Exon 8:Intron 8:20903, PBMC:HC; 21:46694944, POFUT2|| Intron 6:12867, PBMCnotRA; 21:46763239, PBMC:HC; 21:46856099, PBMC:OA; 21:46921982, COL18Al||Intron 31:46559, PBMC:notRA; 21:46955566, SLC19Al||Intron 2:6819|Proximal Promoter: -1024, Bcell:OA_SLE_HC; 21:46975805, PBMC:notRA; 21:46976175, PBMC:notRA; 21:47010818, PBMC:notRA; 21:47054539, PBMCnotRA; 21:47396773, COL6Al||Distal Promoter: -4889, PBMC:OA_SLE_HC; 21:47401492, COL6Al||Proximal Promoter: -170, PBMC:notRA; 21:47845788, PCNT||Exon 33:101753, PBMC:HC; 21:47859926, PCNT||Intron 41:115891, PBMC:notRA; 22:17073884, CCT8L2||Proximal Promoter:-184,TPTEPl||5' Proximal Enhancer: -8916, BcelhHC; 22:17591088, CECR6||3' Proximal Enhancer: 11125|3' Proximal Enhancenl 1169,IL17RA||Exon 13:25238, Tcel HC; 22:18479382, PBMC:notRA; 22:18632433, USP18||Proximal Promoter:-324, PBMCSLE; 22:18635460, USP18||Intron 1:2703,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC;
22:18737348, PBMC:OA_SLE_HC; 22:19119464, DGCR14||Exon 10:12726,TSSK2||Exon 1:1144, PBMC:notRA; 22:19162276, CLTCL1||3' Proximal Enhancenl 16963,SLC25A1||3' Proximal Enhancer:3758|3' Proximal Enhancer:4025, PBMC:HC,PBMC:OA_SLE_HC; 22:19726430, Wholeblood:notRA; 22:20284604, PBMC:notRA; 22:20708652, PBMC:notRA; 22:21399189, LOC400891||Proximal Promoter: -1059,P2RX6P||Proximal Promoter: -651, PBMCSLE; 22:23519916, BCR||Distal Promoter:-2635, PBMC:OA; 22:23521267, BCR||Proximal Promoter:-1284, BcelhHC; 22:23909177, IGLL1||3' Proximal Enhancer: 13318, Bcell:OA_SLE_HC; 22:23922378, IGLLl||Proximal Promoter: 117, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 22:24093826, VPREB3||3' Proximal Enhancer:2804,ZNF70||Proximal Promoter: -547, PBMC:SLE; 22:24095989, C22orfl5||5' Proximal Enhancer:-9218,VPREB3||Intron l :641,ZNF70||Distal Promoter:-2710, BcelhOA; 22:24640743, GGT5||Proximal Promoter:367,POM121L9P||5' Proximal Enhancer: -6845, Bcell:OA_SLE_HC; 22:24823389, ADORA2A|| Proximal Promoter:-140,C22orf45||3' Proximal Enhancer:67394,SPECClL||3' Proximal Enhancer: 156600|3' Proximal Enhancer:85314, BcelhHC; 22:24979964, FAM211B||3' Proximal Enhancer:9071,GGTl ||Proximal Promoter:247, Mono:OA_SLE_HC; 22:24998181, FAM211B||5' Proximal Enhancer:-9146,GGT1 ||5' Proximal Enhancer: -5444|Intron l : 18464|Proximal Promoter:-942|Proximal Promoter:-998, PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 22:25571929,
PBMC:OA_SLE_HC; 22:25594918, CRYBB3||Proximal Promoter: -906, PBMC:notRA; 22:26876075, HPS4||Intron 2:3745|Proximal Promoter:-524,SRRD||Distal Promoter:-3774, PBMC:HC; 22:26898513, TFIPl l ||Intron 7:Intron 8:9924, PBMCnotRA; 22:28249567, PITPNB||Exon 12:65688, PBMCnotRA; 22:30474915, HORMAD2|| Proximal Promoter:-1537, BcelhHC; 22:30721543, SF3A1 ||3' Proximal Enhancer:31370,TBClD10A||Intron 1 : 1412, PBMC:OA_SLE_HC; 22:30779672, CCDC157||3' Proximal Enhancer:27046,RNF215||Intron 5:3630, PBMC:notRA; 22:31689831, PIK3IPl ||Proximal Promoter:-1311, PBMC:HC; 22:32870150, FBX07||Proximal Promoter:- 1073 |Proximal Promoter:-556, Bcell:OA_SLE_HC; 22:37211021, PVALB||Intron 3:4496, PBMC:OA_SLE_HC; 22:37447398, KCTD17||Proximal Promoter: - 380, PBMC:HC; 22:37493737, TMPRSS6||Intron 3:5956, PBMC:notRA; 22:37493863, TMPRSS6||Intron 3:5830, PBMC:notRA; 22:37495019, TMPRSS6||Intron 2:4674, PBMC:OA; 22:38203998, GCAT||Proximal Promoter:87,HlF0||3' Proximal Enhancer:2885, PBMC:notRA; 22:38474147, BAIAP2L2||3' Proximal Enhancer:32529,PICKl ||3' Proximal Enhancer:20886,SLC16A8||Exon 5:5023, PBMC:HC; 22:39527583, CBX7||Exon 6:20955, PBMC:OA_SLE_HC; 22:39709853, RNU86||3' Proximal Enhancer:3048,RPL3||Intron 7:5817,SNORD43||3' Proximal Enhancer:5265,SNORD83A||3' Proximal Enhancer: 1459,SNORD83B||Proximal Promoter:63, PBMC:notRA; 22:39713532, RNU86||Proximal Promoter:-631,RPL3||Exon 3:2138,SNORD43||3' Proximal Enhancer: 1586,SNORD83A||Proximal Promoter: -2220,SNORD83B||Distal Promoter:-3616, PBMC:OA; 22:39784769, PBMC:HC; 22:39784796, PBMC:HC; 22:40573204, TNRC6B||Intron 4: 132384|Proximal Promoter: -724, Bcell:OA_SLE_HC; 22:41217753, MIR4766||5' Proximal Enhancer: -7791,SLC25A17||Proximal Promoter:-2361,ST13||3' Proximal Enhancer:34934, PBMC:notRA; 22:41460240, PBMC:notRA; 22:41597321, L3MBTL2||Distal Promoter:-3991, Bcel SLE; 22:41986335, PMMl ||Proximal Promoter: -464,PPPDE2||3' Proximal Enhancer:30726, Tcel OA; 22:42325444, CENPM||3' Proximal Enhancer: 10779|3' Proximal Enhancer: 17704,TNFRSF13C||Distal Promoter: -2623, Bcel HC; 22:42347272, BK250D10.8||Proximal Promoter: -918,CENPM||Distal Promoter: -4124, PBMC:SLE; 22:42356813, BK250D10.8||3' Proximal Enhancer: 8623, Bcel OA; 22:42679577, LOC388906||3' Proximal Enhancer: 13819, Bcell:OA_SLE_HC; 22:42950376, SERHL2|| Proximal Promoter:452, PBMC:HC; 22:43807121, MPPEDl ||Proximal Promoter: - 898, Tcell:OA_SLE_HC; 22:44575455, PARVG||Intron l :6620|Proximal Promoter:-1314|Proximal Promoter:-1760|Proximal Promoter: -1801, PBMC:HC; 22:44588350, PARVG||3' Proximal Enhancer: 11135|3' Proximal Enhancer:Intron 8: 11581 Proximal Enhancer: Intron 8: 19515|Intron 8: 11094, PBMC:HC; 22:45018513, LINC00229||Exon 2:2786, PBMC:HC; 22:45022625, LINC00229||Proximal Promoter:-1326, PBMC:notRA; 22:45608516, Mono:HC; 22:45737514, FAM118A||Exon 10:32434|Exon 9:31730,SMC1B||3' Proximal Enhancer:71986,
Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 22:45806309, RIBC2||Distal Promoter:-3264,SMClB||Intron 1 :3191, PBMC:OA_SLE_HC,PBMC:SLE; 22:45809952, RIBC2||Proximal Promoter:379,SMClB||Proximal Promoter: -452, PBMC:OA_SLE_HC; 22:45810043, RIBC2||Proximal Promoter:470,SMClB||Proximal Promoter: -543, PBMC:OA_SLE_HC; 22:46285638, Mono:OA_SLE_HC; 22:46285897, PBMC:HC,PBMC:OA_SLE_HC; 22:46507771, MIR4763 UProximal Promoter:- 1674,MIRLET7A3 |Proximal Promoter:-857,MIRLET7B| |Proximal Promoter: -1794, PBMC:OA; 22:46508451, MIR4763||Proximal Promoter:-994,MIRLET7A3||Proximal Promoter:- 177,MIRLET7B||Proximal Promoter:- 1114, PBMC:notRA; 22:46646882, C22orf40||Proximal Promoter:-689,PKDREJ||3' Proximal Enhancer: 12337,PPARA||3' Proximal Enhancer: 100384, Mono:OA_SLE_HC; 22:46650375, C22orf40||Distal Promoter: -4182,PKDREJ||3' Proximal Enhancer: 8844, Tcell:OA_SLE_HC; 22:46688823, CN5H6.4||3' Proximal Enhancer:3734,GTSEl ||Distal Promoter: - 3814,TTC38||Exon 14:24963, Mono:HC; 22:46833806, CELSRl ||Intron 3:99261, Bcel HC; 22:46972501, BcelhOA; 22:47010440, PBMC:SLE; 22:47027906, GRAMD4||Intron 1 :5249, PBMC:HC,PBMC:notRA; 22:48486164, PBMC:HC; 22:48792702, Mono:OA_SLE_HC; 22:48917166, FAM19A5|| Intron 1 :31879, PBMC:OA; 22:49840886, PBMC:HC; 22:49843259, PBMC:notRA; 22:50243719, ZBED4||Distal Promoter: -3777, PBMC:notRA; 22:50919482, ADM2|| Proximal Promoter:-502|Proximal Promoter: - 670,MIOX||5' Proximal Enhancer:-5730,SBF1 ||5' Proximal Enhancer:-6018, PBMC:HC; 22:50946712, LMF2||Proximal Promoter:-577,NCAPH2||Proximal Promoter:68, PBMC:notRA; 22:50981121, KLHDC7B||5' Proximal Enhancer:-5340,SYCE3||3' Proximal Enhancer:20207, PBMC:SLE; 22:50984368, KLHDC7B| jproximal Promoter:-2093,SYCE3||3' Proximal Enhancer: 16960, PBMC:OA_SLE_HC; 22:50984393, KLHDC7B||Proximal Promoter: -2068,SYCE3||3' Proximal Enhancer: 16935, PBMC:SLE,Tcell:SLE; 22:50986511, KLHDC7B||Proximal Promoter: 50, SYCE3||3' Proximal Enhancer:14817, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:SLE; 22:50986813, KLHDC7B||Proximal Promoter:352,SYCE3||3' Proximal Enhancer:14515, Bcell:SLE,Mono:OA_SLE_HC,PBMC:SLE; 22:50987527, KLHDC7B||Exon 1:1066,SYCE3||3' Proximal Enhancer: 13801 , PBMC:SLE; 22:51016501, CHKB||3' Proximal Enhancer:4927,CHKB-CPTlB||Intron 1 l:4927,CPTlB||Intron l:595|Proximal Promoter:393|Proximal Promoter:5,LOC100144603||Distal Promoter:-4953, PBMC:OA_SLE_HC; 22:51016638, CHKB||3' Proximal Enhancer:4790,CHKB-CPTlB||Intron 1 l:4790,CPTlB||Proximal Promoter:-132|Proximal Promoter:256|Proximal Promoter:458,LOC100144603||Distal Promoter: -4816, PBMC:OA_SLE_HC; 22:51016644, CHKB||3' Proximal Enhancer:4784,CHKB-CPTlB||Intron 1 l:4784,CPTlB||Proximal Promoter:-138|Proximal Promoter:250|Proximal
Promoter:452,LOC100144603||Distal Promoter: -4810, PBMC:OA_SLE_HC; 2:100481106, AFF3||Intron 6:240939|Intron 6:277931, Mono:HC; 2:100677411, AFF3||Intron 2:44634|Intron 3:81626, PBMC:HC; 2:100723240, AFF3||Intron l:35797|Proximal Promoter:-l 195, Tcell:OA_SLE_HC; 2:100942198, LONRF2||Distal Promoter:-3003, PBMC:notRA; 2:10146551, GRHL1||3' Proximal Enhancer: 54760, PBMC:notRA; 2:101763598, TBClD8||Intron 1:4248, PBMC:notRA; 2:102870456, PBMC:notRA; 2:102895712, Mono:HC; 2:103035835, IL18RAP||Intron 1:582, PBMC:notRA; 2:10340837, C2orf48||Intron 2:58857,MIR4261||5' Proximal Enhancer: -8040, PBMC:notRA; 2:10445016, HPCALl||Intron 1:1191|Intron 1:1977, PBMC:OA_SLE_HC; 2:104996109, LOC100287010||Exon 3:28681, Bcel OA; 2:10517352, HPCALl||Intron l:73527|Intron 1:74313, PBMC:SLE,Tcell:SLE; 2:10517361, HPCALl||Intron l:73536|Intron 1:74322, PBMC:SLE,Tcell:SLE; 2:105459775, LOC100506421||Intron 1:8159, PBMC:OA; 2:105488038, PBMC:HC; 2:105857955, GPR45|| Proximal Promoter: -244, Tcel OA; 2:106512578, NCK2||3' Proximal Enhancer:151059|3' Proximal Enhancer:44375, BcelhOA; 2:106713059, UXSl||Intron 13:Intron 14:97736|Intron 9:42278, PBMC:HC; 2:107084911, RGPD3||Proximal Promoter:- 110, PBMC:notRA; 2:108157524, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2:10830698, NOL10||Proximal Promoter: -586, Mono:HC; 2:108964526, SULTlC2Pl||Intron 3:25833, PBMC:notRA; 2:109251064, LIMSl ||Intron l:100254|Intron 1: 13363 |Intron l:27448|Intron l:46143|Intron 1:46308, PBMC:OA_SLE_HC; 2:10942687, PDIA6||Exon 2:10273, PBMC:notRA; 2:109747207, LOC100287216||Proximal Promoter:-632,SH3RF3||Intron 1:1211, BcelhOA; 2:109826107, PBMC:notRA; 2:10984512, Wholeblood:notRA; 2:109855574, PBMC:HC; 2:110370440, ANKRD57||Proximal Promoter:-1470,SEPT10||Intron 1:1343, PBMC:notRA; 2:111633044, ACOXL||Intron 10:142895, Mono:HC; 2:111857973, ACOXL||Intron 17:367824, PBMC:OA_SLE_HC; 2:112293267, Mono:HC; 2:11286089, C2orf50||Intron 3:12911,PQLC3||5' Proximal Enhancer: -9450, PBMC:OA_SLE_HC; 2:112939562, FBLN7||Intron 4:Intron 5:43601, PBMC:SLE; 2:113012627, ZC3H8||Proximal Promoter:37, PBMC:notRA; 2:113298655, POLRlB||Proximal Promoter:-836,TTL||3' Proximal Enhancer: 58913, Tcel SLE; 2:113956634, PSD4||Intron 15:25075, Tcel HC; 2:113957041, PSD4||Intron 16:25482, PBMC:HC; 2:114196058, CBWD2||Intron 1:791, PBMC:notRA; 2:114361162, DDXllL2||Proximal Promoter: -2009|Proximal Promoter:132,RPL23AP7||3' Proximal Enhancer:23553,WASH2P||3' Proximal Enhancer: 19933, PBMC:notRA; 2:114426529, PBMC:notRA; 2:1151809, SNTG2||Intron 6:205256, TcelhOA; 2:11680144, GREBl||Distal Promoter: -2706|Intron l:5903|Proximal Promoter:65,MIR4429||3' Proximal Enhancer:659, PBMC:OA_SLE_HC; 2:11728079, GREBl||Intron 9:45229, PBMC:notRA; 2:119616769, TcelhOA; 2:120436039, TMEM177||Proximal Promoter: -703, PBMC:notRA; 2:121347402, Tcel OA; 2:121691795, GLI2||Intron 2:136929, Bcel OA; 2:121697428, GLI2||Intron 2:142562, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,PBMC:SLE; 2: 124971544, CNTNAP5||Intron 1:188681, PBMC:OA_SLE_HC; 2:125077436, CNTNAP5||Intron 3:294573, Bcel HC; 2:128569178, WDR33||Proximal Promoter:-417, Wholeblood:notRA; 2:128994402, TcelhOA; 2:129231478, Bcell:HC,PBMC:HC; 2:130989361, PBMC:notRA; 2:131010647, Bcel SLE; 2:131046122, PBMC:SLE; 2:131368380, PBMC:notRA; 2:131509767, FAM123C||Distal Promoter:-3309|Distal Promoter:-3456|Distal Promoter:-4096, PBMC:notRA; 2:131585563, Bcell:OA_SLE_HC; 2:132202527, LOC401010||Proximal Promoter:-60, PBMC:notRA; 2:132233784, MZT2A||3' Proximal Enhancer: 16280,TUBA3D||Proximal Promoter:205, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 2:132435951, PBMC:notRA; 2:132480958, C2orf27A||Intron 1:895, PBMC:notRA; 2:132481826, C2orf27A||Intron 1:1763, PBMC:OA_SLE_HC; 2:132559058, C2orf27B||Proximal Promoter:176, Wholeblood:notRA; 2:132765062, PBMC:OA_SLE_HC; 2:133039779, Tcell:OA_SLE_HC; 2:134180560, NCKAP5||Intron 3:145471, PBMC:HC; 2:134548875, PBMC:notRA; 2:134949671, PBMC:notRA; 2:138845177, PBMC:OA; 2:139538746, NXPH2||Proximal Promoter:-935, PBMC:HC; 2:139654347, LOC647012||Proximal Promoter:-546, BcelhHC; 2:1425560, TPO||Intron l:7381|Intron 2:8328, Mono:OA; 2:143632190, KYNU|| Distal Promoter: -3004, PBMC:OA; 2:144462886, ARHGAP 151 |Intron 13:575988, PBMC:notRA; 2:145226929, ZEB2||Intron 2:51029, PBMC:OA_SLE_HC; 2:145268533, ZEB2||3' Proximal Enhancer:Intron 2:9425,ZEB2-AS1||3' Proximal Enhancer:9933, Mono:HC; 2:145278485, ZEB2||Proximal Promoter:-527,ZEB2-ASl||Proximal Promoter:-19, PBMC:HC; 2:145278564, ZEB2||Proximal Promoter:-606,ZEB2-ASl||Proximal Promoter:-98, Bcell:HC,PBMC:HC; 2:148753294, ORC4||Intron l:25012|Intron l:25022|Intron l:25035|Intron l:25036|Intron l:25169|Intron 1:25879, PBMC:notRA; 2:149478494, EPC2||Intron 2:75935, Mono:OA_SLE_HC; 2:149894539, LYPD6B||Proximal Promoter:-441, Mono:OA_SLE_HC,Mono:SLE; 2:150222839, LYPD6||Intron 1:3581 l|Intron 1:36341, Bcell:OA; 2:150977441, Bcell:HC; 2:151444499, PBMC:OA; 2:151469837, Mono:SLE; 2:151889577, PBMC:HC; 2:152831214, CACNB4||Intron 2:124021|Intron 2:124379|Proximal Promoter: -729, PBMC:OA; 2:154143677, PBMC:notRA; 2:154143768, PBMC:notRA; 2:155433424, PBMC:notRA; 2:157323390, GPD2||Intron l:30491|Intron 1:31426, Mono:SLE; 2:159651813, DAPLl||Proximal Promoter:-15, PBMC:notRA; 2:159736477, PBMC:HC; 2:161228737, RBMSl||Intron 1:121581, PBMC:notRA; 2:161236088, RBMSl||Intron 1:114230, Bcell:HC; 2:162095662, TANK||3' Proximal Enhancer: 102197|3' Proximal Enhancer:78724, PBMC:OA; 2:162101262, TANK||3' Proximal Enhancer:107797|3' Proximal Enhancer:84324, Mono:OA; 2:164590272, FIGN||Intron 2:2241, PBMC:HC; 2:166930521, SCNlA||Intron 2:75121|Proximal Promoter: -372, PBMC:OA_SLE_HC; 2:168673805, B3GALTl||Proximal Promoter:- 1376, PBMC:HC,PBMC:OA_SLE_HC; 2:168675205,
B3GALTl||Proximal Promoter:24, PBMC:HC; 2:169355957, CERS6||Intron 1:43123, PBMC:notRA; 2:169506620, Mono:SLE; 2:170264540, Bcell:OA; 2:173539091, Mono:OA_SLE_HC; 2:174024669, ZAK||Intron 2:84105, PBMC:HC; 2:174265733, PBMC:HC; 2:175594739, Bcell:OA; 2:176946509, EVX2||Intron 2:2181, Mono:OA_SLE_HC; 2:177503639, LOC375295||Proximal Promoter:-1337, PBMC:HC; 2:177518121, Bcell:HC; 2:182543706, NEURODl||Intron 1:1686, PBMC:notRA; 2:184395412, PBMC:notRA; 2:188269443, CALCRL||Intron 1:43578, PBMC:OA_SLE_HC; 2:190126396, PBMC:HC; 2:190192866, PBMCSLE; 2:190399258, Mono:HC; 2:190506593, Bcell:OA_SLE_HC; 2:191276183, MFSD6|| Intron 1:3103, PBMC:HC; 2:191401926, TMEM194B||Proximal Promoter: -2458, PBMC:notRA; 2:192198841, MY01B||Intron 4:88588|Intron 4:88735, Bcell:HC; 2:197070128, HECW2||Intron 28:387207, Tcell:OA; 2:197122104, HECW2||Intron 18:335231, PBMC:OA_SLE_HC,PBMC:notRA; 2:198062750, ANKRD44||Intron 1:112771, PBMC:HC; 2:198077081, ANKRD44||Intron 1:98440, PBMC:HC; 2:198134173, ANKRD44||Intron 1:41348, PBMC:HC; 2:198379584, HSPEl-MOB4||Intron 2:14864,MOB4||Proximal Promoter:- 1182|Proximal Promoter:-1437|Proximal Promoter: -710, Tcell:HC,Tcell:OA_SLE_HC; 2:198383542, HSPE1- MOB4||Intron 2:18822,MOB4||Intron l:2521|Intron l:2776|Intron 1:3248, PBMC:notRA; 2:200718119, FONG||Proximal Promoter:-2223, PBMC:OA; 2:200778865, C2orf69|| Intron 1:2887, PBMCnotRA; 2:201173897, SPATS2L||Intron l:2542|Intron l:2913|Intron 1:3294, Tcell:SLE; 2:201194453, SPATS2L||Intron 2:23098|Intron 2:23469|Intron 2:23850, Tcell:OA_SLE_HC; 2:201242945, SPATS2L||Intron 2:71590|Intron 2:71961|Intron 2:72342, Bcell:SLE,Tcell:SLE; 2:201245077, SPATS2L||Intron 2:73722|Intron 2:74093 |Intron 2:74474, PBMC:SLE,Tcell:SLE; 2:201289756, SPATS2L||Intron 6:118401|Intron 6:118772|Intron 6:119153, PBMCnotRA; 2:201601406, AOX2P||Intron 5:40961,LOC100507140||Proximal Promoter:- 1506, PBMCnotRA; 2:202163482, ALS2CR12||Intron 12:58619, PBMC:HC,PBMC:OA_SLE_HC; 2:202484320, ALS2CRll||Proximal Promoter: - 415,TMEM237||3' Proximal Enhancer:23090|3' Proximal Enhancer:23904, Bcell:OA_SLE_HC; 2:203134514, NOP58||Intron 1:4000,SNORD70||5' Proximal Enhancer:-6639, PBMC:notRA; 2:203504161, FAM117B||Intron 1:4261, Bcell:HC; 2:203639072, FAM117B||3' Proximal Enhancer:139172,ICAlL||Exon 14:97299, PBMC:notRA; 2:203642154, FAM117B||3' Proximal Enhancer: 142254,ICAlL||Exon 14:94217, PBMC:HC,PBMC:OA_SLE_HC; 2:204570033, CD28||Proximal Promoter:- 1164, PBMC:HC; 2:207147089, ZDBF2||Intron 3:7567, Mono:OA_SLE_HC; 2:207307150, ADAM23||Proximal Promoter: - 1217, PBMC:OA_SLE_HC; 2:207847811, Mono:SLE; 2:208027870, BcelhSLE; 2:208572165, CCNYLl||Distal Promoter: -4098, PBMC:HC; 2:20869434, GDF7||Intron 1:3011, PBMC:OA_SLE_HC; 2:209271875, PTH2R||Proximal Promoter:320, Mono:OA_SLE_HC; 2:21266995, APOB||Proximal Promoter:-50, Tcel HC; 2:213406960, PBMC:OA_SLE_HC; 2:213969340, IKZF2||Intron 3:45718|Intron 4:46993, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Mono:SLE; 2:214017104, IKZF2||Proximal Promoter: - 2046|Proximal Promoter:-771, PBMC:HC,PBMC:notRA; 2:218048915, PBMC:notRA; 2:21869305, PBMC:OA_SLE_HC; 2:218842585, Bcel HC; 2:218933280, CXCR2P1||5' Proximal Enhancer: - 7267,RUFY4||Intron 3:33624|Proximal Promoter: -457, PBMCnotRA; 2:219001517, CXCR2||Exon 3:10782|Exon 4:11505, PBMC:notRA; 2:219610103, TTLL4||Intron 6:34536, PBMC:HC; 2:219841474, FEV||3' Proximal Enhancer:8905,LOC151300||Proximal Promoter:469, Tcell:OA_SLE_HC; 2:220007315, NHEJl||Intron 5:18272, PBMC:notRA; 2:220381734, ACCN4||Intron 1:2843, PBMC:SLE; 2:220716794, PBMC:notRA; 2:224806760, WDFYl||Intron 1:3292, TcelhHC; 2:224897425, SERPINE2|| Intron l:5932|Intron 1:6611, PBMC:notRA; 2:225244609, FAM124B||Exon 2:Exon 3:22102, PBMC:SLE; 2:225266843, FAM124B||Proximal Promoter: -132, BcelhHC; 2:230876010, FBX036||Exon 4:88804, PBMC:notRA; 2:231089641, SP110||Distal Promoter:-4814|Intron l:803,SP140||Proximal Promoter:-803, BcelhOA; 2:231658979, CAB39||Intron 4:80717|Intron 4:81423, PBMC:HC,PBMC:OA_SLE_HC; 2:231714995, Mono:OA_SLE_HC; 2:232186992, ARMC9|| Intron 19: 123651, BcelhSLE; 2:232213012, ARMC9||3' Proximal Enhancer: 149671, PBMC:HC; 2:232263126, B3GNT7||Exon 2:2792, PBMC:notRA; 2:232393064, NMURl ||Exon 2:2118, PBMC:HC; 2:232393196, NMURl ||Exon 2: 1986, PBMC:HC; 2:233246431, ALPP||Exon 11 :3084,ECEL1P2||3' Proximal Enhancer:5323, PBMC:HC; 2:233351921, ECELl ||Intron 1 :611, PBMC:notRA; 2:233412831, CHRNG||3' Proximal Enhancer:8395,EIF4E2||Distal Promoter: -2525,TIGDl ||Exon 1 :2395, PBMC:notRA; 2:23358444, PBMC:notRA; 2:234775274, MSL3Pl ||Exon 2: 1781, PBMC:notRA; 2:235408237, ARL4C|| Distal Promoter:-2544, PBMC:SLE; 2:235902088, SH3BP4||Intron 1 :41461, PBMC:OA; 2:235952729, SH3BP4|| Intron 4:92102, Mono:HC; 2:236923454, AGAPl ||Intron 12:Intron 13:520722, PBMC:HC,PBMC:OA_SLE_HC; 2:236923534, AGAPl ||Intron 12:Intron 13:520802, PBMC:OA_SLE_HC; 2:236963462, AGAPl ||Intron 15:Intron 16:560730, PBMC:OA_SLE_HC; 2:237027592, AGAPl ||Intron 15:Intron 16:624860, PBMC:notRA; 2:237035495, AGAPl ||Exon 17:Exon 18:632763, Mono:OA; 2:237083222, GBX2||5' Proximal Enhancer: - 6570, Tcell:HC; 2:237592822, PBMC:notRA; 2:238341793, PBMC:HC; 2:238350541, PBMC:HC; 2:238380390, PBMC:notRA; 2:23839710, KLHL29||Intron 3:231413, PBMC:SLE; 2:23840268, KLHL29||Intron 3:231971, PBMC:SLE; 2:23840282, KLHL29|| Intron 3:231985, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 2:238410067, MLPH||Intron 2: 14190, PBMC:OA_SLE_HC; 2:238500081, RAB17||Proximal Promoter: -312, PBMC:OA_SLE_HC; 2:23851985, KLHL29||Intron 3:243688, PBMC:SLE; 2:23852064, KLHL29||Intron 3:243767, PBMC:OA_SLE_HC,PBMC:SLE; 2:239008943, ESPNL||Proximal Promoter:-7,SCLY||3' Proximal Enhancer:39379,UBE2F-SCLY||3' Proximal Enhancer: 133357, Mono:HC; 2:239140024, HES6||3' Proximal Enhancer:8657,LOC151174||Proximal Promoter:294,LOC643387||Proximal Promoter:-302, PBMC:notRA; 2:239140032, HES6||3' Proximal Enhancer:8649,LOC151174||Proximal
Promoter:286,LOC643387||Proximal Promoter: -294, PBMC:notRA; 2:239140182, HES6||3' Proximal Enhancer:8499,LOC151174||Proximal Promoter: 136,LOC643387||Proximal Promoter:-144, PBMC:notRA; 2:239140190, HES6||3' Proximal Enhancer:8491,LOC151174||Proximal
Promoter: 128,LOC643387||Proximal Promoter:-136, PBMC:notRA; 2:240019103, PBMC:SLE; 2:240020028, PBMC:OA_SLE_HC,PBMC:notRA; 2:240153791, PBMC:HC,PBMC:OA_SLE_HC; 2:240362425, PBMC:OA_SLE_HC; 2:240751167, PBMC:OA_SLE_HC; 2:240872433, MIR4786||3' Proximal Enhancer: 10078, PBMC:notRA; 2:240874769, MIR4786||3' Proximal Enhancer:7742, PBMC:HC,PBMC:OA_SLE_HC; 2:240884925, MIR4786|| Proximal Promoter: -2414, PBMC:HC; 2:240965916, NDUFA10||Proximal Promoter:-1097,OR6B2||3' Proximal Enhancer:3930, PBMC:notRA; 2:241262389, BcelhHC; 2:241389258, GPCl ||Intron 1 : 14144,MIR149||5' Proximal Enhancer: - 6159,PP14571 ||Exon 2:6859, PBMC:notRA; 2:24162256, UBXN2A||Proximal Promoter:-l 119, PBMC:HC; 2:241807859, AGXT|| Proximal Promoter: -302, PBMC:HC; 2:241834907, C2orf54||Distal Promoter: -3455|Exon 1 :666, PBMC:OA_SLE_HC; 2:241900108, LOC200772||Intron 3:6760, Bcell:OA_SLE_HC; 2:241975140, SNEDl ||Intron 4:36886, PBMC:HC; 2:242003078, SNEDl pxon 18:64824, Bcell:SLE,Mono:SLE,PBMC:SLE,PBMC:notRA; 2:242174797, HDLBP||Intron 22:37449|Intron 22:80318, PBMC:HC; 2:242490217, BOK||5' Proximal Enhancer:-7928,BOK-ASl ||Intron 1:8341, PBMC:notRA; 2:242556858, THAP4|| Intron 2: 19867|Proximal Promoter:58, Tcell:OA_SLE_HC; 2:242702553, D2HGDH||Intron 9:28524, PBMC:HC; 2:242769324, PBMC:OA; 2:242802009, CXXC11 ||5' Proximal Enhancer:-9876,PDCDl ||Proximal Promoter:-951, PBMC:HC; 2:242843504, PBMC:notRA; 2:242881634, Tcell:OA_SLE_HC; 2:242887344, PBMC:HC; 2:242904738, PBMC:SLE; 2:242904768, PBMC:SLE; 2:242927047, PBMC:OA; 2:24307957, SF3B14||5' Proximal Enhancer: - 8643,TP53I3||Proximal Promoter:-756|Proximal Promoter: 128, PBMC:HC; 2:24367828, LOC375190||Intron 5:21479, PBMC:notRA; 2:25964061, ASXL2||Exon 12: 137251, PBMC:HC; 2:26213508, KIF3C||5' Proximal Enhancer:-8065, PBMC:HC; 2:26635591, CCDC164||Intron 1 : 10808, Mono:SLE; 2:27233872, MAPRE3||Intron 1 :40348, PBMC:HC; 2:27301943, AGBL5||3' Proximal Enhancer:27453,EMILINl ||Exon 1 :509,KHK||5' Proximal Enhancer:-7667,OST4||5' Proximal Enhancer: - 7376, PBMC:HC,PBMC:OA_SLE_HC; 2:2732624, PBMC:HC,PBMC:OA_SLE_HC; 2:27988724, MRPL33||5' Proximal Enhancer:-5859, Mono:HC; 2:28497669, PBMC:HC; 2:30371484, YPEL5||Intron l :Intron 2: 1735, PBMC:HC; 2:30371990, YPEL5||Intron l :Intron 2:2241, PBMC:HC; 2:30457110, LBH||Intron 1 :2714, PBMC:HC; 2:30458365, LBH||Intron 2:3969, PBMC:HC; 2:3063115, Wholeblood:notRA; 2:31378999, Tcel HC; 2:31397283, CAPN14||Exon 22:43128, PBMC:HC; 2:31806234, SRD5A2||Proximal Promoter:-194, PBMC:notRA; 2:31806275, SRD5A2||Proximal Promoter:-235, PBMCnotRA; 2:3184399, TSSC1 ||3' Proximal Enhancer: 197254, PBMC:notRA,Tcell:HC; 2:33359529, LTBPl ||Intron 4: 187161 |Proximal Promoter: -134, PBMC:HC; 2:33359688, LTBPl ||Intron 4: 187320|Proximal Promoter:25, PBMC:HC; 2:33905480, PBMC:SLE; 2:33954043, MYADML|| Proximal Promoter: -759, PBMC:notRA; 2:37035865, VIT||Exon 13:Exon 14:Exon 15: 112033, PBMC:SLE; 2:3704530, ALLC|| Proximal Promoter:-1255, PBMC:HC; 2:37416819, LOC100505876||5' Proximal Enhancer:-6815,SULT6Bl ||Proximal Promoter:-! 129, PBMC:HC; 2:37418009, LOC100505876||5' Proximal Enhancer:-5625,SULT6Bl ||Proximal Promoter: -2319, Mono:HC; 2:37551108, PRKD3||5' Proximal Enhancer:-6886, Tcell:OA_SLE_HC; 2:3776067, PBMC:OA_SLE_HC; 2:38070667, TcelhOA SLE HC; 2:3828216, PBMC:HC; 2:3828286, PBMC:OA_SLE_HC; 2:38892846, GALM||Proximal Promoter:-205, Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:notRA,Tcell:SLE; 2:38892887, GALM||Proximal Promoter:- 164,
Mono:OA_SLE_HC,Mono: SLE,PBMC:OA_SLE_HC,PBMC: SLE; 2:38892901 , GALM| |Proximal Promoter:-150, Mono:HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE; 2:38893237, GALM||Proximal Promoter: 186, PBMCSLE; 2:38893251, GALM|| Proximal Promoter:200, PBMC:OA_SLE_HC,PBMC:SLE; 2:38893519, GALM|| Proximal Promoter:468, PBMC:SLE; 2:38976288, SRSF7||Intron 3:2348, PBMC:notRA; 2:39003850, GEMIN6|| Proximal Promoter: -1476, PBMCnotRA; 2:39812572, LOC728730||Intron 5: 148016, PBMC:HC; 2:42123725, LOC388942||3' Proximal Enhancer: 19031, PBMC:HC; 2:42303177, PBMC:SLE,PBMC:notRA; 2:42345201, PBMC:HC; 2:426252, PBMC:SLE; 2:4295357, PBMC:OA_SLE_HC; 2:43023945, HAAO||Distal Promoter: -4194, PBMC:HC; 2:43041125, PBMC:notRA; 2:43158610, Bcell:HC,PBMC:HC; 2:43195545, PBMC:HC; 2:43278552, PBMC:notRA; 2:43398079, PBMC:SLE; 2:43398171, PBMC:SLE; 2:43398339, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2:43405947, PBMC:HC; 2:45159457, SIX3||5' Proximal Enhancer:-9579, Tcell:OA; 2:45234140, SIX2||Intron 1 :2402, PBMC:OA; 2:45239247, SIX2||Distal Promoter:-2705, Tcell:HC; 2:47008202, Bcell:HC; 2:47100912, PBMC:HC; 2:47716097, MSH2||3' Proximal Enhancer:85835, Mono:SLE; 2:47750631, KCNK12||Intron 1 :46839, PBMC:HC,PBMC:notRA; 2:47798396, KCNK12||Proximal Promoter:-926, PBMC:OA; 2:48401950, PBMC:HC; 2:506174, PBMC:OA; 2:51378948, PBMC:notRA; 2:52796128, PBMC:notRA; 2:55281781, RTN4||5' Proximal Enhancer:-5455|Distal Promoter: -4047, Mono:HC; 2:55393977, C2orf63||3' Proximal Enhancer:65472|3' Proximal Enhancer:65722, PBMC:OA_SLE_HC; 2:55450823, C2orf63||Intron l :8876|Intron 2:8626,RPS27A||5' Proximal Enhancer:-8215|5' Proximal Enhancer:-8717|5' Proximal Enhancer:-8990, PBMC:OA_SLE_HC; 2:55919983, PNPTl ||Intron 1 : 1028, Tcell:SLE; 2:56216320, MIR216A||Proximal Promoter:-126,MIR217||5' Proximal Enhancer:-6109, PBMCnotRA; 2:58989427, FLJ30838||Intron 2:241540, BcelhOA SLE HC; 2:593391, PBMC:HC; 2:60815558, PBMC:notRA; 2:60983087, PAPOLG||Proximal Promoter: -277, PBMC:SLE; 2:61153802, REL||3' Proximal Enhancer:45051, PBMC:OA_SLE_HC; 2:61991905, PBMC:OA; 2:63843856, MDH1 ||3' Proximal Enhancer:27572|3' Proximal Enhancer:28114, PBMC:HC; 2:63849775, PBMC:notRA; 2:64440295, LINC00309||5' Proximal Enhancer:-7676, PBMC:HC; 2:64885581, SERTAD2||Distal Promoter: -4535, PBMC:HC; 2:65212362, SLClA4||Distal Promoter:-3216|Distal Promoter:-4132,
Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 2:65861662, PBMCSLE; 2:662396, TMEM18||3' Proximal Enhancer: 15043, BcelhSLE; 2:66648797, PBMC:OA_SLE_HC; 2:66657913, MEISl ||Distal Promoter: -4618, BcelhOA; 2:66664960, MEISl ||Exon 2:2429, Bcel OA; 2:66763598, MEISl ||Intron 8: 101067, PBMC:OA; 2:66770400, MEISl ||Intron 8: 107869, PBMC:notRA; 2:6910518, LINC00487||Proximal Promoter:-76,
Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 2:6952860, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2:69812277, PBMC:OA_SLE_HC,PBMC:SLE; 2:7004578, CMPK2||Intron 1 : 1358, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC;
2:7006627, CMPK2||Proximal Promoter: -691, PBMC:SLE; 2:70106252, GMCLl pxon 14:49435, PBMC:notRA; 2:70175826, MXD1 ||3' Proximal Enhancer:33654, Wholeblood:notRA; 2:70268913, PCBPl-ASl ||Intron 6:45234, PBMC:HC; 2:71558577, ZNF638||Proximal Promoter:-307, PBMC:notRA; 2:71695338, DYSF||Intron l : 14586|Intron 1 : 1507, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 2:7171869, RNF144A||Intron 8: 114347, Mono:OA; 2:731298, PBMC:notRA; 2:73144353, EMXl ||Proximal Promoter: -250, PBMC:notRA; 2:731519, PBMC:notRA; 2:731561, PBMC:notRA; 2:731594, PBMC:notRA; 2:73215647, SFXN5||Intron 9:83318, PBMCnotRA; 2:73429084, NOTO|| Proximal Promoter:-301, PBMC:notRA; 2:73964834, TPRKB||Proximal Promoter: -317, PBMC:HC; 2:74210857, Mono:OA; 2:74280825, TET3||Intron 1 :7376, PBMC:HC; 2:74669387, RTKN||Proximal Promoter: - 1677|Proximal Promoter:-327, PBMC:HC; 2:74697095, CCDC142||3' Proximal Enhancer: 13262,INO80B- WBP1 ||3' Proximal Enhancer: 14946,MOGS||Distal Promoter:-4558,MRPL53||3' Proximal Enhancer:2847,WBPl ||3' Proximal Enhancer: 11569, PBMC:OA_SLE_HC,PBMC:notRA; 2:74811430, C2orf65||Intron 4:63734, PBMC:notRA; 2:74981960, PBMC:notRA; 2:792213, LOC339822||Intron 3:71899, PBMC:OA_SLE_HC,PBMC:SLE; 2:7975491, PBMC:HC; 2:82120996, Bcel HC; 2:8453529, LINC00299||Intron 2: 15020, PBMC:HC; 2:85060011, C2orf89|| Intron 3:48241, Mono:HC; 2:85153928, PBMC:OA; 2:8628196, Mono:SLE; 2:87012810, CD8A||Exon 5:Exon 6:Exon 7:6027|Exon 9:22709,RMND5A||3' Proximal Enhancer:65397, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2:87015813, CD8A||Intron 3:Intron 4:Intron 5:3024|Intron 7: 19706, Tcell:OA_SLE_HC; 2:87019612, CD8A||Intron 3: 15907|Proximal Promoter: -775, Tcell:OA_SLE_HC; 2:87020937, CD8A||Intron 3: 14582|Proximal Promoter:-2100, Tcell:OA_SLE_HC; 2:87048489, CD8B||Intron 3:Intron 4:Intron 5:Intron 6:40558, Tcell:OA_SLE_HC; 2:87048747, CD8B||Intron 3:Intron 4:Intron 5:Intron 6:40300, PBMC:OA_SLE_HC,PBMC:SLE; 2:8724414, PBMC:HC; 2:875437, PBMC:notRA; 2:87572542, Bcell:OA_SLE_HC; 2:88124876, RGPDl||Intron l: 160433,RGPD2||Proximal Promoter:410, PBMC:notRA; 2:8818497, ID2||Distal Promoter:-3615, Mono:OA; 2:8819139, ID2||Distal Promoter: -2973, PBMC:notRA; 2:88390376, MIR4780||5' Proximal Enhancer:-8258,SMYDl||Intron 3:23078, Mono:OA; 2:88583845, Mono:HC; 2:88826245, C2orf51||Intron 3:2077, PBMC:notRA; 2:89060884, ANKRD36BP211 Distal Promoter:-4534, Tcell:SLE; 2:89128093, PBMC:notRA; 2:91638344, PBMC:notRA; 2:91758369, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 2:91816806, LOC654342||3' Proximal Enhancer:31169, PBMC:HC,Wholeblood:notRA; 2:91844528, LOC654342||Intron 1:3447, PBMC:HC; 2:91932949, PBMC:OA_SLE_HC; 2:92031119, PBMC:notRA; 2:92276136, PBMCnotRA; 2:9283270, Tcell:OA; 2:928720, PBMC:OA_SLE_HC,PBMC:notRA; 2:928750, PBMC:HC,PBMC:notRA; 2:9409242, ASAP2||Intron 1:62349, Wholeblood:notRA; 2:95529853, ANKRD20A8P||5' Proximal Enhancer:-7033,LOC442028||3' Proximal Enhancer: 83234,TEKT4||5' Proximal Enhancer:-7378, PBMC:notRA; 2:95536219, LOC442028||Exon 10:76868,TEKT4||Proximal Promoter: - 1012, Wholeblood:notRA; 2:95537197, LOC442028||Intron 9:75890,TEKT4||Proximal Promoter:-34, Wholeblood:notRA; 2:95664359, Bcell:OA_SLE_HC; 2:95692352, MAL||Intron 1:874, PBMC:OA; 2:96830479, Bcel HC; 2:97166422, NEURL3||Exon 2:7424, PBMC:SLE; 2:97169033, NEURL3|| Intron 1:4813, Bcel HC; 2:97205147, ARID5A||Intron 1:2684, PBMC:HC; 2:97505599, ANKRD231 jlntron 7:4159,ANKRD39||3' Proximal Enhancer: 18157,C NM3||3' Proximal Enhancer:23609, Wholeblood:notRA; 2:98443701, TMEM131||Intron 11:168653, PBMC:notRA; 2:98827491, VWA3B||Intron 12:123897, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 3: 10052611, CIDECP||3' Proximal Enhancer:15209,LOC401052||Proximal Promoter: 168, PBMCnotRA; 3:100712058, ABI3BP||Proximal Promoter:276, PBMC:notRA; 3: 101901234, Mono:HC,PBMC:HC; 3:104238223, PBMC:notRA; 3: 10479218, PBMC:HC; 3: 107416903, BBX||Intron 3:175121, PBMC:notRA; 3: 10780469, PBMC:SLE; 3: 107805635, CD47||Intron 1:4300, Mono:HC,PBMC:HC,Tcell:HC; 3:108020727, HHLA2|| Proximal Promoter: -604, PBMC:HC; 3: 108021293, HHLA2|| Proximal Promoter:-38, PBMC:notRA; 3: 109128895, FLJ25363||Proximal Promoter:59, PBMC:notRA; 3: 11102832, PBMC:OA_SLE_HC; 3:111522050, PHLDB2||Intron l:70724,PLCXD2||Intron 3:Intron 4:128528,
Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 3: 111676660, PHLDB2||Intron l l:Intron 12:98634|Intron 12:225334|Intron 12:98093, PBMC:OA_SLE_HC; 3: 11211081, HRHl||Intron l: 14868|Intron 1:32303, PBMC:OA; 3:112218510, BTLA|| Proximal Promoter: -102, Mono:HC; 3:112693867, CD200Rl||Proximal Promoter:70, PBMC:OA_SLE_HC; 3: 113235015, SPICE l||Proximal Promoter:-981, Mono:OA_SLE_HC; 3: 113822317, PBMC:notRA; 3:114325713, PBMCnotRA; 3: 114864747, PBMC:SLE; 3: 115155686, Tcell:OA_SLE_HC; 3: 115837501, L SAMP || Intron 1:326884, PBMC:SLE; 3: 11643368, VGLL4||Exon 2:42030|Exon 3: 118852, Tcell:OA_SLE_HC; 3:118892305, UPKlB||Proximal Promoter:- 119, Tcel HC; 3: 119044523, ARHGAP311 |Intron 1:31304, Bcell:OA_SLE_HC; 3:119279147, CD80||Proximal Promoter: - 666, Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 3: 121491382, IQCBl||Intron l l:Intron 14:62544, PBMC:HC; 3: 121902499, CASR|| Proximal Promoter:-30|Proximal Promoter:-681, Bcel OA; 3:122281881, DTX3L|| Proximal Promoter:-1303,PARP9||Intron l: 1266|Intron l:1313|Intron 1: 1642, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 3:122281939, DTX3L||Proximal Promoter: - 1245,PARP9||Intron l:1208|Intron l:1255|Intron 1: 1584,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC;
3:122281975, DTX3L|| Proximal Promoter:-1209,PARP9||Intron l: 1172|Intron l:1219|Intron 1: 1548, PBMC:HC,PBMC:OA_SLE_HC; 3:122284215, DTX3L||Intron l: 1031,PARP9||Proximal Promoter: - 1021|Proximal Promoter: -10681 Proximal Promoter: -692, Bcell:OA_SLE_HC,Bcell:SLE; 3: 122400474, PARP14||Intron 1:803, Bcel SLE; 3:122401300, PARP14||Intron 1: 1629,
Bcell:OA_SLE_HC,Tcell:OA_SLE_HC; 3: 122401343, PARP14||Intron 1: 1672,
PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 3: 122509111, DIRC2||Distal Promoter: -4789,HSPBAPl||Intron 1:3555, PBMC:HC; 3: 123417080, MYLK||Intron 17:Intron 18: 186069, PBMC:notRA; 3: 123476518, MYLK||Intron 4: 126631, PBMC:SLE; 3:124306820, KALRN|| Intron l:3315|Intron 34:493263, PBMC:notRA; 3:124491657, ITGB5||Intron 11:114487, PBMC:HC; 3:12528629, TSEN2||Intron l:2620|Intron 1:2699, PBMC:notRA; 3:125896282, ALDHlLl||Intron 1:3203, PBMC:notRA; 3:12595473, LOC100129480||5' Proximal Enhancer:-8510,MKRN2||Distal Promoter: -3120,
PBMC:OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 3:12595696, LOC100129480||5' Proximal Enhancer: - 8733,MKRN2||Distal Promoter:-2897, PBMC:OA_SLE_HC; 3: 12595852, LOC100129480||5' Proximal Enhancer: - 8889,MKRN21 |Distal Promoter: -2741,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 3:126194923, UROCl||3' Proximal Enhancer:41693,ZXDC||Proximal Promoter:- 161, BcelhOA; 3: 126278943, C3orf22||Proximal Promoter:-! 185, Mono:OA_SLE_HC,Mono:OA_SLE_HC 12; 3: 126668502, CHCHD6||Intron 6:245385, PBMC:notRA; 3:127481599, MGLL|| Intron 3:60102|Intron 3:60452, PBMC:HC; 3: 128420513, PBMC:HC; 3:128484036, RAB7A||Intron 1:39058, PBMC:HC; 3: 12856409, CAND2||Intron 5:Intron 7: 18239, PBMC:OA; 3: 129118538, C3orf25||3' Proximal Enhancer:28956,RPL32P3||Proximal Promoter: -256, SNORA7B||Proximal Promoter:-2347, Bcell:OA; 3: 129147694, C3orf25||Proximal Promoter: -200,MBD4||3' Proximal Enhancer: 11158, PBMC:SLE; 3: 129155354, C3orf25||5' Proximal Enhancer:-7860,IFT122||Distal Promoter:-3613,MBD4||Exon 3:3498, PBMC:notRA; 3:129160135, IFT122||Intron 1:1168,MBD4||Proximal Promoter:-1283, PBMC : SLE,PBMC :notRA; 3:129160154, IFT122||Intron 1:1187,MBD4||Proximal Promoter:- 1302, PBMC:SLE,Tcell:OA_SLE_HC; 3:12937954, IQSEC1||3' Proximal Enhancer:176663|3' Proximal Enhancer:71006, PBMC:HC; 3: 129384521, TMCCl||Intron 2:23054|Intron 4:214881|Intron 4:227898, PBMC:notRA; 3: 129694392, TRH||Intron 1:1279, PBMC:OA; 3:129722676, PBMC:notRA; 3:130171080, COL6A5||Intron 36:106722, PBMC:notRA; 3: 13019649, IQSECl||Intron 1:94968, BcelhOA SLE HC; 3: 13039396, IQSECl||Intron 1:75221, PBMCnotRA; 3:130682432, ATP2Cl||Intron 10:Intron l l:113064|Intron 1 l:68999|Intron 11:69141 |Intron 1 l:69528|Intron 12:69574|Intron 12:69598, PBMC:notRA; 3: 131081177, LOC339874||Intron 2:19142,NUDT16Pl||Proximal Promoter:460|Proximal Promoter:489, Tcell:OA; 3:133255001, Mono:SLE; 3:133294854, CDV3||Intron 2:1554|Intron 2:2421, PBMC:OA_SLE_HC; 3: 133744113, SLC02Al||Intron 1:4807, PBMC:notRA; 3: 134093850, AMOTL2||Proximal Promoter:-444, Mono:OA; 3:134282543, CEP63||Exon 12:Intron 1 l:77969|Exon 13:77647|Exon 16:77497, PBMC:notRA; 3:13462465, NUP210||Proximal Promoter:-656, PBMC:HC; 3: 13462496, NUP210||Proximal Promoter:-687, PBMC:HC; 3: 135702110, PPP2R3A||Intron 1:17596, Bcell:OA_SLE_HC; 3:13591084, FBLN2|| Proximal Promoter:460, Mono:HC; 3:136539113, TMEM22||Intron 1:1253, PBMC:OA; 3:136714183, IL20RB||Intron 5:37477, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE;
3: 137838021, A4GNT||3' Proximal Enhancer:13208,DZIPlL||5' Proximal Enhancer:-5699|Distal Promoter: - 3570, Mono:OA; 3: 138065751, MRAS||Proximal Promoter:-1756|Proximal Promoter:-1940|Proximal Promoter: -2218|Proximal Promoter:-738, PBMC:notRA; 3: 138085169, MRAS||Intron l:17200|Intron l: 17478|Intron l: 17662|Intron 1: 18680, Tcell:OA; 3: 138660387, C3orf72||5' Proximal Enhancer: - 5688,FOXL2||3' Proximal Enhancer:5595, Bcell:SLE; 3:138668349, C3orf72||Intron l:2274,FOXL2||Proximal Promoter:-2367, Tcell:OA_SLE_HC; 3: 139970779, CLSTN2||Intron 2:316753, PBMC:SLE; 3: 140987789, ACPL2||Intron 2:Intron 4:37108, PBMC:OA_SLE_HC; 3: 141012746, ACPL2||Exon 6:Exon 8:62065, Tcell:HC; 3: 141456305, RNF7|| Proximal Promoter:-745, Mono:HC; 3: 141762780, TFDP2||Intron 3:Intron 4: 105606, PBMC:notRA; 3:142165032, ATR||3' Proximal Enhancer:132636,XRNl||Intron 1:1821, Bcell:SLE; 3: 142296671, ATR||Intron 1:997, Bcell:OA_SLE_HC; 3: 142296843, ATR||Intron 1:825, PBMC:HC; 3: 14320523, PBMC:HC; 3: 146187037, PLSCR2||Intron 1:2674 l|Proximal Promoter:51, PBMC:notRA; 3: 147112143, ZIC4||Intron 2:Intron 3:12453|Intron 3: 11164|Intron 3:9928|Proximal Promoter: -1926, Wholeblood:notRA; 3: 148708821, GYGl||Proximal Promoter:-373, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 3: 148846750, HPS3|| Proximal Promoter: -620, PBMC:HC; 3:149182974, TM4SF4||5' Proximal Enhancer:-9393, PBMC:notRA; 3: 149697815, LOC646903||3' Proximal Enhancer:8750,PFN2||5' Proximal Enhancer: -9074, PBMCnotRA; 3: 150329458, SELT||Intron 1:8393, PBMC:notRA; 3: 150420821, FAM194A||Intron 1:921, PBMC:SLE; 3: 150917888, GPR171||Intron 2:3100,MED12L||Intron 14:113213, PBMC:HC,Tcell:HC; 3:150921051, GPR171||Proximal Promoter:-63,MED12L||Intron 14:116376,P2RY14||3' Proximal Enhancer:45947|3' Proximal Enhancer: 75179, Mono:HC; 3:151058527, P2RY12||Exon 2:44017|Proximal Promoter:58, PBMC:HC; 3:151613372, Mono:SLE,PBMC:SLE,Tcell:SLE; 3: 152017240, MBNLl||Exon 2:31412|Proximal Promoter:47, Mono:SLE; 3: 152856773, PBMC:notRA; 3: 15311183, SH3BP5||Intron 4:62921|Intron 4:71718, TcelhSLE; 3:15377670, SH3BP5||Distal Promoter:-3566|Intron 1:5231, PBMC:notRA; 3:15384168, SH3BP5|| Proximal Promoter:-1267, TcelhOA; 3:155570809, SLC33Al||Intron 1: 1439, Wholeblood:notRA; 3: 155585263, GMPS||Distal Promoter:-3061, BcelhOA; 3: 155860278, KCNABl||Intron l:21942|Proximal Promoter:-472, PBMC:notRA; 3: 156543471, LEKR1|| Proximal Promoter:-624|Proximal Promoter:-676, Wholeblood:notRA; 3: 156544586, LEKRl||Proximal Promoter:439|Proximal Promoter:491, PBMC:SLE; 3:156807691, LOC100498859||Proximal Promoter:22,LOC339894||Intron 3:33100, BcelhOA; 3: 156848003, Mono:HC; 3: 157815145, SHOX2||Exon 5:Exon 6:8807, PBMC:HC; 3:157816403, SHOX2||Intron 4:Intron 5:7549, PBMC:HC; 3: 15919583, MIR563||3' Proximal Enhancer:4306, PBMC:notRA; 3:159557552, SCHIPl||Proximal Promoter: -97, PBMC:HC,PBMC:OA_SLE_HC; 3: 159557779, SCHIPl||Proximal Promoter: 130, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 3: 159558031, SCHIPl||Proximal Promoter:382, PBMC:HC,PBMC:OA_SLE_HC; 3: 159646501, PBMC:HC; 3:160121821, IFT80||Distal Promoter: - 4501,MIR15B||Proximal Promoter:-554,MIR16-2||Proximal Promoter:-711,SMC4||Intron 3:3475|Intron 4:4392, PBMC:OA_SLE_HC; 3:16577697, PBMC:HC; 3: 16712515, PBMC:notRA; 3: 167238645, WDR49||Intron 12:132644, PBMC:HC; 3:167370529, WDR49||Intron 1:760, Mono:SLE; 3:16843387, PBMC:HC; 3:169042374, MECOM||Intron l:Intron 2:339189, PBMC:HC; 3: 169531864, LRRC34||Proximal Promoter:-1290,LRRIQ4||5' Proximal Enhancer:-7845, Tcell:HC,Wholeblood:notRA; 3: 170136539, CLDNl l||Proximal Promoter:-l 13|Proximal Promoter: -2488,
Mono:HC,Mono:OA_SLE_HC; 3: 171685460, PBMC:notRA; 3: 171755923, FNDC3B|| Proximal Promoter:-1494|Proximal Promoter: -2420, PBMC:HC; 3: 171759519, FNDC3B||Intron l:1176|Intron 1:2102, PBMC:HC; 3: 171805805, FNDC3B||Intron l:47462|Intron 1:48388, Bcell:OA_SLE_HC; 3: 173302303, NLGNl||Intron 2:186060, Tcell:OA; 3:175554437, Mono:OA_SLE_HC; 3: 176741225, TBLlXRl||Exon 16: 173823, PBMC:notRA; 3:177309023, PBMC:SLE; 3:177352093, PBMC:notRA; 3:177391387, PBMC:HC; 3:178984841, KCNMB3||5' Proximal Enhancer:-7162|Proximal Promoter:-3, PBMC:OA_SLE_HC; 3: 178984910, KCNMB3||5' Proximal Enhancer:-7231|Proximal Promoter:-72, PBMC:OA_SLE_HC; 3: 179061771, MFNl||Distal Promoter:-3708,ZNF639||3' Proximal Enhancer:20221, Mono:OA; 3: 179501588, USP13||Intron 20:130656, PBMC:notRA; 3:180546915, PBMC:SLE; 3: 181412965, SOX2-OT||Intron 2:84815, PBMC:HC; 3:182876556, LAMP3||Intron 1:4111, PBMC:HC; 3: 182929273, MCF2L2||Intron 22:216582, Mono:HC; 3:183309985, PBMCSLE; 3: 183353451, KLHL24||Proximal Promoter:41, PBMC:notRA; 3:183533873, MAP6Dl||Exon 3:9520,YEATS2||3' Proximal Enhancer: 118268, TcelhHC; 3: 185476452, Wholeblood:notRA; 3: 185788716, ETV5||Intron 7:38185, PBMC:OA_SLE_HC,PBMC:SLE; 3:186718821, ST6GALl||Intron 2:70507, Mono:HC; 3: 186881368, PBMC:notRA; 3: 187336889, PBMC:OA_SLE_HC; 3:187942570, LPP||Intron l: 11850|Proximal Promoter:-622, PBMC:notRA; 3:188425256, LPP||Intron 6:482064|Intron 6:494536, PBMC:HC; 3: 189349323, TP63||Proximal Promoter: 108, PBMC:HC; 3:190683048, PBMC:notRA; 3: 192135072, FGF12||5' Proximal Enhancer:-8234|Intron 2:310316, PBMC:HC,PBMC:OA_SLE_HC; 3: 192577951, MB21D2|| Intron 1:57999, PBMC:OA_SLE_HC; 3:192634364, MB21D2||Intron 1: 1586, PBMC:OA; 3:193711643, LOC100128023||Proximal Promoter:384,LOC647323||Intron 1:9805, PBMC:notRA; 3:193921641, Wholeblood:notRA; 3: 193922037, Wholeblood:notRA; 3:194089473, LRRC15||Intron 1:999, PBMC:SLE; 3: 194797099, XXYLTl||Intron 3:194796, PBMC:HC; 3: 194868790, XXYLTl||Intron 3: 123105, PBMC:HC; 3:195268648, PPPlR2||Intron 1:1576, BcelhHC; 3:195576629, PBMC:HC; 3: 195632915, TNK2||Intron 1:2965, PBMC:OA_SLE_HC; 3: 195709661, SDHAPl ||Intron 5:7489, PBMC:notRA; 3:195750746, PBMC:notRA; 3:195943198, OSTalpha||Proximal Promoter:- 184,ZDHHC19||Distal Promoter: -4898, Mono:OA; 3:195943579, OSTalpha||Proximal Promoter: 197,ZDHHC19||5' Proximal Enhancer: -5279, PBMC:OA; 3:196325238, FBX045||3' Proximal Enhancer:29514, PBMC:HC,PBMC:OA_SLE_HC; 3:196325552, FBX045||3' Proximal Enhancer:29828, PBMC:HC; 3:196373751, LRRC33||Intron 1:7096, PBMC:HC; 3:196705629, PIGZ||5' Proximal Enhancer:-9925, PBMC:notRA; 3:196705742, PBMC:notRA; 3:196705855, PBMC:notRA; 3: 196705884, PBMC:notRA; 3: 196705898, PBMC:notRA; 3: 196757701, MFI2|| Proximal Promoter:- 1015, PBMC:notRA; 3: 197180978, Mono:HC; 3: 197812210, ANKRD 18DP| |Distal Promoter: -4668, PBMC:OA_SLE_HC; 3:197837441, PBMC:notRA; 3:19850542, Bcel HC; 3:19930780, EFHB||Intron 9:44926, PBMC:HC,PBMC:OA_SLE_HC; 3:21447391, VENTXP7|| Proximal Promoter:174, PBMC:notRA; 3:21584249, ZNF385D||Intron 3:208567, Wholeblood:notRA; 3:22412385, Mono:SLE; 3:22412746, Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 3:22413232, Mono:SLE,PBMC:SLE; 3:22422855, PBMC:OA_SLE_HC; 3:23782847, PBMC:HC,PBMC:OA_SLE_HC; 3:24034017, PBMC:HC; 3:25728479, PBMC:notRA; 3:26664308, LRRC3B||Proximal Promoter:9, Bcel OA; 3:28282245, CMCl||Proximal Promoter:-878, PBMC:HC,PBMC:OA_SLE_HC; 3:28389645, AZI2||Intron 1:973, PBMC:SLE; 3:29141029, BcelhOA; 3:30327579, PBMC:HC; 3:31935279, OSBPL10||Intron 1:88063, Mono:OA_SLE_HC,PBMC:OA,PBMC:OA_SLE_HC; 3:32015661, OSBPL10||Intron 1:7681,ZNF860||5' Proximal Enhancer: -7604, Mono:OA_SLE_HC; 3:36986992, TRANK1 ||Proximal Promoter: -444, PBMC:OA_SLE_HC; 3:37848209, ITGA9||Intron 27:354397, PBMC:HC; 3:39230226, XIRPlpxon 2:3851|Exon 2:3859, PBMC:OA; 3:39309355, CX3CRl||Intron l:12172|Intron l: 12575|Intron l: 13409|Intron 1: 13871, PBMC:HC; 3:39322541, CX3CRl||Intron 1:685 |Proximal Promoter: - 1014|Proximal Promoter:-61 l|Proximal Promoter:223, PBMC:SLE; 3:39452635, RPSA||Intron 3:3525|Intron 4:4432,SNORA6||3' Proximal Enhancer:2754,SNORA62||Proximal Promoter:91, PBMC:notRA; 3:42139507, TRAKl||Intron 1:6762, PBMC:notRA; 3:42544618, VIPRl||Intron l: 13828|Intron 1:515, PBMC:HC; 3:42976884, KRBOXl||Proximal Promoter:-949, PBMC:OA_SLE_HC; 3:42978026, KRBOXl||Proximal Promoter: 193, PBMC:HC; 3:44622831, ZNF167||3' Proximal Enhancer:Intron 5:26119,ZNF660||Distal Promoter:-3624, PBMC:notRA; 3:45268633, TMEM158||Proximal Promoter:-819, Mono:OA; 3:45957664, FYC01||3' Proximal Enhancer:79652, PBMC:HC; 3:45981161, CXCR6||Distal Promoter:-3811,FYC01||Intron 14:56155, Mono:OA; 3:46037592, PBMC:OA_SLE_HC,PBMC:SLE; 3:46600244, LRRC2||Intron 1:7796, PBMC:notRA; 3:46918266, PTH1R||5' Proximal Enhancer:-5472|Proximal Promoter: -969, PBMC:OA; 3:46996484, CCDC12||Intron 1:21786, PBMC:HC; 3:47517819, SCAP||Proximal Promoter:-374, PBMC:SLE; 3:4794020, EGOT||Proximal Promoter:-746,ITPRl||Intron 40:Intron 41:Intron 43:258989, PBMC:HC; 3:48412245, FBXW12||Proximal Promoter:-1463, PBMC:notRA; 3:48507087, ATRIP||3' Proximal Enhancer: 18870,SHISA5||3' Proximal Enhancer:34574,TREXl||Proximal Promoter:- 141, PBMC:HC; 3:48965611, ARIH2||Intron 3:9331,C3orf71||5' Proximal Enhancer:-8793, PBMC:notRA; 3:49396193, GPXl||Proximal Promoter: -402,RHOA||3' Proximal Enhancer:53333, PBMC:HC; 3:5023310, BHLHE40||Intron 4:2214, PBMC:notRA; 3:5024125, BHLHE40||Intron 4:3029, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 3:5065165, PBMC:HC; 3:51987688, GPR62||Proximal Promoter: -1641,PARP3 Proximal Enhancer: 11328,PCBP4||3' Proximal Enhancer: 13762|3' Proximal Enhancer:13794|3' Proximal Enhancer:9220, PBMC:HC; 3:52721831, GLT8D1||3' Proximal Enhancer: 15791 |3' Proximal Enhancer: 18217,GNL3||Intron 4:1896,PBRM1||5' Proximal Enhancer: - 8092|Proximal Promoter:-1965,SNORD19||Proximal Promoter:-1424,SNORD19B||Distal Promoter:- 2922,SNORD69||Distal Promoter: -4920, Bcel HC; 3:52828628, ITIH1||3' Proximal Enhancer: 14687|3' Proximal Enhancer: 14692|3' Proximal Enhancer: 16120|3' Proximal Enhancer: 17027,ITIH3||Proximal Promoter:-155, PBMC:notRA; 3:52865592, ITIH4|| Proximal Promoter:-875,MUSTNl||3' Proximal Enhancer:3643,TMEM110||3' Proximal Enhancer:66005,TMEMl 10-MUSTN1||3' Proximal Enhancer:66005, PBMC:notRA; 3:52909345, TMEMl 10||Intron 1:22252,TMEM110-MUSTNl||Intron 1:22252, Mono:HC; 3:53321205, DCPlA||Exon 10:60449, Mono:HC; 3:53321215, DCPlA||Exon 10:60439, Mono:HC; 3:54674405, CACNA2D3||Intron 10:517713,ESRG||Proximal Promoter: -521, Wholeblood:notRA; 3:55508460, WNT5A||Exon 4: 12871, PBMC:notRA; 3:55556197, ERC2||Intron 16:946194, PBMC:notRA; 3:55673955, ERC2||Intron 16:828436, PBMC:OA_SLE_HC; 3:55920018, PBMC:HC; 3:57530799, DNAH12||Proximal Promoter:-728, BcelhOA; 3:57680278, FAM116A||Proximal Promoter:-1462, PBMC:notRA; 3:58246371, ABHD6||Intron 2:23113, Tcel SLE; 3:58413668, PDHB||Exon 10:Exon l l:5911|Exon 9:5898,PXK||3' Proximal Enhancer:95052, PBMC:OA_SLE_HC; 3:58483777, ACOX2||3' Proximal Enhancer:39152,KCTD6||Intron l:5955|Proximal Promoter: -314, PBMC:notRA; 3:58509780, ACOX2||Intron 11:13149, Bcell:OA_SLE_HC; 3:59718904, Mono:OA_SLE_HC; 3:61237223, FHIT||Proximal Promoter: -90, PBMC:OA_SLE_HC; 3:63955727, ATXN7||Intron l:2308|Intron 4:71653 |Intron 5: 105495, PBMC:SLE; 3:64572729, ADAMTS9||Intron 28:100636, Mono:OA_SLE_HC; 3:66444122, LRIGl||Intron 12: 106723, PBMC:OA_SLE_HC; 3:66853898, PBMC:HC; 3:67705285, SUCLG2||Proximal Promoter:-247, PBMC:SLE; 3:68316096, FAM19Al||Intron 2:262738|Intron 2:275363, Wholeblood:notRA; 3:6904261, GRM7||Intron 1:1460, PBMC:OA; 3:69482656, Mono:SLE; 3:69997232, MITF||3' Proximal Enhancenlntron 4:11482|Intron 5: 18427 l|Intron 5: 184526|Intron 5:208647|Intron 5:81858, Bcel OA; 3:71804859, EIF4E3|| Proximal Promoter:-1327|Proximal Promoter:-935,GPR27||3' Proximal Enhancer: 1659, PBMC:HC; 3:72305082, Mono:OA_SLE_HC; 3:72440793, RYBP||Intron 1:54981, PBMC:HC; 3:75669109, PBMC:notRA; 3:75956119, Wholeblood:notRA; 3:78917133, ROB01||Intron 2: 151476|Intron 4:899926, BcelhHC; 3:79174694, ROB01||Intron 2:642365, Wholeblood:notRA; 3:8041501, PBMC:OA_SLE_HC; 3:81887543, Mono:HC; 3:8704494, PBMC:HC; 3:93780275, DHFRLlpxon 2: 1556|Exon 2: 1792,NSUN3||Proximal Promoter: -1579, PBMC:notRA; 3:96844879, EPHA6||Intron 3:311455, BcelhHC; 3:97887864, OR5H15||Proximal Promoter:321, PBMC:notRA; 3:9956823, IL17RC|| Proximal Promoter:-1934|Proximal Promoter:-1958,IL17RE||Intron 15:12312|Intron 16: 12528, PBMC:OA_SLE_HC; 4: 10009916, SLC2A9||Intron 2: 13198|Intron 3:31956, PBMC:OA_SLE_HC; 4: 100868748, DNAJB14||Proximal Promoter:-869,H2AFZ||3' Proximal Enhancer:2764,LOC256880||Distal Promoter: - 2887, BcelhHC; 4: 10101400, PBMC:HC; 4:103131830, PBMC:notRA; 4:103172826, SLC39A8||3' Proximal Enhancer:72643|3' Proximal Enhancer:93522|3' Proximal Enhancer:93829|Exon 11:93584, PBMC:notRA; 4: 103269584, SLC39A8||Distal Promoter: -2929|Distal Promoter:-3174|Distal Promoter: - 3236, PBMC:notRA; 4: 103740913, UBE2D3|| Intron l:49090|Intron l:7427|Intron 2:49119|Intron 2:7795|Intron 2:8192|Intron 2:8394, PBMC:HC; 4:104020949, BDH2||Proximal Promoter:75,CENPE||3' Proximal Enhancer:98617, PBMC:SLE; 4: 106009831, PBMC:notRA; 4:109034555, LEFl||Intron 3:53398|Intron 3:55557, Bcel OA; 4: 109038130, LEFl||Intron 3:49823|Intron 3:51982, Mono:HC; 4: 109087419, LEFl||Intron l:2693|Intron l:534,LOC641518||5' Proximal Enhancer:-5856|Proximal Promoter: -1261, Mono:OA_SLE_HC,Mono:SLE; 4:109994039, COL25Al||Intron 2:Intron 3:229484|Intron 3:229760, PBMC:HC; 4: 111531975, PITX2||3' Proximal Enhancer: 12279|3' Proximal Enhancer:31304, Mono:OA; 4:11157341, PBMC:SLE; 4: 11398983, HS3ST1||3' Proximal Enhancer:31554, Mono:HC; 4: 114238277, Wholeblood:notRA; 4:11431253, HS3STl||Proximal Promoter: -716, PBMC:HC; 4: 114694440, PBMC:notRA; 4:1166270, SPON2||Intron 2:729|Intron 3:36480|Proximal Promoter:387, Mono:OA; 4: 119888794, SYNP02|| Intron 1:78799, Bcell:OA_SLE_HC; 4: 1202694, CTBP1||3' Proximal Enhancer:40214,LOC100130872||Proximal Promoter:56,SPON2||Proximal Promoter:56, PBMC:notRA; 4: 120974344, MAD2L1||3' Proximal Enhancer: 13669, PBMC:HC; 4:121991645, NDNF||Intron 1:2028, PBMC:HC; 4:122078167, TNIP3||Intron 4:7328|Intron 7:59615|Intron 7:70454, PBMC:HC,PBMC:OA_SLE_HC; 4:122687481, PP12613||Exon l:1742,TMEM155||Proximal Promoter: - 1141, PBMC:HC; 4:123711095, PBMC:notRA; 4:124154293, SPATA5|| Intron 14:310069, Mono:SLE; 4: 124155479, SPATA5|| Intron 14:311255, Mono:SLE; 4: 124180616, SPATA5||Intron 15:336392, PBMC:HC; 4: 1243980, C4orf42||Exon 2:753,CTBPl||Proximal Promoter:- 1072, PBMC:HC; 4:124400196, Tcell:OA; 4:1244006, C4orf42||Exon 2:779,CTBPl||Proximal Promoter:- 1098, PBMC:HC; 4:1244017, C4orf42||Exon 2:790,CTBPl||Proximal Promoter:- 1109, Tcel HC; 4: 1244024, C4orf42||Exon 2:797,CTBPl||Proximal Promoter:-1116, Tcel HC; 4: 1244042, C4orf42||Exon 2:815,CTBPl||Proximal Promoter:- 1134, Tcell:HC; 4:1244086, C4orf42||Exon 2:859,CTBPl||Proximal Promoter:-1178, PBMC:HC; 4: 124694178, LOC285419||Intron 2: 120239|Proximal Promoter:-1240, PBMC:notRA; 4: 128800215, PLK4||Proximal Promoter:-1800|Proximal Promoter:-2183, PBMC:OA; 4:128981486, LARPlB||Proximal Promoter:- 1016, Bcell:OA_SLE_HC; 4:1291382, MAEA||Intron 1:7711, Mono:HC; 4: 1305425, MAEA|| Intron 1:21754, PBMC:SLE; 4: 134070416, PCDH10||Proximal Promoter:-53, PBMC:OA; 4:13538807, LOC285547||5' Proximal Enhancer:-5766,LOC285548||3' Proximal Enhancer:10641,NKX3-2||3' Proximal Enhancer:7307, Bcell:OA_SLE_HC; 4: 135865584, PBMC:notRA; 4: 139408972, PBMC:OA_SLE_HC; 4:139840467, PBMC:HC; 4:140620573, MGST2||Intron 2:Intron 3:33652, PBMC:notRA; 4:140952109, MAML3||Intron 1: 123124, PBMC:notRA; 4: 141079462, MAML3||Distal Promoter:-4229, Mono:SLE; 4:141490354, UCPl||Proximal Promoter:-395, PBMC:OA; 4: 141490428, UCPl||Proximal Promoter:-469, PBMC:OA; 4:142790226, PBMCnotRA; 4:144831061, GYPE||Distal Promoter:-4345, Mono:HC; 4:144833511, GYPE||5' Proximal Enhancer:-6795, Wholeblood:notRA; 4:144939574, GYPB||Intron 1:922, PBMC:notRA; 4:147866863, TTC29||Proximal Promoter:171, PBMC:notRA; 4: 148721238, PBMC:notRA; 4:148767763, Tcell:OA_SLE_HC,Tcell:SLE; 4: 149362435, NR3C2||Intron 1: 1237, PBMC:HC; 4:15007205, CPEB2||Intron l:2908,LOC441009||Distal Promoter:-3536, Bcell:OA_SLE_HC; 4:1520151, Tcell:HC; 4: 152097288, SH3D19||Intron 6:50372|Intron 6:51894|Proximal Promoter:-584, PBMC:notRA; 4: 152198109, PRSS48||Proximal Promoter: -215, PBMC:notRA; 4: 152249812, PBMC:notRA; 4:152329364, FAM160Al||Proximal Promoter:-1033, Mono:OA; 4:152996165, PBMC:HC,PBMC:OA_SLE_HC; 4:153896257, FHDCl||Exon 11:32123, Bcell:HC; 4: 154073616, TRIM2|| Proximal Promoter: -653, PBMCSLE; 4:154092267, TRIM2|| Intron 1: 17998, PBMC:OA_SLE_HC; 4: 154220167, ANXA2P1||3' Proximal Enhancer:9796,TRIM2||Intron 6: 145898|Intron 6:94570, PBMC:notRA; 4:154386540, KIAA0922||Proximal Promoter: -957, PBMC:HC,PBMC:OA_SLE_HC; 4: 154601692, TLR2|| Distal Promoter:-3748, PBMC:notRA; 4: 155548532, PBMC:SLE; 4:155662375, LRAT||Distal Promoter:-2787, PBMC:HC; 4:1558451, Wholeblood:notRA; 4:156134067, NPY2R||Intron 1:4287, PBMC:notRA; 4: 160118923, Mono:OA_SLE_HC; 4: 160299446, PBMC:notRA; 4:1607111, PBMC:OA_SLE_HC; 4:1607291, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 4: 16214868, TAPTl||Intron 2: 13293, PBMC:notRA; 4: 1625012, Wholeblood:notRA; 4: 1625181, Wholeblood:notRA; 4:163085403, FSTL5||Proximal Promoter: -217, Bcel OA; 4:165109574, ANP32C||3' Proximal Enhancer:9289,MARCHl||Intron 1: 194833, PBMC:notRA; 4: 165109834, ANP32C||3' Proximal Enhancer:9029,MARCHl||Intron 1:194573, PBMC:notRA; 4: 169239131, DDX60||Intron 1:827,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 4: 169242366, DDX60||Proximal Promoter:-2408, PBMC:SLE,Tcell:OA_SLE_HC; 4: 169791918, PALLD||Intron 10:373702|Intron 1:387631 Intron 9:239151, Bcell:OA,Bcell:OA_SLE_HC; 4:173905761, GALNTL6||Intron 10:1171187, PBMC:notRA; 4: 174430487, PBMC:OA; 4: 174431730, PBMC:HC; 4: 17580680, LAP3||Intron 1: 1754,
Bcell:OA_SLE_HC,Bcell:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 4:1762460, PBMC:notRA; 4: 1764152, Bcell:HC; 4: 176711190, GPM6A||Intron l:22992|Intron l:Intron 2:212458, PBMCnotRA; 4: 180982754, Mono:OA; 4:183062301, MGC45800||Exon 4:3367, PBMC:OA; 4: 183727013, ODZ3||3' Proximal Enhancer:481877, Bcell:OA; 4:183727862, ODZ3||3' Proximal Enhancer:482726, PBMC:HC; 4: 184578976, RWDD4||Intron l: 1355,TRAPPCl l||Proximal Promoter:-1443, PBMC:HC; 4:184680264, PBMC:notRA; 4: 185017300, ENPP6||Intron 7:121814, Bcell:HC; 4:185961240, PBMC:notRA; 4: 186048714, PBMC:OA; 4: 186732837, SORBS2||Exon l:555|Exon l:573|Intron l:145033|Proximal Promoter:-612|Proximal Promoter:-789, PBMC:OA_SLE_HC; 4: 186732932, SORB S2|| Intron l:144938|Proximal Promoter:-707|Proximal Promoter:-884|Proximal Promoter:460|Proximal Promoter:478, PBMC:OA_SLE_HC; 4:186733024, SORBS2||Intron 1: 1448461 Proximal Promoter:-799|Proximal Promoter: -976|Proximal Promoter:368|Proximal Promoter:386, PBMC:OA_SLE_HC; 4: 186960904, Mono:OA_SLE_HC; 4: 187125413, CYP4V2|| Intron 7: 12740, PBMC:notRA; 4:187751549, PBMC:notRA; 4: 187761401, Bcell:HC; 4:187855570, PBMC:HC; 4: 188140222, Wholeblood:notRA; 4: 188963324, Tcell:HC; 4:189042690, PBMC:notRA; 4: 189376704, LOC401164||Proximal Promoter: -27, PBMC:HC; 4: 190236439, PBMC:OA_SLE_HC; 4:190728249, PBMCnotRA; 4:190962794, PBMC:OA_SLE_HC; 4:204382, ZNF876P||Proximal Promoter:-2006, Bcell:SLE; 4:20852337, KCNIP4||Intron l:31996|Intron 1:453192|Intron l:693942|Intron l:846981|Intron 2: 1098037|Proximal Promoter:-46, Mono:OA; 4:20986246, KCNIP4|| Intron l:319283|Intron l:560033|Intron l:713072|Intron 2:964128, PBMC:SLE; 4:21546029, KCNIP4|| Intron l:153289|Intron 2:404345|Proximal Promoter:250, PBMC:SLE; 4:2341196, ZFYVE28||Exon 3:Exon 4:79174|Exon 4:25408, PBMC:HC,Tcell:HC; 4:23776092, Mono:HC; 4:23934534, PBMC:OA_SLE_HC; 4:23936764, PBMC:SLE; 4:2431872, LOC402160||Intron 2: 11172, PBMC:HC; 4:2432313, LOC402160||Intron 2: 11613, PBMC:HC; 4:24913973, CCDC1491| Intron l :627|Intron 1 :67853, TcelhHC; 4:25032305, LGI2|| Proximal Promoter: 109, Bcell:OA; 4:25487481, PBMC:notRA; 4:298277, ZNF732||5' Proximal Enhancer:-8333, PBMC:notRA; 4:3295736, PBMC:notRA; 4:3373006, RGS12||Intron l : 1283|Intron 3:57133, PBMC:notRA; 4:3464702, DOK7|| Proximal Promoter:- 330, PBMC:notRA; 4:3480318, DOK7||Intron 4: 15286, PBMC:OA_SLE_HC; 4:3486204, DOK7||Intron 4:21172, BcelhOA; 4:3736042, PBMC:notRA; 4:37585660, C4orfl9||Intron 2: 130109|Proximal Promoter:- 194,RELL1 ||3' Proximal Enhancer: 102339, PBMC:OA_SLE_HC; 4:37668528, RELLl ||Intron 1 : 19471, PBMC:HC,PBMC:OA_SLE_HC; 4:3785927, Mono:OA_SLE_HC; 4:38073835, PBMC:HC; 4:38667430, FLJ13197||Proximal Promoter:-l 181,KLF3||Intron 1 : 1641, PBMC:SLE; 4:38673130, FLJ13197||5' Proximal Enhancer:-6881,KLF3||Intron 1 :7341, PBMC : SLE,PBMC :notRA; 4:38871320, FAM114Al ||Intron l :Intron 2: 1967,MIR574||3' Proximal Enhancer: 1668, PBMC:OA; 4:39531927, UGDH||Distal Promoter: -2709, PBMC:notRA; 4:40267141, PBMC:SLE; 4:4117213, PBMC:notRA; 4:41314429, PBMC:HC; 4:41366989, LIMCHl ||Intron 1 :4186, PBMC:OA_SLE_HC,PBMC:SLE; 4:41430667, LIMCHl ||Intron 1 :67864, PBMC:OA_SLE_HC; 4:41540115, LIMCH1 || Intron 3: 177312, Mono:SLE; 4:41746614, PHOX2B||Exon 3:4373, BcelhOA; 4:42403471, ATP8A1 ||3' Proximal Enhancer:255651,SHISA3||Exon 2:3616, Mono:OA; 4:4310922, ZBTB49||Intron 4: 18999, PBMC:notRA; 4:43900946, PBMC:notRA; 4:43901032, PBMC:notRA; 4:43901084, PBMC:notRA; 4:44450358, KCTD8||Proximal Promoter:466, PBMC:OA; 4:47465011, COMMD8||Intron 1 :665, PBMC:SLE; 4:48045040, NIPAL1 ||3' Proximal Enhancer:26250, Mono:HC; 4:48136452, TEC||3' Proximal Enhancer: 135362,TXK||Proximal Promoter: -179, PBMC:HC; 4:48496404, FRYL||3' Proximal Enhancer:285912,SLC10A4||3' Proximal Enhancer: l 1045,ZARl ||Exon 4:4096, Bcel OA; 4:4867638, MSX1 ||3' Proximal Enhancer:6247, TcelhOA; 4:5374425, STK32B||Intron 4:320899, PBMC:OA_SLE_HC,PBMC:notRA; 4:54630659, PBMC:OA_SLE_HC; 4:55019140, PBMC:notRA; 4:55143269, PDGFRA||Intron 12:48006, PBMC:OA_SLE_HC; 4:55143285, PDGFRA||Intron 12:48022, PBMC:HC,PBMC:OA_SLE_HC; 4:56231727, LOC100506462||3' Proximal
Enhancer:20020,SRD5A3||Intron 3: 19340, Wholeblood:notRA; 4:56262833, TMEM165||Intron 1 :744, PBMC:notRA; 4:5637894, EVC2||Intron 10:72400|Intron 10:73381, Wholeblood:notRA; 4:56685972, LOC644145||Proximal Promoter: -264, PBMC:OA; 4:5754217, EVC||Intron 8:41294, Mono:OA; 4:57623913, PBMC:HC; 4:57824450, ΝΟΑ1 ||3' Proximal Enhancer: 19376, PBMC:HC,Tcell:HC; 4:58061859, LOC255130||Intron 2:85932, PBMC:notRA; 4:58309519, PBMC:OA_SLE_HC; 4:5889238, CRMPl ||Intron l : 1077|Intron 1 :5547, BcelhOA; 4:5991345, PBMC:OA; 4:62707027, LPHN3||Intron 6:344189, PBMC:HC; 4:6537163, PPP2R2C||Intron l :20242|Intron 1 :28164, PBMC:notRA; 4:66534326, EPHA5||Intron l : 1327,LOC100144602||Proximal Promoter:-1352, TcelhOA; 4:66536550, EPHA5||Proximal Promoter:-897,LOC100144602||Intron 1 :872, PBMC:OA; 4:6659735, PBMC:notRA; 4:6695614, S100P||Proximal Promoter:49, PBMC:HC; 4:6717681, CNO||Proximal Promoter: - 160,MRFAP1L1 ||5' Proximal Enhancer:-6075, PBMC:notRA; 4:68424256, STAPl ||Proximal Promoter:- 189, PBMC:notRA; 4:69207281, YTHDCl ||Intron 1 :8543, Mono:OA; 4:6940915, TBClD14||Intron 2:2942 l |Intron 2:29745, Mono:OA; 4:6988209, TBClD14||Intron 3:76715|Intron 3:77039|Proximal Promoter:-679, Tcel HC; 4:70626128, SULTlBl ||Proximal Promoter:302, Tcell:OA_SLE_HC; 4:710272, PCGF3||Intron 1 : 10700, Tcel OA; 4:71382958, AMTN|| Proximal Promoter:- 1339, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 4:71557171, UTP3||3' Proximal Enhancer:2976, Mono:SLE; 4:71587640, RUFY3||Intron l : 16987|Proximal Promoter:-55, Mono:HC; 4:72248830, SLC4A4||Intron 3:44061 |Intron 6: 195828, TcelhOA; 4:736485, PCGF3||Intron 6:36913, PBMC:notRA; 4:74486558, RASSF6||Proximal Promoter:-218|Proximal Promoter: -424, PBMC:SLE; 4:74853779, CXCL5||3' Proximal Enhancer: 10637,PF4||5' Proximal Enhancer: -6064,PPBP||Proximal Promoter: 128, Mono:OA; 4:74865270, CXCL5||Proximal Promoter:-854, BcelhHC; 4:74920559, PPBPL2||Exon 1 :557, Bcell:OA_SLE_HC; 4:7512425, Wholeblood:notRA; 4:7518360, PBMC:notRA; 4:76438412, RCHYl ||Intron l : 1228,THAP6||Proximal Promoter: -1241, PBMC:notRA; 4:7648627, PBMC:notRA; 4:7735312, PBMC:OA_SLE_HC; 4:77618676, Tcell:OA_SLE_HC,Tcell:SLE; 4:7810640, AFAPl ||Intron 9: 131013, PBMC:notRA; 4:786718, CPLXl ||Intron 2:33227, PBMC:notRA; 4:79102901, FRASl ||Intron 2: 124178, PBMC:notRA; 4:79103244, FRASl ||Intron 2: 124521, PBMC:notRA; 4:81953202, BMP3||Intron 1 : 1084, Mono:OA; 4:82283507, Mono:HC; 4:8230689, SH3TCl ||Intron 12:29630, PBMC:HC; 4:8268962, HTRA3||Distal Promoter:-2526, PBMCnotRA; 4:83323642, PBMC:notRA; 4:8374429, ACOX3||Intron 15:Intron 16:68023, Mono:OA_SLE_HC; 4:8527460, PBMC:notRA; 4:8569129, PBMC:HC; 4:8643029, PBMC:HC; 4:87282697, MAPK10||Intron l :91586|Proximal Promoter:-1322,
PBMC:HC,PBMC:OA_SLE_HC; 4:87374944, MAPK10||Proximal Promoter:-661, PBMC:notRA; 4:88364394, NUDT9||Intron 3:Intron 4:20667|Intron 4:20646, PBMC:notRA; 4:89299173, HERC6||Proximal Promoter: -717, PBMC:OA_SLE_HC; 4:89299874, HERC6||Proximal Promoter:-16, Tcell:SLE; 4:89302999, HERC6||Intron 1 :3109, PBMC:SLE,Tcell:OA_SLE_HC; 4:90816310, MMRNl ||Proximal Promoter:259, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 4:9355351, LOC728369||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:-9503|Proximal Promoter:-12,LOC728373||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:- 9503|Proximal Promoter:-12,LOC728379||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:-9503|Proximal Promoter:-12,LOC728393||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:-9503|Proximal Promoter:-12,LOC728400||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:-9503|Proximal Promoter:- 12,LOC728405||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer: - 9503|Proximal Promoter:-12,USP17||5' Proximal Enhancer:-9503|Distal Promoter: -4757|Proximal Promoter:-12,USP17L5||3' Proximal Enhancer:4733|3' Proximal Enhancer:9478|5' Proximal Enhancer:- 9503|Proximal Promoter:-12, PBMC:notRA; 4:94566151, GRID2||Intron 14: 1340602, PBMC:OA_SLE_HC; 4:9475346, PBMC:notRA; 4:96760945, PDHA2||Proximal Promoter: -293, PBMC:notRA; 4:99851008, EIF4E||Exon l :778|Proximal Promoter:-765, PBMC:HC; 4:99851060, EIF4E||Exon l :726|Proximal Promoter:-817, PBMC:HC; 4:99851115, EIF4E||Exon l :671 |Proximal Promoter: -872, PBMC:HC; 4:99851211, EIF4E||Exon l :575|Proximal Promoter:-968, PBMC:HC; 5: 10091925, PBMC:HC; 5: 101119084, PBMC:OA_SLE_HC; 5: 101119420, PBMC:OA_SLE_HC; 5: 1020718, NKD2||Intron 3: 11551, PBMCnotRA; 5: 102201128, PAM|| Proximal Promoter:-398, PBMC:SLE; 5: 103876192, PBMC:HC; 5: 10701439, DAP||Intron 2:59948, BcelhOA; 5: 110105162, SLC25A46||3' Proximal Enhancer: 30409, Mono:SLE,PBMC:SLE; 5: 110948135, LOC100505678||Intron 1 : 100212, Mono:OA; 5: 1113320, PBMC:HC; 5: 111506044, EPB41L4A||Exon 20:248966,EPB41L4A- AS1 ||3' Proximal Enhancer:9822,SNORA13||3' Proximal Enhancer:8863, Tcell:OA_SLE_HC; 5: 111963982, PBMC:HC; 5: 112483149, MCC||Intron 2: 147463|Intron 4:341378, PBMC:notRA; 5: 114884044, FEMlQDistal Promoter:-3453, PBMC:notRA; 5: 115178810, AP3Sl ||Intron l : 1192,ATG12||Proximal Promoter: -1262, Mono:SLE; 5: 115284110, PBMC:notRA; 5: 115299646, AQPEP||Intron 1 : 1496, PBMC:notRA; 5: 115387951, LOC644100||Intron 1 :789, PBMC:notRA; 5: 115696151, PBMC:HC; 5: 118623661, TNFAIP8||Intron 1 : 19244, PBMC:HC; 5: 119799384, PRR16||Proximal Promoter: -634, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 5: 119801643, PRR16||Intron 1 : 1625, Mono:SLE; 5: 119802022, PRR16||Intron 1 :2004,
Bcell:HC,Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:HC,PBMC:OA_SLE_HC ,PBMC:SLE; 5: 122110361, SNX2|| Proximal Promoter:-388, Mono:HC; 5: 1225434, SLC6A18||Proximal Promoter: -35,SLC6A19||3' Proximal Enhancer:23725, PBMC:notRA; 5: 122621186, PBMC:OA; 5: 1228214, SLC6A18||Intron 1 :2745,SLC6A19||3' Proximal Enhancer:26505, PBMC:SLE; 5: 122971951, PBMC:notRA; 5: 125171542, PBMC:notRA; 5: 125762736, GRAMD3||Intron l :3868|Intron 1 :66949, PBMC:notRA; 5: 126220247, MARCH3||Intron 3: 146193, Mono:SLE; 5: 126405711, C5orf63||Intron 2:3473, PBMC:notRA; 5: 127420219, FLJ33630||Proximal Promoter:-1453,SLC12A2||Exon 1 :737, PBMC:notRA; 5: 127420842, FLJ33630||Proximal Promoter:-2076,SLC12A2||Intron 1 : 1360, PBMC:OA_SLE_HC; 5: 130510020, HINT1 ||5' Proximal Enhancer:-8986|5' Proximal Enhancer: - 8994,LYRM7||Intron 1 :3380, Mono:HC; 5: 131831745, IRF1 ||5' Proximal Enhancer:-5280, PBMC:notRA; 5: 131879310, IL5||Proximal Promoter:-96, PBMC:HC; 5: 132114055, SEPT8||Proximal Promoter: - 494|Proximal Promoter: -988, Bcell:OA_SLE_HC; 5: 132150128, ANKRD43||Exon 1 : 1096,SHROOM1 ||3' Proximal Enhancer: 11874|3' Proximal Enhancer: 16462, PBMC:OA; 5: 132163787, SHROOMl ||Intron 1 :2803 IProximal Promoter:- 1785, Bcel HC; 5: 133436368, PBMC:HC; 5: 133451625, TCF7||Exon 3: 1224|Proximal Promoter:276|Proximal Promoter:328, Mono:HC; 5: 134259545, MIR4461 ||Distal Promoter: -4183,PCBD2||Intron 2: 18736, PBMC:notRA; 5: 134303703, CATSPER3||Proximal Promoter: 108, PBMC:notRA; 5: 134356114, CATSPER3||3' Proximal Enhancer:52519,PITXl ||3' Proximal Enhancer: 13850, PBMC:HC,PBMC:OA_SLE_HC; 5: 134361983, PITX1 ||3' Proximal Enhancer: 7981, BcelhHC; 5: 134544423, Mono:OA; 5: 134915085, CXCL14||Proximal Promoter:- 116, Bcel OA; 5: 134990285, LOC340074||Proximal Promoter:-661, Bcel HC; 5: 13664584,
Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 5: 138714337, MZB1||3' Proximal Enhancer: 11268,PAIP2||3' Proximal Enhancer:36204|3' Proximal
Enhancer:36819,SLC23Al ||Exon 10:4702, PBMC:HC,PBMC:notRA; 5: 138723394, C5orf65||3' Proximal Enhancer:7491,MZBl ||Exon 4:221 l,SLC23Al ||Distal Promoter: -4355,SPATA24||3' Proximal Enhancer: 16382, PBMC:HC; 5: 139039026, CXXC5||Intron 1 : 10726, PBMC:OA_SLE_HC; 5: 139062471, CXXC5||Exon 3:34171, PBMC:HC,PBMC:OA_SLE_HC; 5: 139062493, CXXC5||Exon 3:34193, PBMC:OA_SLE_HC,PBMC:SLE; 5: 139176077, PSD2||Intron 1 :672, BcelhOA; 5: 140038675, WDR55||5' Proximal Enhancer:-5708, PBMC:notRA; 5: 140090300, VTRNAl-l ||Proximal Promoter:-560,VTRNA1- 2||5' Proximal Enhancer:-8210,ZMAT2||3' Proximal Enhancer: 10269, PBMC:SLE; 5: 140098230, VTRNA1-1 ||3' Proximal Enhancer: 7370,VTRNAl-2||Proximal Promoter:-280,VTRNA1-3||5' Proximal Enhancer:-7513, PBMC:notRA; 5: 140105405, VTRNA1-2||3' Proximal Enhancer:6895,VTRNAl- 3||Proximal Promoter:-338, PBMCnotRA; 5:140235510, PCDHAl||Intron l:69635,PCDHA10||Proximal Promoter: - 123 ,PCDHA2| | Intron 1:61067,PCDHA311 Intron 1 : 54728,PCDHA4| | Intron l:48839,PCDHA5||Intron l:34150,PCDHA6||Intron l:27861,PCDHA7||Intron l:21542,PCDHA8||Intron 1:14604,PCDHA9||3' Proximal Enhancer:Intron 1:8154, PBMC:notRA; 5: 140419819, PBMC:OA; 5: 140475049, PCDHB2||Exon 1:813,PCDHB3||5' Proximal Enhancer:-5184, PBMC:notRA; 5: 140480967, PCDHB2||3' Proximal Enhancer: 673 l,PCDHB3||Exon 1:734, TcelhHC; 5: 140503531, PCDHB4||Exon 1:1951, PBMC:OA; 5: 140514711, PCDHB4||3' Proximal Enhancer: 1313 l,PCDHB5||Proximal Promoter:- 88, Mono:OA_SLE_HC; 5:140534684, PCDHB17||Proximal Promoter:-895,PCDHB6||3' Proximal Enhancer:4846, PBMC:notRA; 5: 140593332, PCDHB12||3' Proximal Enhancer:5042,PCDHB13||Proximal Promoter:-176,PCDHB14||5' Proximal Enhancer:-9745, PBMC:HC; 5: 140593443, PCDHB12||3' Proximal Enhancer:5153,PCDHB13||Proximal Promoter:-65,PCDHB14||5' Proximal Enhancer: -9634, PBMC:OA_SLE_HC; 5:140595722, PCDHB12||3' Proximal Enhancer: 7432,PCDHB13||Exon 1:2214,PCDHB14||5' Proximal Enhancer:-7355, PBMC:OA; 5:140603034, PCDHB13||3' Proximal Enhancer:9526,PCDHB14||Proximal Promoter: -43, PBMC:notRA; 5: 140612229, PCDHB14||3' Proximal Enhancer:9152,PCDHB18||Proximal Promoter:-1708,PCDHB19P||5' Proximal Enhancer: -7459, PBMC:HC; 5: 140712209, PCDHGAl||Exon 1:1958,PCDHGA2||5' Proximal Enhancer: -6144, Mono:HC,PBMC:HC; 5: 140734931, PCDHGAl||Intron l:24680,PCDHGA2||Intron 1:16578,PCDHGA3||3' Proximal Enhancer:Intron l: 11331,PCDHGA4||Proximal Promoter: 164,PCDHGA5||5' Proximal Enhancer: - 8966,PCDHGB1||3' Proximal Enhancenlntron l:5104,PCDHGB2||Distal Promoter:-4771, Mono:HC; 5: 140739260, PCDHGAl||Intron l:29009,PCDHGA2||Intron l:20907,PCDHGA3||Intron
1:15660,PCDHGA4||3' Proximal Enhancenlntron l:4493,PCDHGA5||Distal Promoter: -4637,PCDHGB1||3' Proximal Enhancer:Intron l:9433,PCDHGB2||Proximal Promoter:-442, PBMC:notRA; 5: 140753570, PCDHGAl||Intron 1:43319,PCDHGA2||Intron 1:35217,PCDHGA3||Intron l:29970,PCDHGA4||Intron 1:18803,PCDHGA5||3' Proximal Enhancer: Intron l:9673,PCDHGA6||Proximal Promoter:- 80,PCDHGA7||5' Proximal Enhancer:-8896,PCDHGBl||Intron l:23743,PCDHGB2||Intron 1: 13868,PCDHGB3||3' Proximal Enhancer: Intron 1:3609, PBMC:OA; 5:140754451, PCDHGAljjlntron l:44200,PCDHGA2||Intron l:36098,PCDHGA3||Intron l:30851,PCDHGA4||Intron 1:19684,PCDHGA5||3' Proximal Enhancer: Intron l:10554,PCDHGA6||Exon 1:801,PCDHGA7||5' Proximal Enhancer: - 8015,PCDHGBl||Intron l:24624,PCDHGB2||Intron 1:14749,PCDHGB3||3' Proximal Enhancer:Intron 1:4490, PBMC:HC; 5:141485167, NDFIPl||Distal Promoter:-3156, PBMC:OA_SLE_HC; 5:141813298, Mono:SLE; 5: 142078020, FGFl||Proximal Promoter: -385, Mono:OA; 5:143584273, KCTD16||Intron 2:33837, Mono:OA; 5:143735715, KCTD16||Intron 3:185279, PBMC:OA_SLE_HC; 5: 145236262, GRXCR2||3' Proximal Enhancer: 16269, PBMC:HC; 5:146716604, STK32A|| Intron 5:102026, PBMC:notRA; 5: 14707001, ANKH||Exon 12:164886,FAM105B||3' Proximal Enhancer:42219, PBMC:HC; 5: 147647955, SPINK13||Proximal Promoter:-467, Bcel OA; 5:147777756, FBX038||Intron 2:14211, PBMC:HC; 5: 148033473, HTR4|| Proximal Promoter:266, PBMCnotRA; 5: 148209341, ADRB2||3' Proximal Enhancer:3186, Mono:HC; 5: 148398804, SH3TC2||Intron 12:43933, Bcel HC; 5:148443366, SH3TC2||Proximal Promoter: -629, PBMC:notRA; 5:148520669, ABLIM3||Proximal Promoter: -384, PBMC:notRA; 5:148520854, ABLIM3||Proximal Promoter:-199, PBMC:HC; 5:148651144, AFAPlLl||Proximal Promoter: -256, PBMC:OA; 5:14870594, PBMC:OA_SLE_HC; 5:14870666, Tcell:HC,Tcell:OA_SLE_HC; 5: 148785846, MIR143HG||Proximal Promoter:-593, Bcel HC; 5:148810180, MIR143||3' Proximal Enhancer: 1700,MIR143HG||Exon 3:23741,MIR145||Proximal Promoter: -28, PBMC:HC; 5: 149319112, PDE6A||Intron 1:5244, PBMC:HC; 5: 149493099, CSFlR||Proximal Promoter:-164,PDGFRB||3' Proximal Enhancer:42323, Mono:HC,Mono:OA_SLE_HC; 5: 149953322, Mono:OA; 5: 149997153, SYNPO||Intron l: 16512|Proximal Promoter:-52, Mono:OA; 5: 149997515, SYNPO||Intron l:16874|Proximal Promoter:310, Tcel OA; 5: 150017204, SYNPO||Distal Promoter:-3002|Intron 2:19999|Intron 2:36563, PBMC:OA_SLE_HC; 5: 150051778, MYOZ3||Intron 5:11375, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:OA_SLE_HC; 5: 150081499, DCTN4||3' Proximal Enhancer:56583|3' Proximal Enhancer:57158,RBM22||Proximal Promoter:-830, BcelhHC; 5:150323558, ZNF300Pl||Intron 1:2588, Bcell:OA_SLE_HC; 5:150534782, ANXA6||Intron 1:2661, PBMC:OA_SLE_HC; 5: 1519265, LPCATl||Intron 1:4811, PBMC:HC; 5: 152729842, Bcell:SLE,Mono:HC,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC; 5: 1555791, PBMC:HC; 5: 156594400, FAM71B||Proximal Promoter:- 1121, PBMC:HC; 5:156594470, FAM71B||Proximal Promoter:- 1191, PBMC:HC; 5: 156594725, FAM71B||Proximal Promoter: -1446, Tcell:OA_SLE_HC,Tcell:SLE; 5:156811669, PBMC:HC,PBMC:OA_SLE_HC; 5:156886415, NIPAL4||Proximal Promoter: -611, PBMCSLE; 5: 158537885, PBMC:notRA; 5: 158634905, RNF145||Intron l: 1658|Intron 1:21561 Proximal Promoter:-249|Proximal Promoter: -7 l|Proximal Promoter:235, PBMC:notRA; 5: 159542935, PWWP2A||Intron 1:3517, PBMC:HC,PBMC:OA_SLE_HC; 5: 159545855, PWWP2A||Exon 1:597, PBMC:notRA; 5:159547159, PWWP2A|| Proximal Promoter:-707, BcelhOA; 5: 159595643, PBMC:notRA; 5:1611111, LOC728613||Intron 2:23009, PBMC:HC,Tcell:HC; 5: 162936453, MAT2B||Intron l :3869|Intron 1 :6223, PBMC:SLE,Tcell:OA_SLE_HC; 5: 163723934, PBMC:notRA,Wholeblood:notRA; 5: 164064, PLEKHG4B|| Intron 11 :23692,
PBMC:HC,PBMC:OA_SLE_HC; 5: 167288661, ODZ2||Intron 2:576819, PBMC:notRA; 5: 16785399, MYO10||Intron 4: 150986, PBMC:notRA; 5: 168403541, PBMC:OA_SLE_HC; 5: 16843340, MYOlojjlntron 2:93045, PBMC:SLE; 5: 168728193, PBMC:OA_SLE_HC; 5: 170171246, KCNIP1 ||3' Proximal Enhancer:240199, Bcell:SLE; 5: 17062511 , Tcell:HC; 5: 170743459, TLX3||3' Proximal Enhancer:7172, Mono:OA; 5: 170811643, MIR3912||3' Proximal Enhancer:2121,NPMl ||Distal Promoter: - 3064, PBMC:notRA; 5: 170845058, FGF18||Proximal Promoter:-1608,NPM1 ||3' Proximal Enhancer:30351, Tcell:HC; 5: 171333801, FBXWl l ||Intron 2:Intron 3: 100076, Bcell:OA_SLE_HC; 5: 171430188, FBXWl l ||Intron 1 :3689, PBMC:OA,PBMC:notRA; 5: 171560211, STK10||Intron 2:55135, TcelhOA SLE HC; 5: 172216309, PBMC:OA_SLE_HC; 5: 172280684, ERGICl ||Intron 1 : 19462, PBMC:HC; 5: 172306136, ERGICl ||Intron 1 :44914, Tcell:OA_SLE_HC; 5: 172639423, Bcell:OA; 5: 172717714, PBMC:SLE; 5: 173116776, PBMC:OA_SLE_HC; 5: 173351052, CPEB4||Intron 2:35722, Mono:OA_SLE_HC; 5: 173415991, C5orf47||Proximal Promoter: -170, PBMC:notRA; 5: 173602861, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 5: 1742623, PBMC:OA_SLE_HC; 5: 174350112, PBMC:notRA; 5: 175789238, ARL10||Distal Promoter:-3263,KIAA1191 ||Proximal Promoter: -429, Tcell:HC; 5: 175846914, CLTB|| Distal Promoter:-3344, PBMC:OA_SLE_HC; 5: 176099987, PBMC:notRA; 5: 176101928, Bcell:HC; 5: 176212707, Wholeblood:notRA; 5: 176759170, LMAN2||Exon 8: 19715, PBMC:HC; 5: 177481396, FAM153C||3' Proximal Enhancer:47430, Bcell:OA_SLE_HC,PBMC:notRA; 5: 177614217, GMCLlPl ||Proximal Promoter:216, PBMCnotRA; 5: 177627467, AGXT2L2||3' Proximal Enhancer:32336,HNRNPAB||Distal Promoter:-4040, Mono:SLE; 5: 177811198, COL23Al ||Intron 2:206358, Wholeblood:notRA; 5: 177811349, COL23Al ||Intron 2:206207, Wholeblood:notRA; 5: 177986646, COL23Al ||Intron 2:30910, PBMC:SLE; 5: 178004012, COL23Al ||Intron 1 : 13544, PBMC:OA; 5: 178057845, CLK4||Distal Promoter:-3791, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 5: 178358274, ZFP2||Exon 5:35359,ZNF454||5' Proximal Enhancer:-9919, PBMC:notRA; 5: 178455197, ZNF879||Intron 4:4422, PBMC:notRA; 5: 178478137, ZNF354C||5' Proximal Enhancer:-9469, PBMC:notRA; 5: 178986131, RUFYl ||Intron l :8570|Proximal Promoter:-561, Tcell:HC; 5: 179238472, SQSTM1 ||5' Proximal Enhancer:-9369|Intron l :4470|Intron 1 :5085, PBMC:notRA; 5: 179634688, RASGEFlC||Intron 1 : 1442, Wholeblood:notRA; 5: 180288995, ZFP62||Proximal Promoter: -709, PBMC:notRA; 5: 180597400, Mono:OA; 5: 180597642, PBMC:OA_SLE_HC; 5: 1841622, Mono:OA; 5: 1912167, Tcell:OA; 5: 191492, LRRC14B||Proximal Promoter:-133,PLEKHG4B||3' Proximal Enhancer:51120, PBMC:OA_SLE_HC; 5: 19928399, CDH18||Intron 2:59954, PBMC:OA; 5:23506738, PRDM9||Proximal Promoter:-985, Tcell:OA; 5:2416025, PBMC:notRA; 5:27038782, CDH9||Proximal Promoter: -93, Bcell:SLE; 5:2743124, C5orG8||5' Proximal Enhancer:-9137,IRX2||3' Proximal Enhancer: 8645, PBMC:notRA; 5:27532684, Mono:SLE; 5:2753852, C5orG8||Intron 3: 1591,IRX2||Proximal Promoter:-2083, PBMC:HC; 5:2759441, C5orG8||3' Proximal Enhancer:7180,IRX2||5' Proximal Enhancer: -7672, BcelhHC; 5:28809037, Bcel HC; 5:31361135, PBMC:OA_SLE_HC; 5:31769846, BcelhHC; 5:31798797, PDZD2||Proximal Promoter: -233, PBMC:OA_SLE_HC; 5:32018601, Mono:SLE; 5:32233621, MTMR12||Intron 15:79493, Mono:OA_SLE_HC; 5:3301621, PBMC:SLE,Wholeblood:notRA; 5:33321127,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 5:36149258, LMBRD2||Intron 1 :2757,MIR5801| Proximal Promoter:-1168,SKP2||Distal Promoter:-2886, PBMC:notRA; 5:36157329, LMBRD2||5' Proximal Enhancer:-5314,MIR580||5' Proximal Enhancer:-9239,SKP2||Intron 2:5185, PBMC:OA_SLE_HC; 5:36273196, RANBP3L||Intron 1 :28815, PBMC:OA_SLE_HC; 5:36606102, SLC 1 A31| Proximal Promoter: - 2328|Proximal Promoter:-354, PBMC:notRA; 5:37840725, GDNF||5' Proximal Enhancer:-5132|Distal Promoter: -4796|Proximal Promoter: -943, Tcel OA; 5:3787906, Wholeblood:notRA; 5:38426404, EGFLAM||Intron 13: 167894|Intron 8:22771, PBMC:notRA; 5:39219632, FYB||Intron 1 :51127|Proximal Promoter:48, PBMC:HC; 5:39220260, FYB||Intron l :50499|Proximal Promoter:-580, PBMC:notRA; 5:39721601, PBMC:notRA; 5:39721720, PBMC:notRA; 5:40834228, CARD6||5' Proximal Enhancer:- 7181,LOC100506548||Distal Promoter: -4984,RPL37||Intron 3: 1159,SNORD72||Proximal Promoter: -1391, Mono:OA_SLE_HC; 5:42757171, CCDC152||Proximal Promoter:252, PBMC:SLE; 5:42840698, Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC; 5:43003251, PBMC:notRA; 5:43602116, NT||Proximal Promoter:- 1112|Proximal Promoter: -674, PBMC:notRA; 5:44048305, PBMC:HC; 5:44389282, FGF10||Proximal Promoter: -498, TcelhOA; 5:49397, PBMC:notRA; 5:49737492, EMB||Proximal Promoter: -258, PBMC:notRA; 5:49737773, EMB||Proximal Promoter:-539, Wholeblood:notRA; 5:49959703, PARP8||Distal Promoter:-3068|Proximal Promoter:-2029, PBMC:HC; 5:50679151, ISLl ||Proximal Promoter: 194, PBMC:OA; 5:5087391, PBMC:OA; 5:5140001, ADAMTS16||Proximal Promoter:-441, PBMC:HC; 5:5252567, AD AMT S 1611 Intron 17: 112125, PBMC:OA; 5:53814625, SNX18||Exon l : 1033|Exon 1 : 1037, PBMC:SLE; 5:54100067, Bcell:OA_SLE_HC; 5:54319996, GZMK||Proximal Promoter:-! 10, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC;
5:54467378, CDC20B||Intron 2: 1627,GPX8||3' Proximal Enhancer: 11395,MIR449A||Proximal Promoter: - 928,MIR449B||Proximal Promoter:-808,MIR449C||3' Proximal Enhancer: 803, PBMC:notRA; 5:54823369, PPAP2A||Intron 1 :7504,RNF138P1 ||3' Proximal Enhancer:7001, PBMC:HC; 5:54831346, PPAP2A||Proximal Promoter:-473,RNF138Pl ||Proximal Promoter:-976, PBMC:SLE; 5:55009832, SLC38A9||Proximal Promoter:- 1669, PBMC:notRA; 5:55237351, IL6ST||Exon 16:Exon 17:53470, PBMC:notRA; 5:56119093, MAP3Kl ||Intron 1 :8194, Mono:HC; 5:561769, PBMC:HC; 5:56595163, PBMC:notRA; 5:56595244, PBMCnotRA; 5:59559218, PDE4D||Intron 1 :224707, PBMC:HC; 5:63933908, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 5:6581849, LOC255167||Proximal Promoter:- 1560|Proximal Promoter:-437, PBMC:OA_SLE_HC; 5:65891188, MAST4||Proximal Promoter: -987, PBMC:OA_SLE_HC; 5:68785451, OCLN||Distal Promoter: -2667|Distal Promoter:-3138, Mono:OA_SLE_HC; 5:71179500, Bcel OA; 5:72512677,
Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 5:72593606, PBMC:OA; 5:72716466, Wholeblood:notRA; 5:72793693, BTF3||Proximal Promoter:-556,
Bcell:OA_SLE_HC,Bcell:SLE,Mono:SLE; 5:72824251, Mono:HC; 5:7287160, PBMC:notRA; 5:72934606, RGNEF||Intron 1 : 12624, PBMC:OA_SLE_HC; 5:73423472, Tcell:OA_SLE_HC; 5:74162809, FAM169A|| Proximal Promoter:-194, Mono:OA; 5:74908125,
PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 5:74908170, PBMC:OA_SLE_HC; 5:75465603, SV2C||Intron 2:86299, BcelhHC; 5:75469904, SV2C||Intron 2:90600, PBMC:notRA; 5:75471166, SV2C||Intron 2:91862, BcelhSLE; 5:75966681, Mono:OA_SLE_HC; 5:77142469, PBMC:notRA; 5:77147141, PBMC:notRA; 5:773167, PBMC:notRA; 5:78279841, ARSB||Intron l :2516|Intron 2: 1925, Bcell:OA_SLE_HC; 5:79479211, SERINC5|| Intron 2:72687, PBMC:HC,PBMC:OA_SLE_HC; 5:79542470, SERINC5|| Intron 1 :9428, PBMC:HC; 5:80257322, RASGRF2||Intron 1 :815, PBMC:SLE,Wholeblood:notRA; 5:81931501, BcelhHC; 5:82845599, VCAN||Intron 10:Intron 8:Intron 9:78107, Bcel SLE; 5:88275243, PBMCnotRA; 5:90466501, GPR98||3' Proximal Enhancer:611885, Mono:SLE; 5:95170808, PBMC:notRA; 5:95187176, C5orf27||Proximal Promoter:-759, PBMC:notRA; 5:95590917, PBMC:HC; 5:96070916, CAST||5' Proximal Enhancer:-8327|Intron 6:32424|Intron 7:73010|Intron 9:73176, PBMC:notRA; 5:9623366, TAS2R1 ||3' Proximal Enhancer:7097, PBMC:notRA; 5:96294187, LNPEP||Intron l :22842|Proximal Promoter:32, PBMC:notRA; 5:98269394, CHD1 ||5' Proximal Enhancer:-7156,LOC100289230||3' Proximal Enhancer:4557, PBMC:OA_SLE_HC; 6: 100059961, PRDM13||Intron 3:5312, PBMC:HC; 6: 100062259, PRDM13||Exon 4:7610, TcelhOA; 6: 100066673, PRDM13||3' Proximal Enhancer: 12024, Bcel OA; 6: 100442105, LOC728012||Proximal Promoter: 192,MCHR2||Proximal Promoter:-6|Proximal Promoter:9, PBMC:HC; 6: 100882035, SIMl ||Intron 8:29516, PBMC:notRA; 6: 101851283, GRIK2||Intron 1 :4423, Mono:OA_SLE_HC; 6: 10426588, LINC00518||3' Proximal Enhancer: 8467, PBMC:OA; 6: 10482947, PBMC:notRA; 6: 10529935, GCNT2||Exon 3:8368, PBMC:HC; 6: 10529972, GCNT2||Exon 3:8405, PBMC:HC; 6: 105389544, PBMC:OA; 6: 10555808, GCNT2||Intron 3:34241 |Proximal Promoter:-140, BcelhOA SLE HC; 6: 106535425, PRDMl ||Intron 1 : 1231, PBMC:HC; 6: 107197558, LOC100422737||Intron 1 :37742, Tcel OA; 6: 1075978, LOC285768||Intron 1 :25589, PBMCSLE; 6: 107813291, SOBP||Intron 1 : 1975, PBMC:notRA; 6: 107977784, SOBP||Intron 6: 166468, Tcell:OA_SLE_HC,Tcell:SLE; 6: 108487078, NR2El ||Proximal Promoter:-136, PBMC:OA; 6: 108487820, NR2El ||Exon 1 :606, Mono:OA; 6: 109611667, CCDC162P||Distal Promoter: -3838, PBMC:OA_SLE_HC; 6: 1101607, LOC285768||Proximal Promoter: -40, PBMC:OA_SLE_HC; 6: 11044877, ELOVL2||Proximal Promoter: -253,LOC100506409||Intron l :887|Proximal Promoter: -46, PBMC:OA; 6: 110618174, C6orfl 86||Intron 4:61301, PBMC:OA_SLE_HC,PBMC:SLE; 6: 110680085, C6orfl 86||Proximal Promoter: - 610, PBMC:notRA; 6: 110736772, DDO||Proximal Promoter:-19,SLC22A16||3' Proximal Enhancer:61072, PBMC:notRA; 6: 110968061, CDK19||Intron 4: 168351, PBMC:notRA; 6: 110968114, CDK19||Intron 4: 168298, PBMC:notRA; 6: 11104957, C6orf228||Intron l : 10692,ERVFRD-l ||Exon 2:7114, PBMC:notRA; 6: 111580120, KIAA1919||Proximal Promoter:-361, Tcel OA; 6: 111659754, REV3L||Intron 21 : 144660, Wholeblood:notRA; 6: 113128231, PBMC:OA_SLE_HC; 6: 113306339, Bcel HC; 6: 11382830, BcelhOA SLE HC; 6: 113993995, PBMC:HC; 6: 114602991, PBMC:HC; 6: 116753994, DSE||Intron 4: 152712|Intron 4:61885, PBMCSLE; 6: 116783807, FAM26F|| Intron 2: 1252, PBMC:HC,PBMC:OA_SLE_HC; 6: 117869857, DCBLDl ||Intron 14:66038, PBMC:HC; 6: 119662024, MANlAl ||Intron 2:8902, Bcel SLE; 6: 119854913, Mono:HC; 6: 122723706, HSF2||Intron 1 :3011, TcelhHC; 6: 125623573, HDDC2||Proximal Promoter:-291, PBMC:SLE; 6: 12593831, PBMC:notRA; 6: 126000798, LOC643623||Intron 1 :5300, PBMC:HC; 6: 128222390, THEMIS||Intron l : 17386|Proximal Promoter: -164, PBMC:HC; 6: 128530306, PTPRK||Intron 6:311513|Intron 6:311564, PBMC:OA_SLE_HC; 6: 130182452, C6orfl91 ||Proximal Promoter:-36, PBMC:OA_SLE_HC; 6: 130544832, SAMD3||5' Proximal Enhancer:-8338|Proximal Promoter:-733, PBMC:HC; 6: 132722810, MOXDl ||Proximal Promoter: -146, PBMC:OA_SLE_HC; 6: 132832336, STX7||Intron 1 :2001, Bcel OA; 6: 132910681, TAAR5|| Proximal Promoter: 196, PBMC:notRA; 6: 133253256, PBMC:SLE; 6: 1335849, PBMC:notRA; 6: 133783544, EYA4||Exon 7:Exon 8:221050, Tcell:OA; 6:13612218, NOL7||Distal Promoter:-3340,RANBP9||3' Proximal Enhancer:99578,SIRT5||3' Proximal Enhancer:Exon 9:37458|Exon 10:37360, PBMC:SLE; 6:137366545, IL20RA||Proximal Promoter:-247, PBMC:notRA; 6:137494924, IL22RA2||Proximal Promoter:- 139, PBMC:OA; 6:138427309, PERP||Intron 1:1351, Bcell:OA_SLE_HC,PBMC:HC; 6:138744549, HEBP2||3' Proximal Enhancer: 19214,NHSLl||Exon 7:149119|Exon 8:76030, PBMC:HC; 6:139454928, HECA||Proximal Promoter:-1320, Tcell:OA_SLE_HC; 6:139470282, HECA||Intron 1:14034, Bcell:OA_SLE_HC; 6:139483193, HECA||Intron 1:26945, Mono:HC; 6:140168822, LOC100132735||Intron 1:76613, Tcell:OA_SLE_HC; 6:14037614, Mono:SLE; 6:1410267, PBMC:OA_SLE_HC,PBMC:SLE; 6:142890973, LOC153910||Intron l:68053|Intron 2:68000, PBMC:HC; 6:143857467, PBMC:OA; 6:144329802, HYMAI||Proximal Promoter:65,PLAGLl||Intron l:55933|Proximal Promoter: -261, Bcell:OA; 6:146759324, GRM1||3' Proximal Enhancer:410543, Tcell:OA; 6:14729030, PBMC:HC; 6:147457355, LOC729178||Intron 3:68395, Bcell:OA; 6:14763072, Bcell:SLE; 6:149785754, ZC3H12D||Intron 2:20394, PBMC:OA_SLE_HC; 6:149805995, ZC3H12D||Proximal Promoter:153, PBMC:SLE; 6:149806732, ZC3H12D||Proximal Promoter: -584, PBMC:SLE; 6:149982378, LATSl||Exon 8:57014, Bcell:OA_SLE_HC; 6:151075493, PLEKHGl||Intron 3:154495, PBMC:OA; 6:151186411, MTHFD 1 L| |Proximal Promoter:- 1057|Proximal Promoter: -403, Bcell:OA_SLE_HC; 6:151670448, AKAP12||Exon 2:23783|Exon 4:109315, Mono:HC; 6:152011415, ESRl||Proximal Promoter:-215, PBMC:OA_SLE_HC,PBMC:SLE; 6:152011666, ESRl||Proximal Promoter:36, PBMC:SLE; 6:152955983, SYNEl||Intron l:2003|Intron 2:2551, PBMC:notRA; 6:15298461, JARID2||Intron 1:51935, Mono:OA_SLE_HC,Mono:SLE; 6:15300007, JARID2|| Intron 1:53481, PBMC:HC; 6:153018721, MYCTl||Proximal Promoter: -308, Mono:OA_SLE_HC; 6:15305678, JARID2||Intron 1:59152, PBMC:HC; 6:154408701, OPRMl||Exon l:1060|Intron l:48259|Intron l:77066|Intron l:Intron 3:77071, PBMC:notRA; 6:154485839, IPCEFl||Intron 11: 19206 ljlntron 12:165376, PBMC:HC; 6:154821545, CNKSR3||Intron 1:10208, PBMC:notRA; 6:15551489, DTNBPl I |Intron 7:Intron 8:111800, PBMC:OA_SLE_HC; 6:155542639, TIAM2||Intron 14:131217|Intron 1:4543, Mono:HC; 6:157041268, Tcell:HC; 6:157876915, ZDHHC14||Intron 1:74359, PBMC:notRA; 6:158013813, Bcell:HC; 6:158403520, SYNJ2||Intron 1:633, PBMC:HC; 6:158508188, SYNJ2||Intron 22:70109|Intron 23:105301, PBMC:HC; 6:158677312, PBMC:notRA; 6:158732256, TULP4||Proximal Promoter:-1435, PBMC:notRA; 6:159331893, C6orl 9||3' Proximal Enhancer:22275, PBMC:SLE; 6:159392353, RSPH3||3' Proximal Enhancer:28845, PBMC:HC; 6:159466458, TAGAP|| Proximal Promoter: -274, PBMC:OA_SLE_HC; 6:160182447, ACAT2||Proximal Promoter: - 541,LOC100129518||Exon 2:917, PBMC:HC; 6:160697625, PBMC:HC; 6:160850749, SLC22A3|| Intron 5:81325, PBMCnotRA; 6:161258922, PBMC:notRA; 6:161259079, PBMC:notRA; 6:16136539, MIR4639||5' Proximal Enhancer: -5238, MYLIP|| Intron 2:7223, PBMC:HC; 6:161607487, Wholeblood:notRA; 6:1619162, FOXCl||3' Proximal Enhancer:8482,GMDS||3' Proximal Enhancer:557063|3' Proximal Enhancer:626706, PBMC:HC; 6:16266437, GMPR|| Intron 4:27627, PBMC:notRA; 6:163543917, PACRG||Intron 4:394916|Intron 5:395754, Bcel SLE; 6:163570371, PACRG||Intron 4:421370|Intron 5:422208,
Mono:HC,Mono:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 6:163606677, PACRG||Intron 4:457676|Intron 5:458514, Mono:OA; 6:164057152, PBMC:notRA; 6:166268631, Mono:OA; 6:166445460, PBMC:HC; 6:166722248, PRR18||Proximal Promoter:-377, PBMC:HC; 6:166824474, RPS6KA2||Exon 21:216252|Exon 22:451297, PBMC:notRA; 6:166825084, RPS6KA2||Exon 21:215642|Exon 22:450687, Tcel HC; 6:166877038, RPS6KA2||Intron ll:163688|Intron 12:398733, PBMC:HC; 6:167189543, PBMC:OA; 6:167195910, PBMC:OA_SLE_HC; 6:167508226, Mono:HC; 6:167524238, CCR6|| Proximal Promoter:-1056, PBMC:HC,PBMC:OA_SLE_HC; 6:167535764, CCR6||Intron l:10470|Proximal Promoter: -476, PBMC:HC; 6:167571324, GPR31||Proximal Promoter: -5, Mono:HC; 6:167571584, GPR31||Proximal Promoter:-265, Mono:HC; 6:167592570, TCP10L2||Exon 6:8490, PBMC:OA_SLE_HC; 6:167704188, UNC93A||Proximal Promoter: -614, PBMC:notRA; 6:167705750, UNC93A||Intron 1:948, PBMC:HC; 6:16802505, PBMC:HC; 6:168045556, PBMC:notRA; 6:168045602, PBMCnotRA; 6:168134760, PBMC:notRA; 6:168533375, PBMC:HC; 6:168533507, PBMC:HC; 6:168533631, PBMC:OA_SLE_HC; 6:168533689, PBMC:OA_SLE_HC; 6:168559456, Mono:OA_SLE_HC; 6:168683006, BcelhHC; 6:168766543, PBMC:HC; 6:168766586, PBMC:HC; 6:169142715, PBMC:OA_SLE_HC; 6:169223825, Mono:OA_SLE_HC; 6:169261475, PBMC:HC; 6:169487533, PBMC:notRA; 6:16962712, PBMC:OA_SLE_HC; 6:169857450, WDR27||Exon 22:Exon 26:244709, PBMC:OA_SLE_HC; 6:169978203, WDR27||Intron 21:Intron 24:123956, PBMC:HC; 6:170189761, C6ori208||Proximal Promoter:-407,C6orf70||3' Proximal Enhancer:38041,LINC00242||Exon 2:9160, PBMC:OA_SLE_HC; 6:170402031, PBMC:SLE; 6:170403557, PBMCSLE; 6:170403583, PBMC:SLE; 6:170455374, PBMC:notRA; 6:170487311, PBMC:notRA; 6:170553133, PBMC:HC; 6:170553364, PBMC:HC,Tcell:HC; 6:170703742, Wholeblood:notRA; 6:170732253, PBMC:notRA; 6:170732353, PBMC:notRA; 6:170816044, PBMC:OA_SLE_HC; 6:1758052, GMDS||Intron 7:418173|Intron 7:487816, PBMCnotRA; 6: 17600994, FAM8Al ||Proximal Promoter:477, Bcell:OA,Mono:OA,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA; 6: 17715219, NUP153||5' Proximal Enhancer:-8401, PBMC:SLE; 6: 18368844, PBMCnotRA; 6:20024319, PBMC:notRA; 6:20211654, MBOATl ||Intron 1 : 1016, PBMC:notRA; 6:2104322, GMDS||Intron 4: 141546|Intron 4:71903, PBMC:HC; 6:22061708, LINC00340||Intron 8:395034, Bcell:OA; 6:24205566, DCDC2||Intron 7: 152714|Intron 8: 177954, PBMC:notRA; 6:24646782, KIAA0319||Proximal Promoter:-399|Proximal Promoter: -533,TDP2||3' Proximal Enhancer:20333, PBMC:OA_SLE_HC,PBMC:notRA; 6:24925385, PBMC:notRA; 6:25167695, Bcell:HC; 6:25180502, Mono:OA_SLE_HC; 6:25652815, SCGN||Proximal Promoter:387, Mono:OA_SLE_HC; 6:25701717, SCGN||Exon 11 :49289, PBMC:OA_SLE_HC; 6:26045788, HISTlH2BB||Proximal Promoter:-1903,HISTlH3C||Proximal Promoter: 150, PBMC:notRA; 6:26086585, HFE||Proximal Promoter: -923, PBMC:HC; 6:26189355, HIST1H2AD||3' Proximal Enhancer: 10116,HIST1H2BE||3' Proximal Enhancer:5332,HISTlH3D||3' Proximal
Enhancer: 10109,HISTlH4D||Proximal Promoter:-51, Bcell:OA,Mono:OA; 6:26195954, HIST1H2AD||3' Proximal Enhancer:3517,HISTlH2BF||Distal Promoter:-3832,HISTlH3D||3' Proximal
Enhancer:3510,HISTlH4D||5' Proximal Enhancer:-6650,HIST1H4E||5' Proximal Enhancer:-8918, PBMC:notRA; 6:26240307, HIST1H1D||5' Proximal Enhancer: -5091,HISTlH4F||Proximal Promoter:- 346,HIST1H4G||3' Proximal Enhancer:6898, PBMC:OA; 6:26330553, PBMC:HC; 6:26330584, PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 6:26331295, PBMCSLE; 6:26382695, BTN2A211 Proximal Promoter:-628|Proximal Promoter: -633 |Proximal Promoter:-743,BTN3A2||3' Proximal Enhancer: 14290|3' Proximal Enhancer: 17226|3' Proximal Enhancer: 17298, PBMC:notRA; 6:27106564, HIST1H2AG||3' Proximal Enhancer:5748,HISTlH2AH||5' Proximal Enhancer:-8343,HIST1H2BJ||5' Proximal Enhancer: -5989,HISTlH2BK||Intron l :8073,HISTlH4I||Proximal Promoter:-523,MIR3143||5' Proximal Enhancer:-8840, Bcell:OA_SLE_HC; 6:27390647, T cell: SLE; 6:27521450, PBMC:notRA; 6:27569671, Wholeblood:notRA; 6:27637520, PBMC:notRA; 6:27670844, LOC100507173||Intron 2:8987|Intron 2:9031, BcelhOA; 6:27706179, Mono:OA_SLE_HC,Mono:SLE; 6:27706275, PBMC:notRA; 6:28248263, PGBDl ||Proximal Promoter:-1050,ZNF187||3' Proximal Enhancer: 13476, PBMC:notRA; 6:28558113, SCAND3||Distal Promoter:-3001, PBMC:OA_SLE_HC; 6:28601324, PBMC:HC; 6:28641622, PBMC:notRA; 6:28661759, Tcel OA; 6:28715138, PBMC:notRA; 6:28733661, PBMC:OA; 6:28911926, TcelhOA SLE HC; 6:29342286, OR12D3||Exon 1 :782, PBMC:OA; 6:29364602, OR12D2||Proximal Promoter: 187, PBMC:notRA; 6:2939878, SERPINB6||3' Proximal Enhancer:32521, PBMC:notRA; 6:29442830, PBMCnotRA; 6:29454672, MASlL||Exon 1 : 1007, Mono:SLE; 6:29454755, MAS lL||Exon 1 :924, Mono:SLE; 6:2953027, SERPINB6||Intron 5:Intron 6: 19372, PBMC:OA_SLE_HC; 6:2953123, SERPINB6||Intron 5:Intron 6: 19276, PBMC:OA_SLE_HC; 6:29576329, GABBRl ||Intron l l : 19676|Intron 15:Intron 16:24633, BcelhHC; 6:29578124, GABBRl ||Intron 13:Intron 14:22838|Intron 9: 17881, PBMC:notRA; 6:29623992, MOG||Proximal Promoter:-765, PBMC:notRA; 6:29629716, MOG||Intron l :Intron 2:4959, PBMC:notRA; 6:29629758, MOG||Intron l :Intron 2:5001, PBMC:notRA; 6:29629986, MOG||Intron l :Intron 2:5229, PBMC:notRA; 6:29634495, MOG||Intron 2:Intron 3:9738,ZFP57||3' Proximal Enhancer: 10436, Mono:HC,PBMC:HC; 6:29635507, MOG||Intron 3:Intron 4: 10750,ZFP57||3' Proximal Enhancer:9424, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 6:29663039, PBMC:notRA; 6:29690056, HLA-F||Proximal Promoter:- 1060,HLA-F-AS1 ||3' Proximal Enhancer:26770, PBMC:notRA; 6:29691832, HLA-F||Intron 2:716,HLA-F-AS1 ||3' Proximal Enhancer:24994, PBMC:notRA; 6:29692035, HLA-F||Exon 3:919,HLA-F-AS1 ||3' Proximal Enhancer:24791, BcelhOA SLE HC; 6:29705939, HLA-F-ASl ||Exon 4:Intron 1 : 10887, Mono:HC; 6:29709366, HLA-F- ASl ||Intron l :Intron 2:7460,IFITM4P||3' Proximal Enhancer:9559, PBMC:notRA; 6:29723301, HLA-F- AS1 ||5' Proximal Enhancer:-6475,IFITM4P||Distal Promoter: -4376, PBMC:notRA; 6:29723315, HLA-F- AS1 ||5' Proximal Enhancer:-6489,IFITM4P||Distal Promoter: -4390, PBMC:notRA; 6:29723320, HLA-F- AS1 ||5' Proximal Enhancer: -6494,IFITM4P||Distal Promoter:-4395, PBMC:notRA; 6:29763945, HCG4||Distal Promoter:-3095,LOC554223||Intron 2:4263, PBMC : SLE,PBMC :notRA; 6:29793526, HLA- G||Proximal Promoter:-1229, PBMC:notRA; 6:29972884, HLA-J||Proximal Promoter:-863,ZNRDl- ASl ||Intron 5:56077, PBMC:notRA; 6:30010457, Tcell:OA_SLE_HC; 6:30067855, TRIM31 ||3' Proximal Enhancer: 13012, Mono:OA_SLE_HC; 6:30070738, TRIM31 ||Exon 9: 10129,
PBMC:HC,PBMC:OA_SLE_HC; 6:30076659, TRIM31 ||Intron 5:4208,
Mono:HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:HC; 6:30079203, TRIM31 ||Intron 3: 1664, PBMC:OA_SLE_HC; 6:30079256, TRIM31 ||Intron 3: 1611, TcelhOA SLE HC; 6:30080782, TRIM31 ||Proximal Promoter:85, BcelhHC; 6:30095174, TRIM40||5' Proximal Enhancer: -9335, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:30095195, TRIM40||5' Proximal Enhancer: -9314, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:30095199, TRIM40||5' Proximal Enhancer: -9310, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:30095248, TRIM40||5' Proximal Enhancer: -9261, PBMC:HC,PBMC:OA_SLE_HC; 6:30095258, TRIM40||5' Proximal Enhancer: -9251, PBMC:HC,PBMC:OA_SLE_HC; 6:30095265, TRIM40||5' Proximal Enhancer: -9244, PBMC:HC,PBMC:OA_SLE_HC; 6:30115829, TRIM10||3' Proximal Enhancer: 12882,TRIM40||Exon 5: 11320, BcelhHC; 6:30122523, TRIM10||Intron 6:6188,TRIM15||5' Proximal Enhancer:-8459,TRIM40||3' Proximal Enhancer: 18014, PBMC:HC; 6:30122593, TRIM10||Intron 6:6118,TRIM15||5' Proximal Enhancer:-8389,TRIM40||3' Proximal Enhancer: 18084,
Mono:OA_SLE_HC,PBMC:HC,Tcell:OA_SLE_HC; 6:30126176, TRIM10||Exon 3:2535,TRIM15||Distal Promoter: -4806,TRIM40||3' Proximal Enhancer:21667, Mono:HC,Mono:OA_SLE_HC; 6:30139592, TRIM15||Intron 6:8610, Tcel OA; 6:30182244, TRIM26||Proximal Promoter: -973, BcelhOA; 6:30227583, HLA-L||Proximal Promoter:245, Mono:OA,PBMC:HC,PBMC:notRA; 6:30231689, HLA-L||Exon 7:4351, BcelhOA; 6:30290408, HCG18||Intron l :4519,TRIM39||Distal Promoter:-4212|Distal Promoter: - 4599,TRIM39-RPP21 ||5' Proximal Enhancer: -6679, Bcel HC; 6:30290603, HCG18||Intron l :4324,TRIM39||Distal Promoter:-4017|Distal Promoter:-4404,TRIM39-RPP21 ||5' Proximal Enhancer:- 6484, PBMC:notRA; 6:30297338, HCG18||Proximal Promoter:-241 l,TRIM39||Exon 3:2331 |Exon 3:2718,TRIM39-RPP21 ||Proximal Promoter:251, PBMC:HC; 6:30302667, HCG18||5' Proximal Enhancer: - 7740,TRIM39||Intron 4:7660|Intron 4:8047,TRIM39-RPP21 ||Intron 2:5580, PBMC:notRA; 6:30307205, RPP21 ||5' Proximal Enhancer:-5700,TRIM39||Intron 5: 12198|Intron 5: 12585,TRIM39-RPP21 ||Intron 3: 10118, PBMC:notRA; 6:30586468, ATAT1 ||5' Proximal Enhancer:-8144|5' Proximal Enhancer:-8146|5' Proximal Enhancer:-8194,MRPS18B||Intron l :983,PPPlR10||Proximal Promoter:-1448,
Wholeblood:notRA; 6:30653191, NRM||3' Proximal Enhancer:5578,PPPlR18||Exon 1 :2481 |Exon 2: 1902, PBMC:HC; 6:30684478, MDCl ||Intron l :980,TUBB||Distal Promoter:-3678, BcelhOA SLE HC; 6:30796209, PBMC:notRA; 6:30882994, GTF2H4||3' Proximal Enhancer:7018,VARS2||Exon 2:Exon 3: 1013|Exon 3:887, PBMC:SLE; 6:30908706, DPCRl ||Proximal Promoter: -70,SFTA2||5' Proximal Enhancer:-8754, PBMC:notRA; 6:30956603, MUC21 ||Exon 3:5119, Wholeblood:notRA; 6:31019494, HCG22||Proximal Promoter: -2489, PBMC:OA_SLE_HC; 6:31146222, POU5F l ||5' Proximal Enhancer: - 7771,PSORSlC3||Proximal Promoter:-546, BcelhHC; 6:31146583, POU5Fl ||5' Proximal Enhancer: - 8132,PSORSlC3||Proximal Promoter: -907, PBMC:HC; 6:31146845, POU5Fl ||5' Proximal Enhancer: - 8394,PSORSlC3||Proximal Promoter:- 1169, PBMC:OA_SLE_HC; 6:31166502, HCG27||Intron 1 :966, PBMC:HC; 6:31166759, HCG27||Intron 1 : 1223, Bcell:OA_SLE_HC; 6:31166799, HCG27||Intron 1 : 1263, TcelhHC; 6:31237199, HLA-C||Intron 6:2714, PBMC:notRA; 6:31238036, HLA-C||Exon 4: 1877, PBMC:HC,Tcell:HC; 6:31238803, HLA-C||Intron 3: 1110, Bcell:SLE,Mono:SLE; 6:31238908, HLA- C||Exon 3: 1005, PBMC:notRA; 6:31240651, HLA-C|| Proximal Promoter:-738, PBMC:HC,PBMC:OA_SLE_HC; 6:31240784, HLA-C||Proximal Promoter:-871, PBMC:HC; 6:31240814, HLA-C||Proximal Promoter:-901, PBMC:HC,PBMC:OA_SLE_HC; 6:31322348, HLA-B||Intron 6:2641, Bcell:OA_SLE_HC; 6:31322577, HLA-B||Intron 5:2412, Bcel SLE; 6:31323677, HLA-B||Intron 3: 1312, Bcell:OA_SLE_HC; 6:31325314, HLA-B||Proximal Promoter:-325, Tcel OA; 6:313464, DUSP22||Intron 3:21364, Tcell:OA_SLE_HC; 6:31373932, MICA||Intron l :2562|Intron l :5460|Intron 1 :6372, PBMC:notRA; 6:31379971, MICApxon 4: 11499|Exon 4: 12411 |Exon 4:8601, PBMC:notRA; 6:31382065, MICA||Intron 5: 10695|Intron 5: 13593 |Intron 5: 14505, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 6:31409481, Mono:OA,PBMC:notRA; 6:31431407, HCG26||5' Proximal Enhancer: -7598,HCP5||Proximal Promoter:451, PBMC:OA_SLE_HC; 6:31431503, HCG26||5' Proximal Enhancer:-7502,HCP5||Exon 2:547, PBMC:OA_SLE_HC; 6:31431902, HCG26||5' Proximal Enhancer:-7103,HCP5||Exon 2:946, Bcell:OA_SLE_HC; 6:31461748, MICB||Distal Promoter: -4106, TcelhOA; 6:31464826, MICB||Proximal Promoter:-1028, PBMC:notRA; 6:31468816, MICB||Intron 1 :2962, PBMC:notRA; 6:31470807, MICB||Intron 1 :4953, PBMC:notRA; 6:31529897, LTA||5' Proximal Enhancer: -9978,NFKBIL1 ||3' Proximal Enhancer: 14545|3' Proximal Enhancer: 15270, PBMC:notRA; 6:31539735, LTA||Proximal Promoter:-140|Proximal Promoter:-357,LTB||3' Proximal Enhancer: 10467,TNF||Distal Promoter:-3614, PBMC:HC; 6:31540014, LTA||Proximal Promoter:-78|Proximal Promoter: 139,LTB||3' Proximal Enhancer: 10188,TNF||Distal Promoter:-3335, PBMC:HC; 6:31540114, LTA||Proximal Promoter: 221 Proximal Promoter:239,LTB||3' Proximal Enhancer: 10088,TNF||Distal Promoter:-3235, Tcel HC; 6:31540411, LTA||Intron l :536|Proximal Promoter^ 19,LTB||3' Proximal Enhancer:9791,TNF||Distal Promoter: -2938, PBMC:HC; 6:31544931, LST1 ||5' Proximal Enhancer:-9024|5' Proximal Enhancer:-9544,LTA||3' Proximal Enhancer:4839|3' Proximal Enhancer:5056,LTB||3' Proximal Enhancer:5271,TNF||Exon 4: 1582, PBMC:HC; 6:31544960, LST1 ||5' Proximal Enhancer:-8995|5' Proximal Enhancer:-9515,LTA||3' Proximal Enhancer:4868|3' Proximal Enhancer:5085,LTB||3' Proximal Enhancer:5242,TNF||Exon 4: 1611, PBMC:HC; 6:31548437, LST1 ||5' Proximal Enhancer:-5518|5' Proximal Enhancer:-6038|5' Proximal Enhancer:-6539,LTA||3' Proximal Enhancer:8345|3' Proximal Enhancer:8562,LTB||Exon 3:Exon 4: 1765,NCR3||3' Proximal Enhancer: 12325,TNF||3' Proximal Enhancer:5088, PBMC:OA; 6:31549631, LST1||5' Proximal Enhancer:-5345|Distal Promoter:-4324|Distal Promoter:-4844,LTA||3' Proximal Enhancer:9539|3' Proximal Enhancer:9756,LTB||Exon 2:Intron 1 :571,NCR3||3' Proximal Enhancer: 11131,TNF||3' Proximal Enhancer: 6282, PBMC:HC; 6:31550090, LSTl ||Distal Promoter:-3865|Distal Promoter:-4385|Distal Promoter: -4886,LTA||3' Proximal Enhancer: 10215|3' Proximal Enhancer:9998,LTB||Proximal Promoter: 112,NCR3||3' Proximal Enhancer: 10672,TNF||3' Proximal Enhancer:6741, PBMC:HC; 6:31555016, LSTl ||Exon 2: 1061 |Exon 2:541 |Proximal Promoter:40,LTB||Distal Promoter:-4814,NCR3||3' Proximal Enhancer:5746,TNF||3' Proximal Enhancer: 11667, PBMC:HC; 6:31589196, AIF1 ||3' Proximal Enhancer: 5408|3' Proximal Enhancer:6164|3' Proximal Enhancer: 6203, PRRC2A||Intron l :747,SNORA38||Proximal Promoter:- 1659, PBMC:HC; 6:31607648, BAG6||Intron 22:Intron 23: 12829|Intron 23: 12522, PBMC:HC; 6:31711970, CLIC1 ||5' Proximal Enhancer:-7629,MSH5||Exon 7:4246,MSH5-SAPCDl ||Exon 7:4246, PBMC:notRA; 6:31762353, LSM2||3' Proximal Enhancer: 12408,VARS||Intron 2: 1359, PBMC:OA; 6:32095148, ATF6B||Intron 3:869,FKBPL||3' Proximal Enhancer:2919, Mono:OA; 6:32109801, PRRT1 ||3' Proximal Enhancer:9919, Mono:HC; 6:32121055, LOC100507547||Exon 3:Intron 2: 1087,PPT2||Proximal Promoter:- 173|Proximal Promoter:-720,PPT2-EGFL8||Proximal Promoter: -720,PRRTl ||Proximal Promoter:- 1335, PBMC:OA; 6:32121249, LOC100507547||Exon 3:Intron 2:893,PPT2||Proximal Promoter:-526|Proximal Promoter:21,PPT2-EGFL8||Proximal Promoter:-526,PRRTl ||Proximal Promoter: -1529, PBMC:HC; 6:32141882, AGER||3' Proximal Enhancer: 10217, AGPATl ||Intron l :2034|Intron 1 :4006,EGFL8||3' Proximal Enhancer:9501,PPT2-EGFL8||3' Proximal Enhancer:20107,RNF5||Distal Promoter: - 4279,RNF5Pl ||Distal Promoter:-4349, PBMC:notRA; 6:32178991, NOTCH4|| Intron 17: 12853, PBMC:notRA; 6:32282950, C6orflO||Intron 10:56706, PBMC:OA_SLE_HC; 6:32294577, C6orflO||Intron 10:45079, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:notRA; 6:32295097,
C6orilO||Intron 10:44559, PBMC:HC; 6:32301513, C6orflO||Intron 10:38143, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32306089, C6orflO||Intron 10:33567,
PBMC:OA_SLE_HC; 6:32309323, C6orflO||Intron 9:30333, PBMC:OA_SLE_HC; 6:32311517, C6orflO||Intron 9:28139, BcelhHC; 6:32335060, C6orflO||Intron 4:4596,
Bcell:OA_SLE_HC,Tcell:OA_SLE_HC; 6:32336160, C6orflO||Intron 3:3496, PBMC:HC; 6:32376066, BTNL2||Proximal Promoter:- 1166, TcelhHC; 6:32381449, BTNL2||5' Proximal Enhancer:-6549, TcelhHC; 6:32427751, Mono:HC,PBMC:HC; 6:32427868, PBMC:HC,Tcell:HC; 6:32449961, Mono:HC,Mono:OA,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 6:32451079, PBMC:HC; 6:32487314, HLA-DRB5||Exon 3: 10692, PBMC:HC; 6:32489555, HLA-DRB51 |Intron 2:8451, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA,Tcell:HC; 6:32489750, HLA-DRB5||Exon 2:8256, PBMC:OA_SLE_HC; 6:32489963, HLA-DRB511 Intron 1 :8043, BcelhSLE; 6:32490350, HLA- DRB5||Intron 1 :7656, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC,Tcell:OA_SLE_HC; 6:32490421, HLA-DRB5||Intron 1 :7585, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32493873, HLA- DRB5||Intron 1 :4133, PBMC:OA_SLE_HC,PBMC:notRA; 6:32493917, HLA-DRB51 |Intron 1 :4089, PBMC:HC,PBMC:OA_SLE_HC; 6:32520916, HLA-DRB6||Intron 5:6863, PBMC:notRA; 6:32522535, HLA-DRB6||Exon 3:5244, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 6:32526342, HLA-DRB6||Intron 1 : 1437, PBMC:notRA; 6:32526366, HLA-DRB6||Intron 1 : 1413, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32526702, HLA-DRB6||Intron 1 : 1077,
PBMC:OA_SLE_HC,PBMC:SLE; 6:32546626, HLA-DRBl ||Exon 6: 10987, PBMC:HC,Tcell:HC; 6:32546665, HLA-DRBl ||Exon 6: 10948,
Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 6:32549361, HLA-DRBl ||Exon 3:8252, PBMC:HC,PBMC:OA_SLE_HC; 6:32549631, HLA-DRB 11 |Intron 2:7982, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC; 6:32551949, HLA-DRB l ||Exon 2:5664, PBMC:OA_SLE_HC,PBMC:SLE; 6:32551954, HLA-DRB l ||Exon 2:5659, PBMC:OA_SLE_HC; 6:32552022, HLA-DRB l ||Exon 2:5591, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32552026, HLA- DRB l ||Exon 2:5587, PBMC:OA_SLE_HC; 6:32552547, HLA-DRB l ||Intron 1 :5066, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 6:32554481, HLA-DRB l ||Intron 1 :3132, PBMC:HC,PBMC:OA_SLE_HC; 6:32557321, HLA-DRB l ||Proximal Promoter:292, PBMC:OA_SLE_HC; 6:32574199, PBMC:notRA; 6:32604564, HLA-DQAl ||Proximal Promoter: -618, PBMC:OA_SLE_HC; 6:32604865, HLA-DQAl ||Proximal Promoter: -317, PBMC:OA_SLE_HC; 6:32606385, HLA-DQAl ||Intron 1 : 1203, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32606845, HLA-DQAl ||Intron 1 : 1663, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32609094, HLA-DQAl ||Exon 2:3912, PBMC:HC,PBMC:OA_SLE_HC; 6:32609130, HLA-DQAl ||Exon 2:3948, PBMC:HC; 6:32609181, HLA-DQAl ||Exon 2:3999, Bcell: OA SLE HC ; 6:32609783, HLA-DQAl ||Exon 3:4601, Bcell:OA_SLE_HC,Mono:HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC; 6:32627885, HLA-DQBl ||Exon 5:Exon 6:6581, PBMC:OA_SLE_HC,PBMC:SLE; 6:32628953, HLA- DQBl ||Intron 4:5513, PBMC:notRA; 6:32629809, HLA-DQBl ||Exon 3:4657, PBMC:notRA; 6:32632106, HLA-DQB 11 |Intron 2:2360, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:32632108, HLA- DQBl ||Intron 2:2358, Mono:OA,PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:32632159, HLA- DQB l jjlntron 2:2307, PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC; 6:32632565, HLA-DQB l ||Intron 2: 1901, Bcel OA; 6:32633102, HLA-DQB l ||Intron 1 : 1364, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 6:32640493, HLA-DQB 1 ||5' Proximal Enhancer: -6027, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC; 6:32797488, TAP2||Intron 10:9059, PBMC:OA_SLE_HC; 6:32803111, LOC100507463||5' Proximal Enhancer:-8751,PSMB8||3' Proximal Enhancer:8705|3' Proximal Enhancer:9601,TAPl ||3' Proximal Enhancer: 18637,TAP2||Exon 5:3436, Tcell:SLE; 6:32803210, LOC100507463||5' Proximal Enhancer: - 8652,PSMB8||3' Proximal Enhancer:8606|3' Proximal Enhancer:9502,TAPl ||3' Proximal Enhancer: 18538,TAP2||Intron 4:3337, Tcell:SLE; 6:32805692, LOC100507463||5' Proximal Enhancer:- 6170,PSMB8||3' Proximal Enhancer: 6124|3' Proximal Enhancer: 7020,TAP1 ||3' Proximal Enhancer: 16056,TAP2||Exon 2:855, PBMC:SLE; 6:32808918, LOCI 00507463 ||Distal Promoter: - 2944,PSMB8||Intron 5:2898|Intron 5:3794,TAP1 ||3' Proximal Enhancer: 12830,TAP2||Proximal Promoter: - 2371, Tcell:OA_SLE_HC; 6:32810706, LOCI 00507463 ||Proximal Promoter:-1156,PSMB8||Intron 2: 1110|Intron 2:2006,TAP1 ||3' Proximal Enhancer: 11042,TAP2||Distal Promoter: -4159, PBMC:OA_SLE_HC; 6:32810742, LOC100507463||Proximal Promoter:-l 120,PSMB8||Exon 2: 1074|Exon 2: 1970,TAP1 ||3' Proximal Enhancer: 11006,TAP2||Distal Promoter: -4195, BcelhSLE; 6:32820102, LOC100507463||3' Proximal Enhancer:8240,PSMB8||5' Proximal Enhancer:-7390|5' Proximal Enhancer: - 8286,PSMB9||Proximal Promoter:-1835,TAPl ||Intron 2: 1646, Bcell:OA_SLE_HC; 6:32820355, LOC100507463||3' Proximal Enhancer:8493,PSMB8||5' Proximal Enhancer:-7643|5' Proximal Enhancer: - 8539,PSMB9||Proximal Promoter:- 1582,TAPl ||Intron 1 : 1393, Bcell:OA_SLE_HC,Bcell:SLE; 6:32822911, LOC100507463||3' Proximal Enhancer: l 1049,PSMB9||Intron l :974,TAPl ||Proximal Promoter:-l 163, PBMC:SLE; 6:32823566, LOC100507463||3' Proximal Enhancen l 1704,PSMB9||Intron l : 1629,TAPl ||Proximal Promoter:-1818, PBMC:notRA; 6:32823941, LOC100507463||3' Proximal Enhancer: 12079,PSMB9||Exon 2:2004,TAPl ||Proximal Promoter: -2193, Tcell:OA_SLE_HC; 6:32845816, PBMC:notRA; 6:32847112, PBMC:notRA; 6:32847675, PBMC:HC; 6:32909282, HLA-DMA||3' Proximal Enhancer: 11617,HLA-DMB||Proximal Promoter: -435, PBMC:SLE; 6:33033312, HLA-DPAl ||Intron 4:8142|Intron 5: 15243, PBMC:OA_SLE_HC,PBMC:notRA; 6:33039500, HLA-DPAl ||Intron l : 1954|Intron 2:9055,HLA-DPBl ||Distal Promoter:-4202, PBMC:HC; 6:33048558, HLA-DPA1 ||5' Proximal Enhancer: - 7104|Proximal Promoter: -3, HLA-DPBl ||Exon 2:4856, PBMC:HC; 6:33084420, HLA-DPB2|| Intron 1 :4128, PBMC:notRA; 6:33085577, HLA-DPB2||Intron 2:5285, PBMC:notRA; 6:33085590, HLA-DPB2||Intron 2:5298, PBMC:notRA; 6:33090304, HLA-DPB2||Intron 2: 10012, PBMC:notRA; 6:33091567, HLA- DPB2||Intron 2: 11275, PBMCnotRA; 6:33091795, HLA-DPB2|| Intron 2: 11503, PBMC:notRA; 6:33096303, HLA-DPB2|| Intron 3: 16011, PBMC:notRA; 6:33096312, HLA-DPB2||Intron 3: 16020, PBMC:notRA; 6:33128825, COLl lA2||3' Proximal Enhancer: 31420, PBMC:notRA,Tcell:HC; 6:33269769, RGL2||Distal Promoter:-2604,TAPBP||3' Proximal Enhancer:Intron 6:Intron 7: 12395, PBMC:HC,PBMC:OA_SLE_HC; 6:33400505, SYNGAPl ||Exon 5: 12659, PBMC:HC; 6:33903528, PBMC:OA_SLE_HC; 6:34102222, GRM4|| Proximal Promoter: -779,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 6:3455459, SLC22A23||Intron 1: 1334, PBMC:SLE; 6:35490818, Mono:SLE; 6:35696870, ARMC12||5' Proximal Enhancer: - 7988,LOC285847||Intron 7:7854, PBMC:HC; 6:3610600, PBMC:OA; 6:36515676, STK38||Proximal Promoter: -429, PBMC:HC; 6:36611140, Mono:HC; 6:3753083, PXDCl ||Proximal Promoter:-837, PBMC:OA_SLE_HC; 6:37616410, MDGAl ||Intron 9:49356,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 6:37616482, MDGAl ||Intron 9:49284, PBMC:OA_SLE_HC,PBMC:SLE; 6:37616598, MDGAl ||Intron 9:49168,
PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 6:37904681, ZFAND3||Intron 2: 117375, BcelhHC; 6:3849442, FAM50B||Proximal Promoter:- 189, PBMC:notRA,Tcell:OA; 6:3900192, PBMC:notRA; 6:39761595, DAAM2|| Intron l : 1437|Intron 1 :823, PBMC:SLE; 6:4056654, PRPF4B||Exon 12:35086, PBMC:OA; 6:40904807, BcelhOA; 6:41254825, TREMl ||Proximal Promoter:-368, Mono:OA; 6:41312735, NCR2||Intron 4:Intron 5:9208, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:41344940, PBMC:notRA; 6:42147253, GUCAlA||Exon 6:24110,GUCA1B||3' Proximal Enhancer: 15441, Tcel OA; 6:42417086, TRERF l ||Intron 2:2697, PBMC:OA; 6:42536105, UBR2||Intron 1 :4346, PBMC:notRA; 6:4286300, PBMC:notRA; 6:42951711, PEX6||Distal Promoter: -4730,PPP2R5D||Proximal Promoter: -618, Bcel OA; 6:43655470, MRPS18A||Proximal Promoter:79, Wholeblood:notRA; 6:43655489, MRPS18A||Proximal Promoter:60, Wholeblood:notRA; 6:436594,
Bcell:OA_SLE_HC,Tcell:OA_SLE_HC; 6:43974774, C6orl223||3' Proximal Enhancer:6438, Bcel HC; 6:44537819, Mono:OA_SLE_HC; 6:45295718, RU X2|| Proximal Promoter:-335, PBMC:notRA; 6:45905407, CLIC5||Intron 4: 142678|Intron 4: 78219| Proximal Promoter:-73, Bcell:OA_SLE_HC; 6:46403466, RCAN2||Intron 2:55594|Intron 2:56338, PBMC:OA; 6:47136110, Mono:HC; 6:47624117, GPRl l l ||Proximal Promoter: -208, Wholeblood:notRA; 6:4773278, CDYL|| Distal Promoter:-3401 |Intron 3:66886, PBMC:notRA; 6:4890079, CDYL||Intron l : 113400|Intron l :53748|Intron 3: 183687|Proximal Promoter: -146, PBMC:HC; 6:4890278, CDYL||Intron l : 113599|Intron l :53947|Intron 3: 183886|Proximal Promoter:53, PBMC:HC; 6:50488809, PBMC:HC; 6:5067127, PBMC:notRA; 6:5136301, LYRM4|| Intron 2:Intron 3: 124871, PBMC:HC; 6:51953096, PKHDl ||Proximal Promoter:-673, PBMC:notRA; 6:53228363, PBMC:notRA; 6:53572893, PBMCnotRA; 6:55774999, PBMC:notRA; 6:55778951, PBMC:notRA; 6:56405167, DST||Intron 42: 102527, PBMC:HC; 6:56755566, PBMC:notRA; 6:57970592, PBMCnotRA; 6:62224316, PBMC:notRA; 6:64289969, PTP4Al ||Exon 6:8050, PBMC:notRA; 6:64423797, EYS||3' Proximal Enhancer: 1993321,PHF3||Exon 15:67367, Tcell:OA; 6:6589075, LY86||Proximal Promoter: 142,LY86-ASl ||Intron 1 :33984, Mono:HC; 6:66497885, MCART3P||Proximal Promoter: 114, PBMC:notRA; 6:6677756, Bcell:OA; 6:66804704, PBMCnotRA; 6:68849256, PBMC:notRA; 6:69726000, BAI3||Intron 12:380369, PBMC:HC; 6:69942892, BAI3||Intron 17:597261, Bcell:OA_SLE_HC; 6:71022175, COL9Al ||5' Proximal Enhancer:-9389, Wholeblood:notRA; 6:71571446, B3GAT2||Exon 4:95342,SMAPl ||Exon 10:Exon 11 : 193968, Mono:OA; 6:74104594, DDX43||Proximal Promoter:310, PBMC:notRA; 6:74160206, MB21Dl ||Intron 1 : 1837, PBMC:notRA; 6:74232108, EEFlAl ||Proximal Promoter:- 1353, Bcell:HC; 6:7482473, PBMC:notRA; 6:75381295, Tcell:OA_SLE_HC; 6:7544197, DSP||Intron 1 :2328, PBMC:notRA; 6:75953853, COX7A2||Proximal Promoter: -209,TMEM30A||3' Proximal Enhancer:40779, PBMC:notRA; 6:75953935, COX7A2||Proximal Promoter: -291,TMEM30A||3' Proximal Enhancer:40697, PBMC:notRA; 6:77563066, PBMC:OA_SLE_HC,PBMC:SLE; 6:7847437, BMP6|| Intron 2: 120427, PBMC:HC,PBMC:OA_SLE_HC; 6:790268, PBMC:SLE; 6:79620031, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 6:7986689, MUTED-TXNDC51 |Intron 4:77958,PIP5KlPl ||Proximal Promoter:355, PBMC:notRA; 6:80247907, LCA5||Proximal Promoter: -760, Bcell:OA; 6:80853625, BCKDHB||Intron 3:37282, Mono:OA_SLE_HC,Mono:SLE; 6:82405786, PBMC:OA_SLE_HC; 6:84568890, CYB 5 R4|| Proximal Promoter: -479,RIPPLY2||3' Proximal Enhancer: 5906, Mono:OA_SLE_HC; 6:84800491, MRAP2||Exon 4:57072, Mono:OA_SLE_HC,Tcell:OA_SLE_HC; 6:88119922, C6orfl65||Intron 2:2233, Bcel OA; 6:88180175, C6orfl65||3' Proximal Enhancer:62486,SLC35Al ||Proximal Promoter:-2467, PBMC:notRA; 6:88862190, CNR1 ||5' Proximal Enhancer:-7134|Intron l :Intron 2: 13577, BcelhSLE; 6:89927485, GABRR1 ||Proximal Promoter: l l, PBMC:HC; 6:91153758, PBMC:HC,PBMC:OA_SLE_HC; 6:93354486, PBMC:notRA; 6:97247547, GPR63||Exon 2:Exon 3:37806, PBMC:notRA; 7: 100144475, AGFG2||Intron 1 :7642, PBMC:HC; 7: 1003645, ADAP1 ||5' Proximal Enhancer: -9356,COX19||3' Proximal Enhancer: 11590, PBMC:OA_SLE_HC; 7: 1003710, ADAP1 ||5' Proximal Enhancer: -9421,COX19||3' Proximal Enhancer: 11525, PBMC:OA_SLE_HC; 7: 100729412, TRIM56||Intron 1 :627, PBMC:OA; 7: 101132009, EMID2||Intron 3: 125888, Tcell:OA_SLE_HC; 7: 101364176, Bcell:OA_SLE_HC; 7: 101961796, PBMC:notRA; 7: 101962123, PBMC:notRA; 7: 102329146, PBMC:notRA; 7: 102782124, NAPEPLD||Intron l :7445,RPL19P12||Exon 1 :726, PBMC:notRA; 7: 105306555, ATXN7Ll ||Intron l : 13054|Intron 3:210476, PBMC:HC,PBMC:notRA; 7: 105399252, ATXN7L1 ||3' Proximal Enhancer:Intron 3: 117779, PBMC:OA_SLE_HC; 7: 105489998, ATXN7Ll ||Intron 2:27033, PBMC:HC; 7: 105632173, CDHR3||Intron 4:28517, PBMC:notRA; 7: 1064100, C7orf50||Intron 2: 113793,MIR339||Proximal Promoter: -1438, PBMC:HC; 7: 107201750, DUS4L||Distal Promoter:-2681,
PBMC:OA_SLE_HC,PBMC:SLE; 7: 107700124, LAMB4|| Intron 23:70677,
PBMC:HC,PBMC:OA_SLE_HC; 7: 1080558, PBMC:notRA; 7: 108108892, PNPLA8||3' Proximal Enhancer:57870|3' Proximal Enhancer:59713, PBMC:OA; 7: 112062682, IFRDl ||Proximal Promoter: -516, PBMC:HC,PBMC:OA_SLE_HC; 7: 1121190, GPER||5' Proximal Enhancer:-5252|5' Proximal Enhancer: - 6532, PBMC:notRA; 7: 112411466, TMEM168||Intron 4: 19012, PBMC:notRA; 7: 112548837, C7orf60||Intron 2:31095, TcelhOA; 7: 112907863, PBMC:notRA; 7: 114026072, FOXP2||Intron 2:299708, PBMC:notRA; 7: 11568529, THSD7A|| Intron 6:303295, PBMC:OA_SLE_HC; 7: 116750996, ST7-AS2||3' Proximal Enhancer:34618, TcelhHC; 7: 116786606, ST7-AS2||Proximal Promoter: -992, BcelhSLE; 7: 117835958, NAA38||Exon 4: 11873, PBMC:notRA; 7: 1180328, PBMC:notRA; 7: 121032965, FAM3C||Intron 1 :3457, PBMC:notRA; 7: 121956643, CADPS2||3' Proximal
Enhancer:570170,LOC154860||3' Proximal Enhancer: 12932, PBMC:OA; 7: 122635026, TAS2R16||Exon 1 :728, Bcell:OA_SLE_HC; 7: 122840109, SLC13Al ||Proximal Promoter:-84, Bcel HC; 7: 123294503, LMOD2||Proximal Promoter:-1357, PBMC:notRA; 7: 123438230, PBMC:HC; 7: 123563992, SPAMl ||Proximal Promoter: -1293 |Proximal Promoter:-1916, PBMC:notRA; 7: 124404324, GPR37||Exon 1 : 1357, PBMC:OA_SLE_HC; 7: 12444095, VWDE|| Proximal Promoter:-243, PBMC:OA; 7: 12444115, VWDE||Proximal Promoter:-263, PBMC:OA; 7: 1245797, PBMC:notRA; 7: 126890254, PBMC:HC; 7: 1277154, UNCX||3' Proximal Enhancer:4501, Bcel OA; 7: 127720749, MIR593||Proximal Promoter:- 1163, PBMCnotRA; 7: 127988331, PRRT4||3' Proximal Enhancer: 13408,RBM28||Distal Promoter: -4369, BcelhHC; 7: 128020864, PBMC:HC; 7: 128045859, IMPDHl ||Exon 2:Exon 3:Exon 4:Intron 3:4177|Proximal Promoter: 165, PBMC:notRA; 7: 128116412, METTL2B||Proximal Promoter: -370, Bcell:OA_SLE_HC,Bcell:SLE,Tcell:SLE; 7: 128579933, IRF5||Intron l : 1663|Intron 1 : 1940| Proximal Promoter:-838, Tcel SLE; 7: 128579964, IRF5||Intron l : 1694|Intron l : 1971 |Proximal Promoter:-807, Tcel SLE; 7: 1286023, UNCX||3' Proximal Enhancer: 13370, PBMC:OA; 7: 129008407, AHCYL2||5' Proximal Enhancer:-7076|Intron l : 143553|Proximal Promoter:444, PBMC:notRA; 7: 129412730, MIR182||Proximal Promoter: -2398,MIR183||3' Proximal Enhancer:2124,MIR96||3' Proximal Enhancer: 1879, PBMCnotRA; 7: 129499233, UBE2H||Intron 3:93550|Intron 3:93567, PBMC:OA_SLE_HC; 7:130646078, FLJ43663||Intron 2:14571 l|Intron 3:147484, Mono:HC; 7:1315546, PBMC:notRA; 7:1329387, PBMC:notRA; 7:134002145, SLC35B4||Proximal Promoter:-318, PBMC:OA; 7:134427910, PBMC:notRA; 7:134832221, TMEM140||Proximal Promoter: -544, PBMC:HC,Tcell:HC; 7:134855509, C7orf49||Proximal Promoter:- 1283 |Proximal Promoter:-233|Proximal
Promoter:69,TMEM140||3' Proximal Enhancer:22744, PBMC:notRA; 7:1350879, PBMC:notRA; 7:135369001, C7orf73||3' Proximal Enhancer:21781,SLC13A4||Exon 15:43932, Tcell:OA; 7:135396089, SLC13A4||Intron 2:16844, Tcell:OA_SLE_HC; 7:136832262, Mono:HC,PBMC:HC,Tcell:HC; 7:138348774, SVOPL||Intron 3:15016|Proximal Promoter:195, PBMC:HC; 7:138803256, ZC3HAV1||5' Proximal Enhancer:-8791, PBMC:OA_SLE_HC; 7:139209511, CLEC2L|| Intron 1:838, PBMCnotRA; 7:139426030, HIPK2||Intron 1:51663, PBMC:HC; 7:139432178, HIPK2||Intron 1:45515, PBMC:HC; 7:139690264, TBXASl||Intron 10:Intron 9:161313|Intron ll:Intron 13:212218, Tcell:OA_SLE_HC; 7:139760375, PARP12||Intron 1:3146, PBMC:SLE,Tcell:SLE; 7:139760671, PARP12||Intron 1:2850, Bcell:SLE,PBMC:SLE; 7:139761087, PARP12||Intron 1:2434,
PBMC:HC,PBMC:OA_SLE_HC,Tcell:SLE; 7:139929429, PBMC:HC; 7:139932132, Wholeblood:notRA; 7:140043078, SLC37A3||Intron 10:Intron 13:55233, PBMC:HC; 7:141176413, LOC100507421||Exon 4:402382, Tcell:OA_SLE_HC; 7:142374345, MTRNR2L6||Proximal Promoter:215, PBMC:notRA; 7:142375072, MTRNR2L6||Exon 1:942, PBMC:OA; 7:142421812, PBMC:HC; 7:142428317, PBMC:notRA; 7:142493732, Tcell:HC; 7:142494148, Tcell:HC; 7:142494204, PBMC:SLE; 7:142494213, PBMC:SLE,Tcell:HC; 7:142494492, PBMC:SLE; 7:143059260, FAM131B||Intron l:580|Proximal Promoter:-87, PBMC:notRA; 7:143211367, PBMC:notRA; 7:143699825, OR6Bl||Proximal Promoter: - 1264, PBMC:OA_SLE_HC; 7:143825736, OR2A14||Proximal Promoter:-469, Wholeblood:notRA; 7:144056518, ARHGEF51 |Intron 1:4030, PBMC:notRA; 7:144273837, TPKl||Intron 6:Intron 7:259309, PBMC:OA; 7:148321082, C7orG3||3' Proximal Enhancer:33426, Mono:OA; 7:148941307, ZNF212||Intron 1:4566, PBMCnotRA; 7:148977647, LOC155060||Distal Promoter:-4724,ZNF783||Intron 5:18386, PBMC:notRA; 7:149318081, ZNF767||Intron 2:Intron 3:3800, Bcell:HC; 7:149414901, KRBAl||Intron 1:2754, PBMC:notRA; 7:149567078, ATP6V0E2|| Distal Promoter:-2978,LOC401431||Intron 3:3873,ZNF862||3' Proximal Enhancer:31570, PBMC:notRA; 7:149582572, ATP6V0E2||3' Proximal Enhancer: 12516, PBMC:notRA; 7:150018095, ACTR3C||Intron l:2663,C7orl29||5' Proximal Enhancer: - 8842,LRRC61||Proximal Promoter: -2200, PBMC:HC; 7:150026567, ACTR3C||5' Proximal Enhancer: - 5809,C7orl29||Proximal Promoter: -370,LRRC61||Intron l:Intron 2:6272,RARRES2||3' Proximal Enhancer: 12196, PBMC:HC,PBMC:notRA; 7:150038502, C7orl29||3' Proximal
Enhancer:11565,LRRC61||3' Proximal Enhancer: 18207,RARRES2||Proximal Promoter:261, PBMC:notRA; 7:150038898, C7orl29||3' Proximal Enhancer: 11961, LRRC61||3' Proximal
Enhancer: 18603,RARRES2||Proximal Promoter:- 135, PBMCnotRA; 7:150105086, LOC728743||Exon 2:2247,ZNF775||3' Proximal Enhancer:28681, BcelhHC; 7:150217056, GIMAP7||Exon 2:5112, PBMC:HC; 7:150263322, GIMAP4|| Proximal Promoter:- 1135, PBMC:SLE,PBMC:notRA; 7:150264284, GIMAP4||Proximal Promoter: -173, PBMC:OA; 7:150451091, LOC100128542||Intron 1:4268, PBMC:OA_SLE_HC; 7:151107285, LOC100131176||Intron l:964,WDR86||Proximal Promoter:- 161, Bcell:OA_SLE_HC; 7:151130479, CRYGN||Intron 3:6620,MIR3907||Proximal Promoter:246, Tcel HC; 7:151723607, GALNTll||Intron 1:830,GALNTL5||3' Proximal Enhancer: 70144, PBMC:notRA; 7:153108684, PBMC:SLE; 7:154006066, DPP6||Intron l:256290|Intron l:3720|Intron 1:421648, Wholeblood:notRA; 7:154455411, DPP6||Intron 6:453065|Intron 6:705635|Intron 6:870993, Tcell:OA_SLE_HC; 7:154586335, DPP6||Intron ll:1001917|Intron ll:583989|Intron 11:836559, Bcell:SLE,PBMC:SLE,Tcell:OA_SLE_HC; 7:154586375, DPP6||Intron ll:1001957|Intron ll:584029|Intron 11:836599, Tcell:OA_SLE_HC; 7:154688294, DPP6||3' Proximal Enhancer:1103876|3' Proximal Enhancer:685948|3' Proximal Enhancer:938518, PBMC:OA_SLE_HC; 7:154836613, PBMC:HC; 7:154877217, HTR5A||Exon 2:14672, PBMC:notRA; 7:155333337, CNPY1||5' Proximal Enhancer:-6798, PBMC:OA_SLE_HC; 7:155595288, SHH||3' Proximal Enhancer:9679, Mono:OA_SLE_HC; 7:155604780, SHH||Proximal Promoter: 187, Bcel OA; 7:155794668, PBMC:notRA; 7:155971032, Mono:HC,Mono:OA_SLE_HC; 7:156429188, C7orfl3||3' Proximal Enhancer:4160,RNF32||5' Proximal Enhancer:-6482|Distal Promoter:-4164|Distal Promoter:-4252, PBMC:notRA; 7:156735466, ΝΟΜ1||5' Proximal Enhancer:-6950, Mono:OA_SLE_HC; 7:156740196, NOMl||Proximal Promoter: -2220, PBMC:OA_SLE_HC; 7:156818079, LOC645249||3' Proximal Enhancer: 14529, Mono:SLE; 7:156869431, Mono:OA; 7:157072813, PBMC:OA; 7:157260189, PBMC:OA_SLE_HC; 7:157362062, MIR153-2||3' Proximal Enhancer:5052,PTPRN2||Intron 19:Intron 20:1018420, PBMC:HC; 7:157474856, Bcel OA; 7:157522373, Bcel HC; 7:157710472, PBMC:notRA; 7:157916279, BcelhOA; 7:157934685, Mono:OA_SLE_HC,PBMC:notRA; 7:157960898, PBMC:OA_SLE_HC,PBMC:notRA; 7:158050299, PBMC:HC; 7:158281138, Mono:OA; 7:158607898, ESYT2||Intron 1:14421, Wholeblood:notRA; 7:158815080, LOC154822||Intron 4:14036,VIPR2||3' Proximal Enhancer: 122569, PBMC:HC; 7:158947138, VIPR2||5' Proximal Enhancer: -9489, PBMCnotRA; 7:158964346, PBMC:HC; 7:16505592, SOSTDCl ||Proximal Promoter:- 118, Wholeblood:notRA; 7: 1688174, PBMC:HC; 7: 1702597, BcelhHC; 7: 171613, PBMC:notRA; 7: 1948947, PBMC:HC; 7: 1966361, PBMC:HC,PBMC:OA_SLE_HC; 7: 1976263, PBMC:OA_SLE_HC; 7: 1982333, PBMC:HC; 7: 1991401, PBMC:notRA; 7:2004389, BcelhOA; 7:2040555, PBMC:HC; 7:20829502, SP8||Distal Promoter:-2994, PBMC:OA_SLE_HC; 7:2099404, BcelhOA SLE HC; 7:2116368, PBMC:HC; 7:2116512, PBMC:HC; 7:2116648, PBMC:HC; 7:2139259, PBMC:notRA; 7:2150016, PBMC:OA_SLE_HC; 7:22145821, PBMC:notRA; 7:22602133, LOC100506178||Proximal Promoter:-822, PBMC:OA; 7:22765321, IL6||Proximal Promoter:-1444, PBMC:notRA; 7:23342917, C7orG0||Intron 2:3978,IGF2BP3||3' Proximal Enhancer: 167078, PBMC:notRA; 7:23509693, IGF2BP3|| Proximal Promoter:302, PBMC:notRA; 7:23719682, C7orf46||Proximal Promoter:-66, PBMC:notRA; 7:2444210, CHST12||Intron 1 : 1016, PBMC:SLE; 7:2444534, CHST12||Intron 1 : 1340, PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC,Tcell:SLE; 7:24797884, DFNA5|| Proximal Promoter: -245|Proximal Promoter:-801, PBMC:OA; 7:25015862, OSBPL3||Intron 1 :3898, PBMC:HC; 7:2551978, LFNG||5' Proximal Enhancer:-5518|5' Proximal Enhancer:-7500|Proximal Promoter: -184, PBMC:OA_SLE_HC; 7:26283764, PBMC:notRA; 7:2638278, IQCE||Intron 16:Intron 17:39647, Bcell:OA; 7:2643340, IQCE||Intron 17:Intron 18:44709, PBMC:OA_SLE_HC; 7:2648222, IQCE||Intron 20:Intron 21 :49591, Mono:OA_SLE_HC,Mono:SLE; 7:2653955, IQCE||Exon 21 :Exon 22:55324, PBMC:HC; 7:2654053, IQCE||Exon 21 :Exon 22:55422, PBMC:HC; 7:26579614, KIAA0087||Proximal Promoter:- 1170, Tcell:OA; 7:26897597, SKAP2||Intron 1 :6744, PBMC:HC; 7:26897612, SKAP2||Intron 1 :6729, PBMC:HC; 7:27192656, HOXA10-HOXA9||3' Proximal Enhancer:27224,HOXA5||5' Proximal Enhancer: -9369,HOXA6||5' Proximal Enhancer: - 5263,HOXA7||3' Proximal Enhancer:3640,HOXA9||3' Proximal Enhancer: 12493,LOC100133311 ||Exon 3: 12674|Exon 3:5875, PBMC:HC; 7:2755000, AMZl ||Exon 7:35838, PBMC:notRA; 7:29256702, CHN2||Intron 1 :22582, Bcel OA; 7:29519297, CHN2||Intron 6:285177|Proximal Promoter: -188, Tcel HC; 7:29606349, PRR15||Exon 2:2923, PBMC:OA_SLE_HC; 7:29721696, DPY19L2P3|| Distal Promoter: - 3073|Distal Promoter:-3991,LOC646762||Intron l :3058,MIR550A3||Proximal Promoter:-1252,ZNRF2P2||3' Proximal Enhancer: 3741, PBMC:HC; 7:30129938, PLEKHA8||3' Proximal EnhancenExon 13:Intron 13:61962, PBMC:HC; 7:30321030, MIR550A1 ||5' Proximal Enhancer:-8379,MIR550B1 ||3' Proximal Enhancer:8476,ZNRF2||Distal Promoter: -2892, Bcell:OA_SLE_HC; 7:30328151, MIR550Al ||Proximal Promoter:-1258,MIR550B1 ||3' Proximal Enhancer: 1355,ZNRF2||Intron 1 :4229, PBMC:HC; 7:30362781, Bcell:OA_SLE_HC; 7:30725669, CRHR2|| Distal Promoter:-3528|Intron 2:Intron 3: 14050, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 7:3134670, PBMC:SLE; 7:31425682, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 7:31557142, CCDC129||Proximal Promoter: 165, PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 7:31685368, CCDC1291| Intron 11 : 128391, PBMC:notRA; 7:32110145, PDElC||Intron l :835|Intron l :900|Intron 3:228238|Proximal Promoter:321, Bcel OA; 7:32526065, AVL9||5' Proximal Enhancer: -9110,LSM5||Exon 5:3958|Exon 5:4410|Exon 5:8805, PBMC:OA_SLE_HC; 7:32771339, MIR550A2||Proximal Promoter:-1253,MIR550B2||3' Proximal Enhancer: 1350,ZNRF2Pl ||3' Proximal Enhancer:3778, PBMC:HC; 7:32919504, KBTBD2||Exon 2: 11964, PBMC:SLE; 7:34416982, AAAl ||Intron 3:Intron 4:380902, Bcell:OA_SLE_HC; 7:35373, PBMC:HC; 7:36020705, PBMCnotRA; 7:36192369, EEPDl ||Proximal Promoter:-466, TcelhOA; 7:36342851, EEPD1 ||3' Proximal Enhancer: 150016, Mono:HC; 7:36382071, KIAA0895||Intron 2:2471 l |Intron 2:2477 l |Intron 2:24779|Intron 2:24807|Intron 3:47663, PBMC:notRA; 7:37024552, PBMC:HC; 7:3713348, SDKl ||Intron 4:372269, PBMC:OA; 7:37991986, EPDR1 ||3' Proximal Enhancer:31066|3' Proximal Enhancer:31824, PBMC:OA; 7:38309984, TARP||Intron 1 :3264, TcelhHC; 7:38316654, TARP||Distal Promoter:-3406, PBMC:HC; 7:38344455, Tcel HC; 7:38403507, LOC100506776||Intron 3:22330, PBMC:notRA; 7:39044924, POU6F2|| Intron 1 :27316, PBMC:OA; 7:39873832, PBMC:notRA; 7:41547329, PBMC:OA; 7:41919892, PBMC:HC; 7:41982337, Wholeblood:notRA; 7:41982375, Mono:OA_SLE_HC; 7:42267337, GLI3||Intron 1 :9281, TcelhHC; 7:4308120, SDKl ||Exon 45:967041 |Intron 19: 138804, Bcell:OA_SLE_HC; 7:43158788, HECWl ||Intron 2:6591, PBMC:OA; 7:43204506, PBMC:HC,PBMC:OA_SLE_HC; 7:43484421, PBMC:SLE; 7:43562162, LOC100506895||Proximal Promoter: -21, Bcell:OA_SLE_HC; 7:43698429, C7orf44||Intron 1 :70654, PBMC:HC; 7:43965451, UBE2D4||Proximal Promoter:-583,URGCP||Intron 1 :545, PBMC:SLE; 7:44083715, DBNL|| Proximal Promoter:-523,FLJ35390||3' Proximal Enhancer:4649|3' Proximal Enhancer:5018,RASA4P||Distal Promoter:-3493, Tcel OA; 7:44365361, CAMK2B|| Proximal Promoter: - 131, PBMC:notRA; 7:44923719, MIR4657||Proximal Promoter:-2320,PURB||Exon 1 : 1241, Bcel OA; 7:45075791, CCM2||Intron l :36005|Intron l :36447|Intron 1 :8559, PBMC:SLE,Tcell:SLE; 7:45617892, ADCYl ||Intron 1 :3768, BcelhOA; 7:45622395, ADCYl ||Intron 1 :8271, PBMC:notRA; 7:4573535, PBMC:notRA; 7:45959833, IGFBP3||Intron 1 : 1038, Wholeblood:notRA; 7:46285461, PBMCSLE; 7:47560215, TNS3||Intron 2:61527, PBMC:HC; 7:47580148, TNS3||Intron 1 :41594, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 7:47711149, C7orf65||3' Proximal Enhancer: 16308, PBMC:HC; 7:47976869, PBMCnotRA; 7:4850260, RADIL||Intron 9:73075, BcelhOA; 7:4859229, RADIL||Intron 6:64106, PBMC:OA_SLE_HC; 7:50450320, IKZFl ||Exon 4:Exon 5:Intron 2:Intron 4: 105943, PBMC:notRA; 7:50632994, Mono:OA_SLE_HC; 7:51170073, COBL||Intron 6:214442, PBMC:OA; 7:5183992, ZNF890P||Proximal Promoter: 185, PBMC:notRA; 7:5184155, ZNF890P||Proximal Promoter:22, PBMC:notRA; 7:5186528, ZNF890P||Proximal Promoter:-2351, PBMC:notRA; 7:5230083, WIPI2||Proximal Promoter:249, PBMC:notRA; 7:5257632, WIPI2||Exon 4:3733|Exon 6:Exon 7:27798, BcelhHC; 7:53254947, PBMC:notRA; 7:53255065, Mono:OA,PBMC:notRA; 7:5352187, SLC29A4||3' Proximal Enhancer:29627,TNRC18||Exon 27: 110990, PBMCnotRA; 7:55516724, PBMC:notRA; 7:55757733, FKBP9L||Intron 3: 14527|Proximal Promoter:-2008|Proximal Promoter:-580|Proximal Promoter: -739, PBMC:notRA; 7:55773068, FKBP9L||Proximal Promoter:-808, PBMC:notRA; 7:56118238, CCT6A||Proximal Promoter:-1139,PSPH||Intron 1 : 1030,SNORA15||5' Proximal Enhancer:- 9924, PBMCnotRA; 7:56553285, PBMC:notRA; 7:56672774, PBMC:notRA; 7:56894857, PBMC:notRA; 7:57271836, PBMC:notRA; 7:57320460, BcelhOA; 7:57484272, Wholeblood:notRA; 7:57512798, ZNF716||Intron 1 :2916, PBMC:notRA; 7:63217221, PBMC:notRA; 7:63222556, Wholeblood:notRA; 7:63250517, Mono:HC; 7:63361617, Mono:HC; 7:63504673, ZNF727||Proximal Promoter:-1147, Bcell:OA_SLE_HC; 7:63505584, ZNF727||Proximal Promoter:-236, PBMC:notRA; 7:63812985, ZNF736||3' Proximal Enhancer:39800, PBMC:notRA; 7:64126140, ZNF107||Proximal Promoter: -370, Mono:SLE,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:SLE; 7:64197047, PBMC:notRA; 7:64197245, PBMC:notRA; 7:65938820, PBMC:notRA; 7:6659785, ZNF853||Intron 2:4259, PBMC:HC; 7:6750462, ZNF12||Distal Promoter:-3896, PBMC:notRA; 7:6893572, PBMC:notRA; 7:68983823, PBMC:notRA; 7:69062082, AUTS2||Proximal Promoter:-1822|Proximal Promoter: -1823, PBMC:HC; 7:70139561, AUTS2||Intron 5: 1075656|Intron 5: 1075657, Tcell:OA_SLE_HC; 7:7015218, Tcell:OA_SLE_HC; 7:71407448, CALNl ||Intron 4:394760|Intron 5:469912, PBMC:notRA; 7:72399451, POM121 ||Intron 6:49516, PBMC:notRA; 7:72838601, FZD9||5' Proximal Enhancer:-9507, Mono:OA; 7:73085754, DNAJC30||3' Proximal Enhancer: 12027, VPS37D||Exon 4:3581, PBMC : SLE,PBMC :notRA; 7:73897230, GTF2IRDl ||Intron 1 :29111, PBMC:HC; 7:74058031, PBMC:HC; 7:74304373, PMS2P5||Distal Promoter: - 2520,STAG3L2||Intron 2:2358, PBMC:notRA; 7:75472540, PBMC:notRA; 7:75582881, SNORA14A||3' Proximal Enhancer:9781, PBMC:HC; 7:75674098, MDH2||Distal Promoter:-3294,STYXLl ||Intron 1 :3223, Bcell:OA; 7:75683547, MDH2||Intron 1 :6155,STYXL1 ||5' Proximal Enhancer:-6226, PBMC:HC; 7:75912349, SRRM3||Exon 14:81134, PBMC:OA; 7:76027001, SRCRB4D||Exon 6: 12011,ZP3||Proximal Promoter: 161, Wholeblood:notRA; 7:76094015, DTX2||Intron l :Intron 2:3044,FDPSL2A||3' Proximal Enhancer: 10302, PBMC:notRA; 7:76139470, DTX2||3' Proximal Enhancer:29644,UPK3B||Proximal Promoter: -274, PBMC:OA_SLE_HC; 7:76221076, LOCI 0013309 l ||Intron 2:42419, PBMCnotRA; 7:76624761, DTX2Pl-UPK3BPl-PMS2Pl l ||Intron 2: 14623, PBMC:notRA; 7:767490, HEATR2|| Intron l : 1153,PRKARlB||Proximal Promoter:-177|Proximal Promoter: -512, TcelhSLE; 7:76829845, CCDC146||Intron 2:77912,FGL2||Proximal Promoter:-695, Mono:SLE; 7:76956562, PION||Intron 22:89155, Bcell:OA_SLE_HC; 7:77044158, PION||Intron 1 : 1559, PBMC:OA_SLE_HC; 7:78368660, BcelhHC; 7:786861, HEATR2||Intron 4:20524, Mono:OA; 7:79083056, MAGI2-AS3||Intron l :Intron 2:784|Proximal Promoter: -219, Mono:OA; 7:8010894, GLCCIl ||Intron 1 :2472, PBMC:OA_SLE_HC,PBMC:SLE; 7:80970, Mono:HC; 7:85930749, PBMC:notRA; 7:86782435, DMTFl ||Intron l :566|Intron 1 :759, PBMC:notRA; 7:91811178, PBMCnotRA; 7:93474158, PBMC:OA_SLE_HC; 7:94144926, CASDl ||Intron 1 :5757, PBMC:notRA; 7:94954059, PONl ||Proximal Promoter:-175, PBMC:SLE; 7:95811907, SLC25A13||Intron 10:Intron 11 : 139552, PBMC:notRA; 7:961457, ADAPl ||Intron 3:32832, PBMC:HC; 7:963471, ADAPl ||Intron 3:30818, PBMC:OA; 7:963768, ADAPl ||Intron 3:30521, PBMC:HC; 7:965485, ADAPl ||Intron 3:28804, PBMC:SLE; 7:96633631, DLX6||Proximal Promoter:-1658,DLX6-ASl ||Intron 1 :9746, PBMC:notRA; 7:96643821, DLX5||3' Proximal Enhancer: 10322,DLX6||3' Proximal Enhancer:8532,DLX6-ASl ||Proximal Promoter: -444, PBMC:HC,PBMC:OA_SLE_HC; 7:97584538, PBMC:notRA; 7:97663876, PBMC:OA_SLE_HC; 7:98739698, SMURFl ||Intron 1 :2045, PBMC: SLE; 7:98741636, SMURFl ||Proximal Promoter: 107, PBMC:notRA; 7:98991138, ARPClB||Intron 8: 18841,PDAP1 ||3' Proximal Enhancer: 15167, PBMC:SLE; 7:99198176, LOC100289187||Intron 2:2275, PBMC:notRA; 7:99277394, CYP3A5||Proximal Promoter:227, PBMC:notRA; 7:99541626, BcelhOA SLE HC; 7:99559579, AZGP1 ||3' Proximal Enhancer: 14156, PBMC:OA_SLE_HC; 7:99680280, COPS6||5' Proximal Enhancer: -6302,ZNF3||Proximal Promoter: -909, PBMC:notRA; 7:99816988, GATS||Intron 4:Intron 5:52867,PVRIG||Proximal Promoter: 118,STAG3||3' Proximal Enhancer:41451, PBMC:HC; 7:99818709, GATS||Intron 4:Intron 5:51146,PVRIG||Exon 6: 1839,STAG3||3' Proximal Enhancer:43172, PBMC:HC; 7:999994, ADAP1 ||5' Proximal Enhancer:-5705,COX19||3' Proximal Enhancer: 15241, PBMC:OA; 8: 101119691, RGS22||Proximal Promoter:- 1347, Bcel HC; 8: 101315498, RNF19A|| Intron l :6829|Proximal Promoter:- 11, PBMC:HC; 8: 101571111, ANKRD46||Intron 1 :901, PBMC:OA_SLE_HC; 8: 102381107, NACAPl ||Proximal Promoter:-13, PBMC:notRA; 8: 103548145, PBMC:HC; 8: 10382165, PRSS55||Proximal Promoter:-890, Bcel HC; 8: 104032819, ATP6VlCl ||Proximal Promoter: -428, PBMC:notRA; 8:104123140, Wholeblood:notRA; 8:104131768, PBMC:OA_SLE_HC; 8:104132683, PBMC:HC; 8:10469310, RPlLlpxon 4:43307, PBMC:notRA; 8:10488231, RPlLl||Intron 1:24386, Mono:OA_SLE_HC,PBMC:SLE; 8:10512459, RPlLl||Proximal Promoter:158, Bcell:HC; 8:10530148, C8orf74||Proximal Promoter:2, Bcell:HC; 8:107227878, PBMC:notRA; 8:107460168, OXRl||Intron 2:177763|Proximal Promoter:17, Mono:OA_SLE_HC; 8:107876626, PBMC:notRA; 8:1080058, PBMC:notRA; 8:110988444, KCNVl||Proximal Promoter:-1485, PBMC:SLE; 8:11141415, MTMR9||Proximal Promoter:-584, PBMC:notRA; 8:111834776, PBMC:notRA; 8:11203954, TDH||Intron 1:6809, PBMC:notRA; 8:11351135, BLK||Proximal Promoter:-385, Mono:HC; 8:11356603, BLK||Intron 1:5083, PBMC:notRA; 8:1136742, PBMC:HC; 8:11413186, BLK||Intron 8:61666, Mono:HC; 8:11499692, PBMC:OA_SLE_HC; 8:11565725, GATA4||Exon 2:4009, PBMC:OA; 8:11567691, GATA4|| Intron 2:5975, TcelhOA SLE HC; 8:116231420, PBMC:HC,Tcell:OA_SLE_HC; 8:116276590, PBMC:OA; 8:11640960, NEIL2||Intron 3:Intron 4:13789, PBMC:HC; 8:11666485, FDFTl||Intron 2:6296, Wholeblood:notRA; 8:117466702, PBMC:HC; 8:11770970, PBMC:notRA; 8:117947783, C8orf85||Distal Promoter:-2680, Bcell:OA_SLE_HC; 8:11882982, PBMC:notRA; 8:119456570, SAMD12||Intron 2:177614, PBMC:SLE; 8:120257063, MAL2||Exon 4:36454, Bcell:HC; 8:1203186, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 8:120886984, DEPTOR||Intron 1:1085, PBMCnotRA; 8:122455018, PBMC:notRA; 8:12429581, LOC100506990||3' Proximal Enhancer: 135060, PBMC:notRA; 8:124412914, ATAD2||Distal Promoter: -4209, PBMC:notRA; 8:125784769, PBMC:HC; 8:126588554, PBMC:HC; 8:126981336, PBMC:notRA; 8:128427306, POU5FlB||Proximal Promoter:-550, Bcell:SLE,PBMC:OA_SLE_HC; 8:128940078, PBMC:notRA; 8:128994030, PBMC:HC; 8:129082086, PBMC:notRA; 8:129180010, Tcell:SLE; 8:129696418, Mono:OA_SLE_HC,Mono:SLE,PBMC:notRA; 8:12990744, DLCl||Intron 5:381685|Proximal Promoter:65, PBMC:OA; 8:129985596, PBMC:HC,PBMC:OA_SLE_HC; 8:130997672, Mono:HC; 8:131265658, PBMC:OA_SLE_HC; 8:131308633, ASAPl-ITl||Proximal Promoter:146, PBMC:HC; 8:131325625, PBMC:HC; 8:134467835, ST3GALl||Exon 10:Exon 9:116348, PBMC:notRA; 8:134559320, ST3GALl||Intron 1:24863, Bcell:OA_SLE_HC; 8:134701487, Bcell:HC; 8:135479018, PBMC:HC,Tcell:HC; 8:135494242, ZFAT||Intron 13:Intron 15:Intron 16:214559|Intron 14:Intron 15:231050, PBMCnotRA; 8:139919163, COL22Al||Intron 1:7073, PBMC:notRA; 8:1400221, PBMC:notRA; 8:140643119, KCNK9||Intron 1:72180, Bcell:SLE; 8:141109051, TRAPPC9||Intron 17:358810|Intron 17:359627, PBMCnotRA; 8:141109731, TRAPPC9||Intron 17:358130|Intron 17:358947, Mono:OA; 8:141342131, TRAPPC9||Intron 9:125730|Intron 9:126547, PBMCnotRA; 8:1418893,
Bcell:OA_SLE_HC,Bcell:SLE,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC ; 8:142219444, SLC45A4||3' Proximal Enhancer: 19229, PBMC:HC; 8:142222685, SLC45A4||Intron 6:15988, PBMC:HC; 8:143214333, PBMC:notRA; 8:143283647, LINC00051||Intron 1:3931,TSNARE1||3' Proximal Enhancer:200896, PBMC:OA; 8:143336052, TSNAREl||Intron 12:148491, PBMC:SLE; 8:143376371, T SNARE l||Intron 10:108172, PBMCnotRA; 8:143516572, PBMC:SLE; 8:143645661, PBMC:OA_SLE_HC; 8:143781340, LOC100288181||3' Proximal Enhancer:27051,LY6K||Proximal Promoter:-188, BcelhOA; 8:143852587, LYNX1||3' Proximal Enhancer:5850|3' Proximal Enhancer: 6157|3' Proximal Enhancer:7053|Intron 3:7052|Proximal Promoter: -1341, PBMC:HC,PBMC:OA_SLE_HC; 8:143926325, GML||Intron 3:10109, TcelhHC; 8:143957809, CYPllBl||Exon 5:3427, PBMC:notRA; 8:144069849, LOC100133669||Intron 1:29958, Tcell:OA_SLE_HC; 8:144070338, LOC100133669||Intron 1:29469, Bcell:OA_SLE_HC; 8:144098888, LOC100133669||Intron l:919,LY6E||Proximal Promoter: - 1013, PBMC:OA_SLE_HC; 8:144099482, LOC100133669||Proximal Promoter:325,LY6E||Proximal Promoter: -419, Mono:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 8: 144102584,
LOC100133669||Distal Promoter: -2777,LY6E||Intron 2:2683,
Bcell:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 8:144103587, LOC100133669||Distal Promoter:- 3780,LY6E||Exon 4:3686, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 8:144105210, LOC100133669||5' Proximal Enhancer:-5403,LY6E||3' Proximal Enhancer:5309, Mono: SLEJcell: SLE; 8:144105259, LOC100133669||5' Proximal Enhancer:-5452,LY6E||3' Proximal Enhancer:5358, PBMC:SLE,Tcell:SLE; 8:144107231, LOC100133669||5' Proximal Enhancer:- 7424,LY6E||3' Proximal Enhancer:7330, TcelhSLE; 8:144156462, PBMC:HC; 8:144255688, PBMC:notRA; 8:144265337, BcelhHC; 8:144365013, GLI4||3' Proximal Enhancer: 15407,ZNF696||5' Proximal Enhancer:-8545, BcelhHC; 8:144371745, ZNF696||Proximal Promoter:-1813, PBMC:notRA; 8:144371779, ZNF696||Proximal Promoter:- 1779, PBMC:notRA; 8:144417263, TOP 1MT|| Proximal Promoter:-213, PBMC:OA_SLE_HC,PBMC:SLE; 8:144544041, ZC3H3||Intron 9:79579, PBMC:HC; 8:144631887, GSDMD||5' Proximal Enhancer:-8589|Distal Promoter:-3669,ZC3H3||5' Proximal Enhancer: - 8267, Wholeblood:notRA; 8:144631915, GSDMD||5' Proximal Enhancer:-8561|Distal Promoter: - 3641,ZC3H3||5' Proximal Enhancer: -8295, Wholeblood:notRA; 8:144917532, NRBP2||Exon 18:5614,PUF60||5' Proximal Enhancer:-5995|5' Proximal Enhancer:-6336,
Bcell:SLE,Mono:SLE,PBMC:SLE; 8:145003776, PLEC||Intron 23:12916|Intron 23:14334|Intron 23:15129|Intron 23:21268|Intron 23:24312|Intron 23:43921|Intron 23:9982|Intron 24:47137, PBMC:SLE,Tcell:OA_SLE_HC; 8: 145017520, MIR661||3' Proximal Enhancer: 1927,PLEC||Distal Promoter:-3762|Intron l: 10568|Intron l: 1385|Intron l:30177|Intron l:590|Intron l:7524|Intron 2:33393|Proximal Promoter:-828, Tcell:OA_SLE_HC; 8:145023013, MIR661||Distal Promoter: - 3566,PLEC||5' Proximal Enhancer:-6321|5' Proximal Enhancer:-9255|Distal Promoter: -4108|Distal Promoter: -4903 |Intron l:2031|Intron l:24684|Intron l:5075|Intron 2:27900, PBMC:HC; 8:145028222, MIR661||5' Proximal Enhancer:-8775,PLEC||5' Proximal Enhancer:-9317|Distal Promoter:-3178|Intron l: 19475|Intron 2:2269 l|Proximal Promoter:-134, PBMC:HC; 8: 145028402, MIR661||5' Proximal Enhancer:-8955,PLEC||5' Proximal Enhancer: -9497|Distal Promoter:-3358|Intron l:19295|Intron 2:225 l l|Proximal Promoter:-314, PBMC:OA_SLE_HC; 8: 145029603, PBMC:HC; 8: 145086427, SPATCl||Proximal Promoter:- 154, Mono:OA; 8:145910754, PBMC:OA; 8: 15807734, Mono:OA; 8: 1649143, DLGAP2|| Intron 11: 199575, Mono:OA_SLE_HC; 8: 17270834, MTMR7|| Proximal Promoter:206, PBMC:OA; 8:17471997, PDGFRL||Intron 3:38056, PBMC:SLE; 8:1789169, ARHGEF 1011 Intron 1: 17021, PBMC:OA_SLE_HC; 8: 1792758, ARHGEF10||Intron 2:20610, Wholeblood:notRA; 8: 1872335, ARHGEF 1011 Intron 21:100187, PBMC:HC; 8:1897969, ARHGEF 1011 Intron 27:125821, PBMC:notRA; 8: 1905131, ARHGEF 10||Exon 29: 132983, PBMC:notRA; 8: 19243209, SH2D4A||Intron 7:Intron 8 : 721291 Intron 8:71723, Bcell:OA_SLE_HC; 8: 19333253, CSGALNACTl||Intron 3:207008|Intron 4: 126803|Intron 4:206841, PBMC:SLE; 8:19409023, C SGALNACT 111 Intron 2:131238|Intron 3:131071|Intron 3:51033, Mono:OA_SLE_HC,PBMC:HC; 8: 1948999, KBTBDl l||Exon 2:26956, Bcel OA; 8: 19540272, CSGALNACTl||Proximal Promoter:- l l|Proximal Promoter:- 178, PBMC:notRA; 8: 1955069, KBTBDl l||Exon 2:33026, Mono:SLE; 8:1959121, KBTBD11||3' Proximal Enhancer:37078, PBMC:OA; 8:20041853, SLC18Al||Proximal Promoter:- 1136, PBMC:notRA; 8:2029571, MYOM2||Intron 13:36414, PBMC:OA; 8:2034467, MYOM2|| Intron 14:41310, PBMC:notRA; 8:21179380, Bcel HC; 8:216453, PBMC:OA_SLE_HC; 8:216703, PBMC:OA_SLE_HC; 8:21824555, XP07||Intron 2:47376, PBMC:HC; 8:21918075, EPB49||Intron l:1390|Intron l:2700|Intron l:5748|Intron 1:6995, Mono:OA,Tcell:SLE; 8:21923551, EPB49||Intron l: 11224|Intron l:12471|Intron l:6866|Intron 1:8176, Mono:OA_SLE_HC; 8:22411211, SORBS3||Intron 1:1961, Mono:HC; 8:22561893, PEBP4||3' Proximal Enhancer:223528, PBMCnotRA; 8:22922124, LOC286059||Distal Promoter: - 3617,TNFRSF10B||Intron 1:4576, BcelhHC; 8:22925656, LOC286059||Proximal Promoter: - 85,TNFRSF10B||Intron 1: 1044, Tcel HC; 8:23100981, CHMP7||Proximal Promoter: -168, PBMC:SLE; 8:23602677, PBMC:HC,PBMC:OA_SLE_HC; 8:2418843, PBMC:OA_SLE_HC; 8:24212569, ADAM28||Exon 23:60990, PBMC:notRA; 8:24768802, NEFM||Distal Promoter:-3652|Proximal Promoter: - 2471, PBMC:notRA; 8:2480426, PBMC:OA_SLE_HC; 8:24855264, PBMC:OA; 8:25072319, DOCK5||Intron 1:30033, PBMC:HC; 8:25227128, DOCK5||Exon 34:184842, Bcell:OA_SLE_HC; 8:2585235, PBMC:notRA; 8:25909385, EBF2||5' Proximal Enhancer:-6745, Tcel OA; 8:2628628, PBMC:notRA; 8:26467541, DPYSL2||Intron 3:31621|Intron 3:32202|Intron 3:95833, PBMC:HC; 8:27117108, STMN4||Proximal Promoter:-1205, PBMC:notRA; 8:27157515, TRIM35||Intron 1:11319, Mono:HC,PBMC:notRA; 8:27449716, CLU||3' Proximal Enhancer: 19238|3' Proximal Enhancer: 19552|3' Proximal Enhancer:22612, Tcel HC; 8:27467783, CLU||Intron 2:1171|Intron 2:1485|Intron 2:4545, Mono:HC,Mono:OA_SLE_HC; 8:27469673, CLU||Intron l:2655|Proximal Promoter: -405|Proximal Promoter:-719, Bcel HC; 8:28174847, PNOC||Proximal Promoter: 199, PBMC:notRA; 8:28174928, PNOC||Proximal Promoter:280, PBMC:notRA; 8:28918821, ΗΜΒΟΧ1||3' Proximal Enhancer: 170597|3' Proximal Enhancer: 170911,KIF13B||3' Proximal Enhancer:201789, PBMC:HC; 8:29086832, KIF13B||Intron 2:33778, PBMC:SLE; 8:29177713, PBMC:HC; 8:29441416, PBMC:HC; 8:29605992, C8ori75||Proximal Promoter:-367, PBMC:notRA; 8:29743492, PBMC:HC; 8:29971104, LEPROTLl||3' Proximal Enhancer: Intron 3:18183, Mono:HC; 8:30279999, RBPMS||Intron 1:38056, PBMC:notRA; 8:30402570, RBPMS||Intron 6:160627, PBMC:HC; 8:33210211, PBMCnotRA; 8:33338897, FUT10||5' Proximal Enhancer:-8233,MAK16||Distal Promoter:-3787, Mono:OA_SLE_HC; 8:33580504, PBMC:notRA; 8:36636824, KCNU1||5' Proximal Enhancer:-5017, PBMC:notRA; 8:37119428, PBMC:SLE; 8:37168415, PBMC:OA; 8:37397163, Tcel OA; 8:37707692, BRF2|| Proximal Promoter: - 261,GPR124||3' Proximal Enhancer:53292,RABl 1FIP1||3' Proximal Enhancer:49323, PBMC:OA_SLE_HC; 8:37773605, PBMC:notRA; 8:38759261, PLEKHA2||Intron 1:509, PBMC:notRA; 8:41004167, PBMC:notRA; 8:41464795, AGPAT6|| Intron 2:29089, Bcel OA; 8:42266931, SLC20A2||3' Proximal Enhancer: 130137,VDAC3||3' Proximal Enhancer:17653, Bcell:OA_SLE_HC; 8:42698936, RNF170||3' Proximal Enhancer: 52930,THAPl||Proximal Promoter: -462, PBMC:HC,PBMC:notRA; 8:42829775, HOOK3||Intron 13:77743, PBMC:notRA; 8:42910303, FNTA|| Proximal Promoter:- 1138, PBMC:notRA; 8:42914541, FNTA||Intron l:Intron 2:3100, PBMC:OA; 8:47015854, PBMC:notRA; 8:47829660, Tcel HC; 8:48091487, LOC100287846||5' Proximal Enhancer:-9442, PBMC:HC; 8:48595620, KIAA0146||Intron 11:422132, PBMC:OA_SLE_HC; 8:49041991, Mono:OA_SLE_HC; 8:49311685, PBMC:OA_SLE_HC; 8:49494724, Bcel HC; 8:50220067, PBMC:notRA; 8:51528401, SNTGl||Intron 13:703805, PBMC:notRA; 8:52322341, PXDNL||Intron 16:399664, PBMC:notRA; 8:52530125, PXDNL||Intron 2: 191880, Tcell:OA; 8:52771466, PCMTDl||Intron 2:40269, PBMC:HC; 8:53352237, Mono:OA; 8:53883763, Tcell:SLE; 8:55375066, SOX17||3' Proximal Enhancer:4572, Wholeblood:notRA; 8:56903623, LYN||Intron 10: 111238, PBMC:HC; 8:57030824, MOS||Distal Promoter: -4283, PBMC:notRA; 8:58121215, PBMC:notRA; 8:58131602, LOC100507651||Proximal Promoter:-45, PBMC:HC; 8:58177661, LOC286177||Intron 2:3877, Bcell:HC; 8:585714, TcelhOA SLE HC; 8:59650783, Mono:HC; 8:599963,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 8:600039, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 8:600233, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC; 8:600429, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Mono:SLE,Tcell:SLE; 8:600488, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC,Tcell:SLE;
8:61088307, Bcell:OA_SLE_HC; 8:61563866, PBMC:HC; 8:61777859, CHD7||Exon 38:186536, Tcell:OA_SLE_HC; 8:62673444, Mono:HC,Mono:OA_SLE_HC; 8:63776642, NKAIN3|| Intron 4:615142, PBMC:notRA; 8:63776762, NKAIN3|| Intron 4:615262, PBMC:notRA; 8:6419438, ANGPT2|| Intron l: 1346,MCPHl||Intron 12:155326, PBMC:HC,PBMC:OA_SLE_HC; 8:6419483, ANGPT2||Intron l: 1301,MCPHl||Intron 12:155371, PBMC:HC,PBMC:OA_SLE_HC; 8:6419570, ANGPT2||Intron l: 1214,MCPHl||Intron 12: 155458, PBMC:HC,PBMC:OA_SLE_HC; 8:6421171, ANGPT2|| Proximal Promoter:-387,MCPHl||Intron 12:157059, PBMC:HC; 8:6638123, Bcell:OA; 8:6655944, Wholeblood:notRA; 8:66582206, MTFRl||Exon 2:25319|Proximal Promoter:99, PBMCnotRA; 8:66751182, PDE7A||Intron 1:2787, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 8:6695409, LOC100652791||Intron 2:2334,XKR5||Proximal Promoter:-2243, PBMC:OA; 8:67587053, C8orf44||Intron l:7267,C8orf44-SGK3||Intron 1:7267,VCPIP1||5' Proximal Enhancer:-7601, PBMC:notRA; 8:67592861, C8orf44||Exon 3:13075,C8orf44-SGK3||Intron 2: 13075, PBMC:SLE,Tcell:OA_SLE_HC; 8:68110902, ARFGEFl||Exon 39:145010,CSPP1||3' Proximal Enhancer: 134300, Mono:HC; 8:6930612, PBMC:notRA; 8:70984270, PRDM14||Proximal Promoter:-708, PBMC:OA; 8:73065416, PBMCnotRA; 8:75418022, PBMC:notRA; 8:756670, Tcell:OA_SLE_HC; 8:77585222, LOC100192378||Exon 2: 10288,ZFHX4||5' Proximal Enhancer:-8292, Tcell:OA_SLE_HC; 8:7874997, PBMC:OA; 8:81177379, Bcell:HC; 8:81178033, PBMC:notRA; 8:8180214, SGK223||Intron 4:59043, PBMC:notRA; 8:81827712, Wholeblood:notRA; 8:83353753, Tcell:HC; 8:840398, Bcell:OA; 8:86089846, E2F5||Proximal Promoter:228, PBMC:notRA; 8:86157641, CA13||Proximal Promoter:-74, Bcell:OA; 8:8679450, MFHASl||Intron 1:71681, PBMC:notRA; 8:900076, PBMC:notRA; 8:90918972, OSGIN2||Intron 1:421 l|Intron 1:4877, PBMC:notRA; 8:91094847, CALBl||Proximal Promoter:260, PBMC:OA; 8:95959531, TP53INPl||Intron 1:2084, Mono:SLE; 8:96258496, C8orG7||Exon 6:22966, PBMCnotRA; 8:96705765, LOC100616530||Intron 2:Intron 3:Intron 4:424702, PBMC:HC; 8:97166036, GDF6||Intron 1:6984, PBMC:OA; 8:9741960, PBMC:SLE; 8:9765583, LOC157627||Distal Promoter: -4744,MIR124- l||Distal Promoter:-4601, Bcell:OA_SLE_HC; 8:97657097, PGCP||Proximal Promoter: -401, PBMC:SLE; 8:97658325, PGCP||Intron 1:827, Tcell:SLE; 8:9766172, LOC157627||5' Proximal Enhancer: - 5333,MIR124-1||5' Proximal Enhancer: -5190, PBMC:HC; 8:98290359, TSPYL5||Proximal Promoter: -183, PBMC:notRA; 8:98438319, PBMC:notRA; 8:98791446, LAPTM4B||Intron 1:3638, PBMC:notRA; 8:99259528, NIPAL2|| Intron 3:47093, Mono:OA_SLE_HC; 9:100000033, BDAGl||Proximal Promoter: - 674,LOC100499484||Proximal Promoter:-674, PBMC:SLE; 9: 100394654, NCBPl||Proximal Promoter: - 1050,TSTD2||Intron 1: 1308, Bcell:OA_SLE_HC,Tcell:SLE; 9: 100850391, NANS||3' Proximal Enhancer:31433,TRIM14||Intron 5:31089|Intron 5:31097, PBMC:OA_SLE_HC; 9: 100881995, COR02A||3' Proximal Enhancer:53179|3' Proximal Enhancer: 72961,TRIM14||Proximal Promoter: - 507|Proximal Promoter:-515, PBMC:notRA; 9: 101869277, TGFBRl||Intron 1: 1866, PBMC:notRA; 9: 102123906, Bcel OA; 9:104160145, MRPL50||Intron l:774,ZNF189||Proximal Promoter:-1017, PBMC:HC; 9: 104249936, C9orfl25||Proximal Promoter: -461, PBMC:HC; 9: 108206805, FSD1L|| Distal Promoter:-3509|Distal Promoter:-3519, Tcel OA; 9:109625179, ZNF462||Proximal Promoter:-198, BcelhHC; 9:109683834, MIR548Q||Intron 2:164882,ZNF462||Intron 1:58457, PBMC:HC; 9: 110266728, BcelhOA SLE HC; 9:112296723, PBMCnotRA; 9:114359, CBWD1||3' Proximal Enhancer:64716,FOXD4||3' Proximal Enhancer:4058, PBMC:notRA; 9: 114428306, DNAJC25- GNG10||Intron l:34675,GNG10||Intron 1:4456, PBMC:OA_SLE_HC; 9:115248156, KIAA1958||Proximal Promoter: -1091, Bcel OA; 9: 116570319, PBMC:OA; 9:117134861, AKNA||Intron 4:21824, Bcel OA; 9: 117694183, TNFSF8||Proximal Promoter:- 1308,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 9: 123688715, TRAFl||Intron
2:2736|Proximal Promoter:458, PBMC:HC; 9:123688745, TRAFl||Intron 2 :2706| Proximal Promoter:428, Mono:HC,PBMC:HC; 9: 124463457, DAB2IP||Intron 3: 134059, BcelhOA SLE HC; 9:124990276, LHX6||5' Proximal Enhancer:-6257|Intron l:815|Proximal Promoter: -41 l|Proximal Promoter:431, PBMC:notRA; 9:126101872, PBMC:notRA; 9:126155038, DE ND1A||3' Proximal Enhancer: Intron 20:537379,MIR601 ||3' Proximal Enhancer:9844, PBMC:HC,PBMC:notRA; 9: 127215669, GPR144||Exon 4:2247, PBMC:OA; 9: 128022358, GAPVDl ||Proximal Promoter:- 1752, PBMC:HC; 9: 128774824, PBMC:notRA; 9: 128776861, PBMC:notRA; 9: 128777132, PBMC:notRA; 9: 129099507, FAM125B||Intron 1 : 10385, PBMC:HC; 9: 129377854, LMXlB||Intron 2: 1133, PBMC:HC; 9: 132096417, PBMC:HC; 9: 132652466, FNBPl ||Exon 17: 153007,USP20||3' Proximal Enhancer:54710|3' Proximal Enhancer:54771, PBMC:HC,PBMC:SLE; 9: 133312912, ASS1 ||5' Proximal Enhancer:-7181, PBMC:SLE; 9: 134127575, FAM78A||3' Proximal Enhancer:24331, PBMC:HC; 9: 134139878, FAM78A||Intron 1 : 12028, PBMC:OA_SLE_HC; 9: 134955070, MED27||Proximal Promoter:204, PBMC:notRA; 9: 135584293, Mono:OA_SLE_HC; 9: 135853992, GFIlB||Proximal Promoter: -105, PBMC:HC; 9: 136134067, ABO||Intron 4: 16563, PBMC:notRA; 9: 136522927, DBH||Intron 11 :21443, SARDH||3' Proximal Enhancer:80552|3' Proximal Enhancer:82150, PBMC:notRA; 9: 136565608, SARDH||Intron 13:37871 |Intron 13:39469, Tcell:SLE; 9: 136567064, SARDH||Intron 13:36415|Intron 13:38013, PBMC:OA_SLE_HC,PBMC:SLE; 9: 136721183, VAV2||Intron 3: 136263, PBMC:HC; 9: 136822302, VAV2||Intron 1 :35144, PBMC:OA_SLE_HC,PBMC:notRA; 9: 137174989, Bcell:SLE; 9: 137302231, PBMC:HC; 9: 137515845, Bcell:OA_SLE_HC,Bcell:SLE,PBMC:notRA,Tcell:OA_SLE_HC;
9: 138375675, PPPlR26||Intron 2:4028, Bcell:HC; 9: 138997380, C9orf69||3' Proximal Enhancer: 13351, PBMC:HC; 9: 139096080, LHX3||Intron l :875|Proximal Promoter:-1076,QSOX2||3' Proximal Enhancer:41607, PBMC:HC; 9: 139607421, FAM69B||Proximal Promoter:398, PBMC:OA_SLE_HC; 9: 139644102, LCN10||5' Proximal Enhancer:-6691,LCN15||3' Proximal Enhancer: 14863,LCN6||Proximal Promoter:-1122,LCN8||3' Proximal Enhancer: 8629,LOC 100128593 ||Exon 3:3490,
Bcell:SLE,PBMC:HC,PBMC:OA_SLE_HC; 9: 139796499, Bcell:OA_SLE_HC,Bcell:SLE,PBMC:SLE; 9: 139926740, ABCA2||Distal Promoter:-3366|Distal Promoter:-4000,C9orfl39||Exon 2:4825,FUT7||Exon 1 :552,NPDC1 ||3' Proximal Enhancer: 13936, PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 9: 140336654, ENTPD8||Proximal Promoter:-753,NELF||3' Proximal Enhancer: 17132,NOXAl ||3' Proximal Enhancer: 18808, PBMC:notRA; 9: 140343854, ENTPD8||5' Proximal Enhancer:-7953,NELF||Exon 14:Exon 15:Exon 16:9932, TcelhSLE; 9: 140356757, NELF||Distal Promoter:-2971,PNPLA7||Exon 30:Exon 31 :88229, Tcel OA; 9: 140388604, PNPLA7|| Intron 18:Intron 19:56382, PBMC:OA; 9: 140687144, PBMC:HC; 9: 140703637, Mono:OA_SLE_HC; 9: 140707378, PBMC : SLE,PBMC :notRA; 9: 17579227, SH3GL2||Proximal Promoter:275, PBMC:OA; 9: 19789383, SLC24A2||Proximal Promoter:- 2366, Wholeblood:notRA; 9:25678683, TUSCl ||Proximal Promoter: 173, BcelhOA; 9:27109293, TEK||Proximal Promoter: 147, PBMC:HC; 9:27610826, PBMC:notRA; 9:32525315, DDX58||Intron 1 : 1007, Bcell:SLE,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:SLE; 9:34726950, FAM205A||Exon 4:2585, PBMC:notRA; 9:34988294, DNAJB5||Proximal Promoter:-1343|Proximal Promoter:-1972,KIAA1045||3' Proximal Enhancer:30103, Tcel HC; 9:35079141, FANCG||Intron 2:872,PIGO||3' Proximal Enhancer: 17405|3' Proximal Enhancer: 17457,VCP||5' Proximal Enhancer: -6402, Mono:OA; 9:35754421, GBA2||5' Proximal Enhancer:-5196,MSMP||Proximal Promoter:-147,RGPl ||3' Proximal Enhancer: 5145, Mono:OA; 9:35908117, HRCT1 ||3' Proximal Enhancer: 1929,LOC158376||Proximal Promoter:-1362, Bcell:OA,Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 9:36985761, Mono:OA; 9:37001111, BcelhHC; 9:37780721, EXOSC3||Exon 3:4346|Exon 4:4344,RG9MTD3||3' Proximal Enhancer:26920, PBMC:notRA; 9:37798519, DCAF10||Proximal Promoter:-2270, PBMC:notRA; 9:38620465, ANKRD18A|| Proximal Promoter:-105,FAM201A||Proximal Promoter:-619, PBMC:notRA; 9:4741011, AK3||Intron l : 1032|Intron l :788|Proximal Promoter: 1421 Proximal Promoter:298, PBMC:notRA; 9:5831674, ERMPl ||Intron 1 : 1407, BcelhHC; 9:6921930, KDM4C|| Intron 8: 164290|Intron 8:201068, PBMC:notRA; 9:71629130, PRKACG||Proximal Promoter:-91, PBMC:notRA; 9:74062096, PBMC:OA; 9:74764495, GDA||Intron l :34985|Proximal Promoter:229, PBMC:OA; 9:74764504, GDA||Intron l :34994|Proximal Promoter:238, PBMC:OA; 9:77502963, TRPM6||Proximal Promoter:-327|Proximal Promoter:-700|Proximal Promoter:47, PBMC:HC; 9:7797524, C9orfl23||Exon 2:2275, PBMC:notRA; 9:79013444, RFK|| Distal Promoter:- 4000,RPSAP9||Proximal Promoter:-70, PBMC:notRA; 9:79488657, PBMC:HC; 9:79791169, LOC100286938||3' Proximal Enhancer: 1664,VPS13 A||Proximal Promoter:- 1191, PBMC:SLE; 9:79792074, LOC100286938||Intron l :759,VPS13A||Proximal Promoter:-286, PBMC:OA,PBMC:OA_SLE_HC; 9:88952877, ZCCHC6||Intron 6:Intron 9: 16525, PBMC:OA_SLE_HC; 9:89348726, Tcell: OA SLE HC ; 9:90407888, CTSL3||3' Proximal Enhancer:20059, PBMC:OA; 9:91091556, SPINl ||Exon 6:88260, PBMC:HC; 9:91398891, Mono:OA; 9:91997686, SEMA4D||Intron 15:96925, Wholeblood:notRA; 9:93840773, LOC100129316||Distal Promoter:-3359, PBMC:notRA; 9:94181612, NFIL3||Intron 1 :4532, PBMC:HC; 9:94351568, PBMC:HC; 9:95473718, BICD2||Exon 7:Exon 8:53365, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 9:96623674, PBMC:HC; 9:97095135, FAM22F||Distal Promoter: -4209,LOC100132077||Proximal Promoter:378, PBMC:HC; 9:97346942, FBP2||Exon 3:9133, PBMC:HC; 9:97405553, FBPl ||Distal Promoter:-3022|Distal Promoter: -3630, PBMC:HC; 9:98054883, FANCC||Intron 1 :24653 |Intron 1 :25108, PBMC:notRA; 9:98280076, PBMC:OA_SLE_HC; 9:98513035, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC,Tcell:SLE; 9:98513318, PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC,Tcell:SLE; 9:99487814, LOC441455||Proximal Promoter: -288, PBMC:notRA; 9:99883682, PBMC:notRA; 9:99962350, PBMC:notRA; X: 100332757, TMEM35||Proximal Promoter:-1078, PBMC:notRA; X:100878328, ARMCX3||Proximal Promoter:- 22|Proximal Promoter:209,ARMCX6||5' Proximal Enhancer: -5337, Mono:OA_SLE_HC,Tcell:HC; X: 100914848, ARMCX2|| Proximal Promoter:15, PBMC:notRA; X: 102024057, LOC100287765||Proximal Promoter: -37, Wholeblood:notRA; X: 102611415, WBP5||Proximal Promoter:36, Mono:OA_SLE_HC; X: 103089404, RAB9B|| Proximal Promoter: -2192, Mono:HC; X:104464033, IL1RAPL2|| Intron 3:653038,TEX13A||Exon 3:1325, PBMC:notRA; X: 104466053, IL1RAPL2|| Intron 3:655058,TEX13A||Proximal Promoter:-695, Wholeblood:notRA; X:105066049, NRK||Proximal Promoter: -486, Wholeblood:notRA; X:105969177, RNF128||Intron 1:32110|Proximal Promoter: -716, Mono:OA_SLE_HC; X:106871544, PRPSl||Proximal Promoter:- 109, Wholeblood:notRA; X:107331058, ATG4A||Distal Promoter:-3840,PSMD10||Exon 4:3816,VSIG1||3' Proximal Enhancer:42859, PBMC:notRA; X: 10851898, Wholeblood:notRA; X: 108717536, GUCY2F||Intron 2:7749, PBMC:OA_SLE_HC; X: 110925365, ALG13||Exon 2:Intron l: 1020|Exon 2:Intron l:968|Proximal Promoter:481, Wholeblood:notRA; X: l 11158281, PBMC:OA_SLE_HC; X: 11157158, ARHGAP6||3' Proximal Enhancer: Exon 13:526663|Exon 13:126937, PBMC:OA_SLE_HC; X: 111623900, ZCCHC16||Intron 2:297648, PBMC:notRA; X: 111623974, ZCCHC16||Intron 2:297722, PBMCnotRA; X: 111624323, ZCCHC16||Intron 2:298071, PBMC:notRA; X: 113818934, HTR2C||Proximal Promoter:384, Bcell:OA_SLE_HC; X:117119877, KLHL13||Intron l:Intron 2: 13095 l|Intron 2: 131426|Proximal Promoter:-501, Wholeblood:notRA; X: 117480243, WDR44|| Proximal Promoter:208, Bcel OA; X: 118370171, PGRMCl||Proximal Promoter:-39, Wholeblood:notRA; X: 119028450, AKAP14||Proximal Promoter:-1485, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; X: 119133091, PBMC:SLE; X: 122319025, GRIA3||Intron 1:930, Bcel OA; X: 122319602, GRIA3||Intron 1: 1507, Wholeblood:notRA; X:129519560, GPR119||Proximal Promoter: -49, Mono:OA; X: 13056184, FAM9C||Intron 7:6733, BcelhSLE; X: 132352415, TFDP3||Proximal Promoter: -39, PBMC:HC; X: 132352420, TFDP3||Proximal Promoter: -44, PBMC:notRA; X:133684399, LOC100506757||Proximal Promoter:346,MGC16121||Distal Promoter:-3739,MIR424||Distal Promoter:-3658,MIR450A1||5' Proximal Enhancer:-9938,MIR450A2||5' Proximal Enhancer: -9762,MIR503||Distal Promoter: -3971,MIR542||5' Proximal Enhancer:-8932, Wholeblood:notRA; X:134156624, FAM127A||5' Proximal Enhancer: - 9708,FAM127C||Proximal Promoter:-58, Bcel OA; X: 134306695, CXorf48||Proximal Promoter: -944, PBMC:notRA; X: 135632947, MIR934||Proximal Promoter: -89, VGLLlpxon 4: 18637, Bcel HC; X: 135847852, ARHGEF6|| Intron 2: 15651, PBMC:notRA; X:136511135, Wholeblood:notRA; X:13711087, RAB9A||Intron 1:3848, Wholeblood:notRA; X:13727132, RAB9A||Exon 2:Exon 3: 19893,TRAPPC2||3' Proximal Enhancer:25622, Bcel OA; X:137794361, LOC100129662||Proximal Promoter:93, Wholeblood:notRA; X: 138530469, SRD5AlPl||Exon 1: 1492, Bcell:OA_SLE_HC; X: 139173571, BcelhOA; X:139584049, SOX3||3' Proximal Enhancer: 3176, Wholeblood:notRA; X:139584816, SOX3||3' Proximal Enhancer:2409, Mono:HC; X:139586086, SOX3||Exon 1: 1139, Wholeblood:notRA; X: 139587335, SOX3||Proximal Promoter:- 110, Bcell:OA_SLE_HC; X: 140336617, SPANXC||Proximal Promoter:29, PBMC:HC; X:14048281, GEMIN8|| Proximal Promoter:-246, Mono:OA; X: 144902062, CXorfl||5' Proximal Enhancer:-6865,SLITRK2||Intron 2:2716|Proximal Promoter:-803, Wholeblood:notRA; X:144903661, CXorfl||5' Proximal Enhancer:-5266,SLITRK2||Exon 2:Intron l:796|Exon 4:4315, Mono:OA_SLE_HC; X:147063165, FMRlNB||Proximal Promoter:317, Wholeblood:notRA; X:147279853, PBMC:notRA; X:150251129, Wholeblood:notRA; X: 151286548, MAGE A 10 -MAGE A511 Intron 2:20502,MAGEA5||Proximal Promoter:-137, Mono:OA; X: 152110833, ZNF185||Intron 13:Intron 14:Intron 15:Intron 16:27848|Intron l:619|Intron 7:24425, Mono:OA_SLE_HC,Mono:SLE; X: 152225366, PNMA3||Exon 2:601, PBMC:HC; X:152913595, DUSP9||Exon 2:5699, Bcel OA; X: 153166595, ARHGAP4||3' Proximal Enhancer:25119,AVPR2||Distal Promoter:-3933|Proximal Promoter:- 1389, PBMC:HC; X: 153166733, ARHGAP4||3' Proximal Enhancer:24981,AVPR2||Distal Promoter:-3795|Proximal Promoter:-1251, Wholeblood:notRA; X: 153236825, HCFCl||Proximal Promoter:-6,MIR3202-l||5' Proximal Enhancer:-9722,MIR3202-2||3' Proximal Enhancer:9802,TMEM187||Proximal Promoter:-1165, Wholeblood:notRA; X: 153238479, HCFCl||Proximal Promoter:-1660,MIR3202-l||5' Proximal Enhancer:-8068,MIR3202-2||3' Proximal Enhancer:8148,TMEM187||Proximal Promoter:489, Wholeblood:notRA; X:153572924, FLNA||3' Proximal Enhancer:30082, PBMC:SLE; X:153979588, GAB3||Proximal Promoter:-240, Wholeblood:notRA; X: 154842718, TMLHE|| Proximal Promoter:-96, Mono:OA; X:15663437, TMEM27||Intron 3:19717, Wholeblood:notRA; X:15768223, CA5B||Exon 2:11812, PBMC:SLE; X:21392334, CNKSR2||Proximal Promoter: -201, Mono:HC; X:23350552, PTCHDl||Proximal Promoter:-2432, Wholeblood:notRA; X:24329623, FAM48B2||Exon 1:1809, PBMC:notRA; X:25029872, ARX||Intron 2:4193, Wholeblood:notRA; X:25035922, ARX||Proximal Promoter:- 1857, Wholeblood:notRA; X:26576402, VENTXPl||Proximal Promoter:-51, BcelhHC; X:26576480, VENTXPl||Proximal Promoter:27, Mono:HC; X:30265350, MAGEBl||Intron 2:3503|Proximal Promoter: 80,MAGEB3||3' Proximal Enhancer:16798,MAGEB4||3' Proximal Enhancer:5294, PBMC:SLE; X:30327782, NR0Bl||Proximal Promoter: -287, Wholeblood:notRA; X:31283706, DMD||Intron 19:889880|Intron l:1318|Intron 34:1146665|Intron 61: 175461 l|Intron 62: 1862838|Intron 62:1862839|Intron 62: 1945967|Intron 62:2074020|Intron 8:242709, Mono:HC; X:33231137, Wholeblood:notRA; X:34675855, TMEM47||Proximal Promoter: -450, Wholeblood:notRA; X:34961618, FAM47B||Exon 1:706, PBMC:notRA; X:3631824, PRKX||Proximal Promoter:-149, Wholeblood:notRA; X:3633155, PRKX||Proximal Promoter:-1480, PBMC:notRA; X:37028050, FAM47C||Exon 1:1619, PBMC:notRA; X:37028774, FAM47C||Exon 1:2343, PBMC:notRA; X:37062005, PBMCnotRA; X:37404389, Mono:HC; X:38210221, OTC||Proximal Promoter:-1514, Wholeblood:notRA; X:39864290, PBMC:notRA; X:40031643, BCOR||Intron 1:4939, Mono:OA; X:40037510, BCOR||Proximal Promoter:-928, PBMC:notRA; X:40594937, MED14||Proximal Promoter:- 133, Bcell:OA; X:46306474, ZNF673||Proximal Promoter: -149, Mono:OA; X:47077266, CDK16||5' Proximal Enhancer:-5150|Proximal Promoter:- 261|Proximal Promoter:-809, Wholeblood:notRA; X:47077361, CDK16||5' Proximal Enhancer: - 5055|Proximal Promoter:-166|Proximal Promoter:-714, Wholeblood:notRA; X:47077403, CDK16||5' Proximal Enhancer:-5013|Proximal Promoter: -124 Proximal Promoter:-672, Wholeblood:notRA; X:47092529, CDK16||3' Proximal Enhancer: 10113|3' Proximal Enhancer: 14454|3' Proximal Enhancer:15002,USPl l||Proximal Promoter:216, Wholeblood:notRA; X:47092560, CDK16||3' Proximal Enhancer: 10144 Proximal Enhancer: 14485|3' Proximal Enhancer:15033,USPl l||Proximal Promoter:247, Wholeblood:notRA; X:47092729, CDK16||3' Proximal Enhancer: 10313 Proximal Enhancer: 14654|3' Proximal Enhancer: 15202,USPl l||Proximal Promoter:416, Wholeblood:notRA; X:47107481, USPl l||Exon 21:15168, Wholeblood:notRA; X:47229908, ZNF157||Proximal Promoter:-90, PBMC:HC; X:48214736, SSX3||Intron 1:1406, PBMC:notRA; X:48217566, SSX3|| Proximal Promoter:-1424, PBMC:notRA; X:48335010, FTSJl||Proximal Promoter:-1369|Proximal Promoter:462,SLC38A5||5' Proximal Enhancer: - 6366, PBMC:SLE; X:49166345, GAGE10||Intron 3:6221, PBMC:SLE; X:49774388, CLCN5||Intron 3:87164,MIR188||3' Proximal Enhancer:6280,MIR362||3' Proximal Enhancer:817,MIR500A||3' Proximal Enhancer:1350,MIR500B||Proximal Promoter: -89 l,MIR501||Proximal Promoter:59,MIR502||Distal Promoter: -4817,MIR532||3' Proximal Enhancer:6635,MIR660||Distal Promoter:-3460, PBMC:notRA; X:53093414, GPR173||Intron 1: 14909, Wholeblood:notRA; X:53117682, GPR173||3' Proximal Enhancer:39177,TSPYL2||Exon 7:6141, Wholeblood:notRA; X:53461386, HSD17B10||Proximal Promoter:-63,RIBCl||3' Proximal Enhancer: 11497|3' Proximal Enhancer: 11548, Wholeblood:notRA; X:55246829, PAGE5||Proximal Promoter:38|Proximal Promoter:39, PBMCnotRA; X:67914130, STARD8||Intron l:649|Intron 2:46620, Tcel HC; X:68114669, Wholeblood:notRA; X:69664722, DLG3||5' Proximal Enhancer:-7432|Proximal Promoter:18, Wholeblood:notRA; X:70585545, TAFl||Proximal Promoter:-568, PBMC:SLE; X:70797539, ACRC|| Proximal Promoter:-334,OGT||3' Proximal Enhancer:44628, Wholeblood:notRA; X:71130538, NHSL2|| Proximal Promoter: -399, Bcel OA; X:71264481, NHSL2||Intron l: 133544,RPS26Pl l||Proximal Promoter:223, PBMC:notRA; X:71352048, RGAG4||Proximal Promoter:-297, Wholeblood:notRA; X: 72068025, DMRTCl||Intron 5:3150,DMRTClB||Intron 5:3150, Mono:SLE,PBMC:SLE; X:72667070, CDX4|| Proximal Promoter:-19, Mono:OA; X:75249519, PBMC:notRA; X:76832207, ATRX||Intron 26:Intron 27:209512, BcelhOA; X:77154916, COX7B||Proximal Promoter:-44,MAGTl||Distal Promoter: -3851, Mono:HC; X:79590882, FAM46D||Proximal Promoter:-120, Wholeblood:notRA; X:83003475, Tcell:HC,Tcell:OA_SLE_HC; X:85402643, DACH2||Proximal Promoter:-811, Mono:OA_SLE_HC,Wholeblood:notRA; X:8751190, FAM9A||3' Proximal Enhancer: 18188| 3' Proximal Enhancer: 18234, TcelhHC; X:8751266, FAM9A||3' Proximal Enhancer: 18112|3' Proximal Enhancer: 18158, TcelhHC; X:8751330, FAM9A||3' Proximal Enhancer: 18048|3' Proximal Enhancer: 18094, Mono:HC,PBMC:HC,Tcell:HC; X:8751402, FAM9A||3' Proximal Enhancer: 17976|3' Proximal Enhancer: 18022, Mono:HC,Tcell:HC; X:8751524, FAM9A||3' Proximal Enhancer:17854|3' Proximal Enhancer: 17900, TcelhHC; X:8751687, FAM9A||3' Proximal Enhancer: 17691 Proximal Enhancer: 17737, TcelhHC
Table 3A
Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:121413182, BAG3||Intron 1:2301, PBMCSLE; 10:86004704, RGR||Proximal Promoter: -104, Tcell:OA; 10:86004761, RGR||Proximal Promoter:-47, Bcell:HC; 10:91093005, IFIT3||Intron l:767|Intron 1:5404, Bcell:SLE,Mono:SLE,PBMC:SLE; 10:91093681, IFIT3||Intron l:1443|Intron 1:6080, Bcell:SLE,Mono:SLE,PBMC:SLE; 10:91151885, IFITl||Proximal Promoter: -436, PBMC:SLE,Tcell:SLE; 10:91153143, IFITl||Intron 1:822, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 11: 1078195, MUC2||Intron 4:3321, Mono:HC; 11:1083178, MUC2||Exon 16:8304, Mono:OA; 11:123776728, OR8D4||Proximal Promoter: -410, PBMC:OA; 11:2720810, KCNQl||Intron 1 l:238127|Intron 11:254590, Bcell:OA; 11:5291692, HBEl||Proximal Promoter:-319, Tcell:OA; 11:614761, PHRF1||3' Proximal Enhancer:38279, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 11:614787, PHRF1||3' Proximal Enhancer:38305, PBMC:SLE,Tcell:SLE; 11:832065, PNPLA2||3' Proximal Enhancer: 13165, Bcell:OA; 12:113415883, OAS2||Proximal Promoter:-390, Mono:SLE; 12:2393684, CACNAlC||Intron 3:231269, Bcell:OA; 12:62490552, FAM19A2|| Intron 1:96068, Tcell:OA; 12:86230557, RASSF9||Proximal Promoter:-239, Bcell:OA; 13:43563347, EPSTIl||Intron 1:3030, Bcell:SLE,PBMC:SLE,Tcell:SLE; 13:43565901, EPSTIl||Proximal Promoter:476, PBMC:SLE; 13:43986655, ENOXl||Intron 4:216958|Intron 4:374461, Bcell:HC; 14:24600569, PSMEl||Distal Promoter: -4808, Tcell:OA; 14:64677007, SYNE2||5' Proximal Enhancer:-5664|Distal Promoter: -3851|Intron 103:357325, Bcell:HC; 15:51060843, SPPL2A||Distal Promoter:-2933, Tcell:OA; 15:77472416, PEAKl||Exon 5:240030, Tcell:SLE; 16:1116010, SSTR5||5' Proximal Enhancer:-6745, Mono:OA; 16:11690918, LITAF||5' Proximal Enhancer: -9596, Tcel OA; 16:24743405, TNRC6A||Intron 2:2357, PBMC:SLE; 16:57496324, COQ9||3' Proximal Enhancer: 14988,DOK4||3' Proximal Enhancer:24061, PBMC:OA; 16:65046268, CDH1 l||Intron 2:109651, BcelhHC; 16:88111009, BANP||3' Proximal Enhancer: 107386|3' Proximal Enhancer: 117533 Proximal Enhancer: 125972, BcelhOA; 17:3379567, ASPA||Proximal Promoter:272|Exon 2:2164, BcelhSLE; 17:41159289, IFI35||Intron 1:548, Bcell:SLE,PBMC:SLE; 17:45798257, TBKBP1||3' Proximal Enhancer:25628, TcelhOA; 17:62252524, TEX2||Intron 6:88129, PBMC:HC; 17:79870317, NPB||3' Proximal Enhancer: 10246, Mono:OA; 17:80337729, UTS2R||3' Proximal Enhancer:5529, Tcel HC; 18:43649078, PSTPIP2||Intron 1:3172, PBMC:OA; 18:60192893, ZCCHC2||Intron 1:2236, Bcell:SLE,PBMC:SLE; 19: 14586979, PTGERl||Proximal Promoter:-805, PBMC:SLE; 19:18109226, KC Nl||Exon 11:47116, Tcel OA; 19:3810782, MATK||5' Proximal Enhancer:-8972, BcelhOA; 19:45449301, APOC2||Proximal Promoter:63,CLPTMl||5' Proximal Enhancer: -9297|5' Proximal Enhancer:-8948|5' Proximal Enhancer:-8540, Mono:HC; 19:51327177, KLKl||Proximal Promoter:-134, BcelhSLE; 19:51875946, NKG7|| Proximal Promoter:14, PBMC:SLE; 1: 153605715, S100A13||5' Proximal Enhancer:-6191|5' Proximal Enhancer:-5971|5' Proximal Enhancer:-5598|5' Proximal Enhancer:-5000|Intron 1:853, BcelhOA; 1:158041312, KIRREL|| Intron 1:78250, PBMC:SLE; 1:173447427, PRDX6||Intron 1:942, PBMC:HC; 1:174844397, RABGAP 1 L| |Proximal Promoter: -258|Intron l:874|Intron 2:75363, Bcell:SLE,Mono:SLE,PBMC:SLE; 1:174844490, RABGAP lL||Proximal Promoter: -165 Intron l:967|Intron 2:75456, Bcell:SLE,Mono:SLE,PBMC:SLE; 1:192548609, RGSlpxon 5:3753, Tcel SLE; 1:2037476, PRKCZ||Intron l: 1322|Intron l:32052|Intron l:32391|Intron 4:55568, BcelhHC; 1:21544521, ECEl||Exon 17:61662|Exon 18:72245|Exon 19:72461|Exon 19:127513, Bcel OA; 1:240612744, FMN2||Intron 16:357560, Mono:OA; 1:57470853, DABl||Intron 16:1245358, BcelhHC; 1:91989267, CDC7||Intron 11:22603 |Intron 11:22864, PBMC:HC; 1:92952467, GFIl||Distal Promoter:-3111|Proximal Promoter:-839|Proximal Promoter:-34, PBMC:SLE; 20:19867026, RIN2||Distal Promoter:-3183|Proximal Promoter:- 138, Mono:HC; 20: 19867145, RIN2||Distal Promoter:-3064|Proximal Promoter:-19, Mono:HC; 20:19869644, RIN2|| Proximal Promoter:-565|Intron 1:2480, TcelhOA; 21:39047855, KCNJ6||Intron 3:240841, Mono:OA; 22:50965373, SC02||Proximal Promoter:- 1340|Proximal Promoter:-1339|Proximal Promoter: -799|Proximal Promoter:-505, Bcell:SLE,PBMC:SLE,Tcell:SLE; 22:50970943, SC02||5' Proximal Enhancer:-6910|5' Proximal Enhancer:-6909|5' Proximal Enhancer:-6369|5' Proximal Enhancer:- 6075, PBMC:SLE; 22:50971109, SC02||5' Proximal Enhancer:-7076|5' Proximal Enhancer:-7075|5' Proximal Enhancer: -6535|5' Proximal Enhancer: -6241, Bcell:SLE,PBMC:SLE; 22:50971140, SC02||5' Proximal Enhancer:-7107|5' Proximal Enhancer:-7106|5' Proximal Enhancer:-6566|5' Proximal Enhancer:- 6272, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 22:50973101, SC02||5' Proximal Enhancer: -9068|5' Proximal Enhancer:-9067|5' Proximal Enhancer: -8527|5' Proximal Enhancer:-8233, Bcell:SLE,Tcell:SLE; 2: 113420964, SLC20Al||Exon 11:17531, Mono:SLE; 2:171676925, GADl||Intron 2:3726, PBMC:SLE; 2:206566025, NRP2||Intron 2: 18802, Bcel HC; 2:220492021, SLC4A3||Proximal Promoter: -270, Mono:OA; 2:242048359, PASK||3' Proximal Enhancer:Intron 15:40560|Intron 16:41035, Bcel SLE; 2:37381088, EIF2AK2||5' Proximal Enhancer:-6123|Intron 1:3102, Mono:SLE,PBMC:SLE; 2:37383568, EIF2AK2||5' Proximal Enhancer:-8603|Intron 1:622, Bcell:SLE,PBMC:SLE,Tcell:SLE; 2:37384708, EIF2AK2||5' Proximal Enhancer: -9743|Proximal Promoter: -518, PBMC:SLE,Tcell:SLE; 2:60685678, BCLl lA||Exon 4:Intron 4:94955, Mono:OA; 2:62428082, B3GNT2||Intron 1:4821, TcelhSLE; 2:7016509, RSAD2||Proximal Promoter:-1286, BcelhSLE; 2:7018020, RSAD2||Proximal Promoter:225, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 2:7018153, RSAD2|| Proximal Promoter:358, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 3:111315344, CD96||Intron 5:Intron 6:54419, Tcell:OA; 3: 111838332, GCET2||3' Proximal Enhancer: 13820, Bcell:HC; 3:128368141, RPNl||Intron 1:1578, Mono:OA; 3:129001312, COPG||3' Proximal Enhancer:32860, BcelhOA; 3:146258875, PLSCRl || Intron 1:3753, Bcell:SLE,PBMC:SLE,Tcell:SLE; 3:146260954, PLSCRl || Intron 1: 1674, Bcell:SLE,Mono:SLE,PBMC:SLE,Tcell:SLE; 3:191048439, UTS2D||Proximal Promoter:-114, TcelhSLE; 3:50190575, SEMA3F||Proximal Promoter: -2272, TcelhOA; 3:56810151, ARHGEF3||Proximal Promoter:- 406|Intron l:25844|Intron 4:303185, Mono:HC; 3:65887859, MAGIl||Intron 1: 136650, PBMC:OA; 3:71111489, FOXPl||Intron l:2585|Intron 2:68603|Intron 3: 182827|Intron 4:242422|Intron 6:481219|Intron 7:521415|Intron 7:521651, PBMC:SLE; 3:71481486, FOXPl||Intron 2: 111222|Intron 3:151418|Intron 3: 151654, PBMC:SLE; 4: 164088478, NAFl||Proximal Promoter:-405, Mono:HC; 4:89379156, HERC5||Intron 1:889, Mono:SLE,PBMC:SLE,Tcell:SLE; 5: 107005390, EFNA5||Intron 1: 1206, Bcell:OA; 5: 110427346, WDR36||Proximal Promoter:-523, PBMC:HC; 5: 127874587, FBN2||Proximal Promoter: - 852, PBMC:OA; 5:135364970, TGFBI|| Proximal Promoter:387, Tcell:OA; 5:1401718, SLC6A3|| Intron 13:43825, PBMC:OA; 5: 172671754, NKX2-5||5' Proximal Enhancer: -9439, PBMC:OA; 5:322735, AHRR||Intron 1: 18445, BcelhOA; 5:399887, AHRR||Intron 4:95597, PBMC:OA; 5:607516, CEP72||Distal Promoter:-4888, BcelhSLE; 5:694438, TPPP||Proximal Promoter: -928, Mono:OA; 6:30703704, FLOTl||Intron 8:6749,IER3||3' Proximal Enhancer: 8623, PBMC:SLE; 6:31082534, PSORSlCl||Proximal Promoter:-73, Bcel HC; 6:32010178, TNXB||Intron 9:3727|Intron 40:66973, Tcel OA; 6:32037474, TNXB||Exon 15:39677, TcelhOA; 6:32943839, BRD2||Exon 4:2979|Exon 4:4468|Exon 5:Exon 6:5175|Exon 5:7403, Bcel OA; 6:34984836, ANKS1A|| Intron 10: 127799, Mono:SLE; 7: 100463985, SRRT||5' Proximal Enhancer: -8715, Bcel HC; 7: 106805823, HBPl||Distal Promoter:-3636|Distal Promoter: -3582, PBMC:OA; 7: 127291444, SNDl||Proximal Promoter: -757, PBMCSLE; 7: 127514192, SNDl||Intron 12:221991, PBMC:HC,Tcell:HC; 7:204337, FAM20C||Intron 2:11369, TcelhOA; 7:5566311, ACTB||3' Proximal Enhancer:3921, PBMC:HC; 7:866102, SUN1||5' Proximal Enhancer:-6039|Intron l:Intron 2:9851|Intron 1: 10909, PBMC:HC; 7:95402733, DYNClIl||Intron 1:916, TcelhOA; 8:28196926, ZNF395||3' Proximal Enhancer:47051, PBMC:HC; 8:99017690, MATN2|| Intron 8: 136380, PBMC:OA; X:20284665, RPS6KA3||Proximal Promoter: 85, Bcel OA
Table 3B
Data are listed as "DML coordinate, optional associated gene| (position relative to optional gene:distance of DML from transcription start site in bases (multiple positions delimited by I), cell population of origin:phenotype comparator;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:111966094, MXIl||Distal Promoter:-3894|Proximal Promoter:-1268, PBMC:notRA; 10: 120802096, EIF3A||Exon 19:38238, PBMC:HC; 10: 124908747, HMX2|| Intron 1: 1110, PBMC:SLE,Tcell:SLE; 10:131529435, MGMT|| Intron 3:263982, Mono:OA_SLE_HC; 10:28571322, MPP7|| Proximal Promoter: - 255, PBMC:HC; 10:35299094, CUL2||Exon 21:64164|Exon 21:80217|Exon 21:80476, PBMCnotRA; 10:35480749, CREM||Distal Promoter:-4080|Distal Promoter:-3305|Intron 3:Intron 4: 16235|Intron 3:Intron 4:24283 |Intron 4:Intron 5:54040|Intron 4:Intron 6:64365|Intron l:Intron 5:64981, PBMC:HC; 10:63683346, ARID5B||Intron 2:22334, PBMC:OA_SLE_HC; 10:63734682, ARID5B||Intron 3:73670, Bcel OA; 10:63753550, ARID5B||Intron 3:92538, Mono:HC; 10:71588009, COL13Al||Intron 3:26366, BcelhSLE; 10:71596731, COL13Al||Intron 3:35088, TcelhHC; 10:72138124, LRRC20||Intron l:3290|Intron 1:4258, PBMC:OA_SLE_HC; 10:73846448, SPOCK2||Intron l:2083|Exon 3:Intron 2:2342, TcelhHC; 10:79314844, KCNMAl||Intron 1:82733, PBMC:notRA; 10:79398838, KCNMAl||Proximal Promoter: - 1261, PBMC:OA_SLE_HC; 10:91093005, IFIT3||Intron l:767|Intron 1:5404, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC,Tcell:SLE;
10:91093681, IFIT3||Intron l:1443|Intron 1:6080,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 10:91151885, IFITl||Proximal Promoter: - 436, Tcell:OA_SLE_HC; 10:91153143, IFITl||Intron 1:822,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 10:94827200, CYP26Cl||Intron 5:6180, PBMC:HC; 10:96990700, PDLIM1||3' Proximal Enhancer:60081, PBMC:HC; 10:96990858, PDLIM1||3' Proximal Enhancer:59923, PBMC:HC; 10:97008920, PDLIMl||Intron 4:41861, Mono:OA; 10:99223744, MMS19||Exon 19:34622, PBMC:HC; 11:102245639, BIRC2||Intron 6:27674, PBMC:notRA; 11:104769087, CASP12||Proximal Promoter:310, PBMC:SLE; 11:104817914, CASP4||Exon 7:9508|Exon 7:21411, PBMC:OA; 11:1107803, MUC2||3' Proximal Enhancer: 32929, PBMC:OA_SLE_HC; 11:111956119, TIMM8B||Exon 2:Exon 3:1403, PBMC:notRA; 11:116664039, APOA5|| Proximal Promoter: -903, PBMC:HC; 11:118213330, CD3G||Proximal Promoter:-1728, Tcell:HC; 11:118214762, CD3G||Proximal Promoter: -296, PBMC:HC; 11:119054921, NLRX1||3' Proximal Enhancer: 15482, PBMC:notRA; 11:122709551, CRTAM||Proximal Promoter:297, PBMC:HC; 11:122954435, CLMP||Exon 4:111572, Tcell:HC,Tcell:OA_SLE_HC; 11:126443490, KIRREL3||Intron 1:427276, PBMC:HC; 11:15200692, INSC||Intron 5:64209|Intron 5:66723, Bcel OA; 11:1892038, LSPl||Proximal Promoter: - 115|Proximal Promoter:-60|Intron l:2136|Intron 2:5644, PBMCSLE; 11:1892043, LSPl||Proximal Promoter:-110|Proximal Promoter:-55|Intron l:2141|Intron 2:5649, PBMC:SLE; 11:1892139, LSPl||Proximal Promoter:-14|Proximal Promoter:41|Intron l:2237|Intron 2:5745, PBMCSLE; 11:1892142, LSPl||Proximal Promoter:- 1 ljproximal Promoter: 44 jlntron l:2240|Intron 2:5748, PBMC:SLE; 11:1892180, LSPl||Proximal Promoter:27|Proximal Promoter: 82 |Intron l:2278|Intron 2:5786, PBMC:SLE; 11:19081590, MRGPRX2||Intron 1:638, PBMC:OA_SLE_HC,PBMC:notRA; 11:2322386, TSPAN32||Proximal Promoter:-856, PBMC:HC; 11:2322507, TSPAN32||Proximal Promoter:-735, PBMC:HC; 11:2322741, TSPAN32||Proximal Promoter: -501, Tcel HC; 11:2322808, TSPAN32||Proximal Promoter: -434, PBMC:HC; 11:2322935, TSPAN32||Proximal Promoter: -307, PBMC:HC; 11:2323801, TSPAN32||Intron 1:559, PBMC:HC; 11:2323896, TSPAN32||Intron 1:654, PBMC:HC; 11:2327755, TSPAN32||Intron 3:4513, Bcel HC; 11:2552843, KCNQl||Intron 2:70160|Intron 2:86623, Mono:OA; 11:2721383, KCNQl||Intron 1 l:238700|Intron 11:255163, PBMC:notRA; 11:45868449, CRY2||Proximal Promoter: -507|Proximal Promoter: -219, Wholeblood:notRA; 11:46709238, ARHGAP 11 |Intron 4:12882, Mono:OA; 11:46879516, LRP4||Exon 38:60657, PBMC:HC; 11:47235900, DDB2||Proximal Promoter:- 592, PBMC:notRA; 11:47377212, MYBPC3||Distal Promoter:-2959, PBMC:HC; 11:569232, PHRF1||5' Proximal Enhancer: -7250, TcelhHC; 11:57159174, PRG2|| Proximal Promoter: -1044, Mono:SLE; 11:613632, PHRF1||3' Proximal Enhancer:37150, PBMC:SLE; 11:613792, PHRF1||3' Proximal Enhancer:37310, Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE; 11:614761, PHRF1||3' Proximal Enhancer:38279, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:614787, PHRF1||3' Proximal Enhancer:38305,
Bcell:SLE,Mono:SLE,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 11:62315034, AHNAK||Proximal Promoter: -702, PBMC:HC; 11:63683744, MARK2||3' Proximal Enhancer:27758|3' Proximal Enhancer:77345, Mono:OA; 11:63687247, MARK2||3' Proximal Enhancer:31261|3' Proximal Enhancer:80848, PBMC:HC; 11:637162, DEAF1||3' Proximal Enhancer:58578, PBMC:HC; 11:65623186, MUS81||Distal Promoter: -4685, PBMC:notRA; 11:660455, DEAFl||Intron 10:35285, PBMC:HC,Tcell:HC; 11:660597, DEAFl||Intron 10:35143, PBMC:HC,PBMC:notRA; 11:66083541, CD248||Exon 1:974, PBMC:SLE,Tcell:SLE; 11:66317822, ACTN3||Intron 1:3432, PBMC:OA_SLE_HC; 11:698201, DEAFl||Proximal Promoter:-2461, Mono:HC; 11:72460551, ARAPl||Intron 1:2883, PBMC:notRA; 11:8160625, RIC3||Intron l:Intron 2:Intron 3:29965, PBMC:notRA; 11:818892, PNPLA2|| Proximal Promoter:-8,RPLP2||3' Proximal Enhancer:8957, PBMC:HC; 11:94278324, FUT4||Exon 1:1308, BcelhOA; 11:94278457, FUT4||Exon 1:1441, Tcel HC; 11:94278595, FUT4||Exon 1:1579, Tcel HC; 11:94278912, FUT4||Exon 1:1896, PBMC:HC; 12:104325856, G N||Proximal Promoter: -1867, PBMC:OA_SLE_HC; 12:109030115, COR01C||3' Proximal Enhancer:95180, PBMC:SLE; 12:109123308, COR01C||Intron 1:1987, BcelhOA; 12:11080457, PRH2|| Proximal Promoter:-1377|Proximal Promoter:-1376, PBMC:HC,PBMC:notRA; 12:113447342, OAS2||Exon 10:Intron 10:31069, Mono:SLE; 12:114299076, RBM19||Intron 21:105100, PBMC:HC; 12:118405988, KSR2||Proximal Promoter:40, PBMC:notRA; 12:120907301, DYNLL11 |Proximal Promoter:-358,GATC||3' Proximal Enhancer:23061, PBMC:notRA; 12:129277140, SLC15A4||3' Proximal Enhancer: 31401, PBMC:SLE; 12:132381902, ULKl||Intron 3:2624, BcelhSLE; 12:1721081, WNT5B||5' Proximal Enhancer: -5140, TcelhHC; 12:1922058, LRTM2||5' Proximal Enhancer: -7374, PBMC:HC; 12:20705789, PDE3A||Intron 1:183611, TcelhOA; 12:33049650, PKP2||Proximal Promoter:130, PBMC:notRA; 12:48120090, RAPGEF3||3' Proximal Enhancer:32091|3' Proximal Enhancer: 32154| 3' Proximal Enhancer:32799, Bcell:OA_SLE_HC; 12:48147034, RAPGEF3||Intron l:5147|Intron 2:5210|Intron 2:5855, PBMC:HC; 12:4919081, KCNA6||Exon 1:740, PBMC:notRA; 12:53183773, KRT3||Exon 9:6119, PBMC:HC; 12:54764371, GPR84||5' Proximal Enhancer:-6101, PBMC:HC; 12:5538415, NTF3||Distal Promoter: -2864, PBMC:notRA; 12:56090600, ITGA7||Intron 12:11086|Intron 12:15489, Tcel OA; 12:56322959, WIBG|| Proximal Promoter: - 2050|Proximal Promoter:-1262, PBMC:HC; 12:63211683, PPMlH||Intron 2:116982, Mono:SLE; 12:63322644, PPMlH||Intron 1:6021, PBMC:notRA; 12:6471251, SC NlA||Exon 3:13139|Exon 4:13654|Exon 4:15272, Tcell:OA_SLE_HC,Tcell:SLE; 12:6473299, SC NlA||Intron l:11091|Intron 2: 11606|Intron 2: 13224, PBMC:HC,PBMC:OA_SLE_HC; 12:6473311, SC NlA||Intron l : 11079|Intron 2: 11594|Intron 2: 13212, PBMC:OA_SLE_HC; 12:6753626, ING4||3' Proximal Enhancer: 18682, PBMC:HC; 12:6976727, USP5||3' Proximal Enhancer: 15437|3' Proximal Enhancer: 15443, Mono:OA_SLE_HC; 12:7023262, EN02||Proximal Promoter:-351, PBMC:SLE; 12:7023346, EN02||Proximal Promoter: -267, PBMC:SLE; 12:7023352, EN02|| Proximal Promoter:-261, PBMC:SLE; 12:76414534, PHLDA1 ||3' Proximal Enhancer: 11022, PBMC:HC,PBMC:OA_SLE_HC; 12:7939674, NANOG||Proximal Promoter: -2320, Bcel HC; 12:86229804, RASSF9||Intron 1 :514, PBMC:notRA; 12:86230176, RASSF9||Proximal Promoter: 142, Mono:OA; 12:86230367, RASSF9||Proximal Promoter: - 49, PBMC:notRA; 12:9065171, PHCl ||Proximal Promoter:-2144,
PBMC:HC,PBMC:OA,PBMC:OA_SLE_HC; 12:9065639, PHCl ||Proximal Promoter:- 1676, PBMCSLE; 12:9162872, KLRGl ||Exon 5:20652, PBMC:HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 12:96188933, NTN4||Distal Promoter: -4397, PBMC:notRA; 13 : 110958977, COL4A2||Proximal Promoter: -653, Tcel OA; 13: 110959647, COL4A2|| Proximal Promoter: 17, PBMC:OA; 13: 111040579, COL4A2|| Intron 4:80949, PBMCnotRA; 13: 111111172, COL4A2||Exon 22: 151542, PBMC:notRA; 13: 111115558, COL4A2||Intron 24: 155928, PBMC:OA_SLE_HC,PBMC:notRA; 13: 111161943, COL4A2||Intron 47:202313, PBMC:OA; 13: 113873353, CUL4A||Exon 3:9423|Exon 3: 10268, PBMC:notRA; 13:21714266, SAP18||Proximal Promoter: -386, PBMC:HC,PBMC:notRA; 13:23754135, SGCG||Proximal Promoter: -924, PBMC:notRA; 13:36871754, SPG20||3' Proximal Enhancer:48892|3' Proximal Enhancer:49180|3' Proximal Enhancer:72563, PBMC:HC; 13:39985790, LHFP||Intron 2: 191566, Bcel HC; 13:40068444, LHFP||Intron 2: 108912, PBMC:OA; 13:43563347, EPSTIl ||Intron 1 :3030, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 13:43565901, EPSTIl ||Proximal Promoter:476, Bcell:SLE,PBMC:OA_SLE_HC,Tcell:SLE; 13:43882349, ENOXl ||Intron 1 l :321264|Intron 11 :478767, PBMC:HC; 13:51482661, RNASEH2B||Proximal Promoter: - 1152, PBMC:HC; 13:92426491, GPC5||Intron 5:375557, TcelhHC; 13:96294131, DZIPl ||Intron 4:2826, Mono:OA; 14: 103415873, CDC42BPB|| Intron 26: 107869, Mono:HC; 14: 103862143, MARK3|| Intron 1 : 10443, PBMC:notRA; 14: 105155327, INF2|| Proximal Promoter: -615, Tcel HC; 14: 105167457, INF2||Intron 1 : 11515, Mono:OA; 14: 105168128, INF2||Intron 2: 12186, Bcell:OA_SLE_HC; 14: 105191118, INF2||3' Proximal Enhancer:35176, Mono:OA; 14: 105613102, JAG2||Intron 19:Intron 20:22059, Bcel HC; 14: 105944604, MTA1 ||3' Proximal Enhancer: 58419,
PBMC:HC,PBMC:OA_SLE_HC; 14: 105944655, MTA1 ||3' Proximal Enhancer:58470, PBMC:HC,PBMC:OA_SLE_HC; 14: 105944942, MTA1 ||3' Proximal Enhancer:58757, PBMC:HC,PBMC:OA_SLE_HC; 14: 105945022, MTA1 ||3' Proximal Enhancer:58837, PBMC:OA_SLE_HC; 14: 105945287, MTA1 ||3' Proximal Enhancer:59102,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 14: 105945685, MTA1 ||3' Proximal Enhancer:59500, PBMC:OA_SLE_HC; 14: 105945699, MTA1 ||3' Proximal Enhancer:59514, PBMC:OA_SLE_HC; 14:23776482, BCL2L2|| Proximal Promoter:414|Exon 2:512, Mono:OA; 14:24615768, PSME1 ||3' Proximal Enhancer: 10391, PBMC:notRA; 14:24780540, LTB4R2||Exon 2: 1184, PBMC:notRA; 14:24780551, LTB4R2||Exon 2: 1195, PBMCnotRA; 14:24780557, LTB4R2||Exon 2: 1201, PBMC:notRA; 14:24780682, LTB4R2||Exon 2: 1326, PBMCnotRA; 14:24780691, LTB4R2||Exon 2: 1335, PBMC:notRA; 14:24780734, LTB4R2||Exon 2: 1378, PBMC:notRA; 14:35587750, KIAA0391 ||Distal Promoter:-4025, Mono:OA; 14:35870184, NFKBIA||3' Proximal Enhancer:3776, PBMC:HC; 14:39573006, SEC23A||Proximal Promoter: -569, PBMCnotRA; 14:63743552, RHOJ||Intron 2:72451, Mono:OA; 14:69341905, ACTNl ||Intron 20:Intron 21 : 104178, PBMCnotRA; 14:75025713, LTBP2||Intron 3:53321, PBMC:OA_SLE_HC; 14:76870544, ESRRB||Intron 1 :32855, PBMC:HC; 14:76873334, ESRRB||Intron 2:35645, PBMC:OA_SLE_HC,PBMC:SLE; 14:79529179, NRXN3||Intron 12:659087, Bcell: OA SLE HC ; 14:91695017, GPR68||3' Proximal Enhancer: 15835 Proximal Enhancer:25207, PBMC:HC; 14:93052501, RIN3||Intron 3:72377, PBMC:notRA; 14:93653027, MOAPl ||Proximal Promoter: -1778, PBMC:HC; 15: 101936156, PCSK6||Intron 7:94031, PBMCnotRA; 15:25451941, PAR4||Distal Promoter:-4897, PBMC:notRA; 15:31624584, KLF13||Intron 1 :5502, Mono:HC; 15:45403733, DUOX2||Exon 6:2626, PBMC:OA; 15:50791560, USP8||Exon 20:Exon 21 :74982, PBMC:notRA; 15:52738117, MY05A||Intron 1 :83130, PBMC:notRA; 15:60863379, RORA||Intron l :21328|Intron l :Intron 2:56350|Intron 2:658123, PBMC:HC; 15:60920441, RORA||Proximal Promoter:-712|Intron 2:601061, PBMC:notRA; 15:61182765, RORA||Intron 1 :338737, Mono:SLE; 15:78802280, IREB2||3' Proximal Enhancer:71763, PBMC:SLE,Tcell:SLE; 15:81122346, KIAA1199||Intron 1 :50635, PBMC:notRA; 15:91192950, CRTC3||3' Proximal Enhancer: 119753, PBMC:HC; 15:92939006, ST8SIA2||Intron 1 : 1867, PBMC:OA_SLE_HC; 15:93595923, RGMA||Intron l :20466|Intron 2:21016|Intron 2:21293|Intron 2:35829|Intron 2:36520, PBMC:SLE; 15:93606698, RGMA||Intron l :9691 |Intron 2: 10241 |Intron 2: 10518|Intron 2:25054|Intron 2:25745, PBMC:OA; 15:93617134, RGMA||Proximal Promoter: -745 |Proximal Promoter:-195|Proximal Promoter:82|Intron l : 14618|Intron 1 : 15309, Bcell:OA_SLE_HC; 16: 11655159, LITAF||Intron l :25070|Intron l :25647|Intron 1 :26163, T cell: SLE; 16:221811, HBA2|| Proximal Promoter:-1034, PBMC:notRA; 16:24759640, TNRC6A||Intron 2: 18592, PBMCnotRA; 16:28635374, SULTlAl ||Proximal Promoter:-467, BcelhHC; 16:30018720, DOC2A||Intron 5:3681, PBMC:SLE; 16:3017902, KREMEN2||Exon 8:Exon 9:3686, PBMC:OA_SLE_HC; 16:3018991, KREMEN2||3' Proximal Enhancer:4775, PBMC:OA_SLE_HC; 16:31106788, VKORCl ||Proximal Promoter:-512, PBMC:SLE; 16:3265228, ZNF200||3' Proximal Enhancer: 19958|3' Proximal Enhancer:20228|3' Proximal Enhancer:20229, PBMC:notRA; 16:4033226, ADCY9||Intron 7: 132960, PBMCSLE; 16:4117281, ADCY9||Intron 2:48905, Tcell:OA_SLE_HC; 16:50769852, CYLD||5' Proximal Enhancer:-6176|5' Proximal Enhancer:-6108, PBMC:HC; 16:5143172, ALG1 ||3' Proximal Enhancer:21363, PBMC:notRA; 16:56703788, MTlH||Proximal Promoter:63, PBMC:notRA; 16:601869, SOLH||Intron 9:24014, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 16:65155141, CDHl l ||Intron 1 :778, PBMC:OA; 16:65155841, CDHl l ||Proximal Promoter:78, PBMC:OA; 16:66969837, CES2||Exon l : 1464|Intron 1 : 1491, PBMCnotRA; 16:67687392, PARD6A||5' Proximal Enhancer: -7458, PBMC:OA; 16:75284882, BCARl ||Distal Promoter:-2658|Intron l :644|Intron 2: 14964|Intron l :Intron 2: 15023|Intron l : 15825|Intron 1 : 17069, PBMC:OA; 16:75300041, BCARl ||Proximal Promoter: - 195|Proximal Promoter:-136|Intron l :666|Intron 1 : 1910, PBMC:OA; 16:75661691, KARSpxon 14:Exon 15: 19894, Mono:OA_SLE_HC,Mono:SLE; 16:81528974, CMIP||Proximal Promoter^ l |Intron 1 :50200, PBMC:HC; 16:81703901, CMIP||Intron 8: 174948|Intron 8:225127,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 16:8619855, TMEM114||Exon 2:2371, Bcel OA; 16:88103117, BANP||Intron 12:99494|Intron 11 : 10964 l |Intron 10:Intron 11 : 118080, Mono:HC; 16:88103629, BANP||Intron 12: 100006|Intron 11 : 110153|Intron 10:Intron 11 : 118592, PBMC:HC; 17: 1280152, YWHAE||Intron 1 :23404, PBMC:OA; 17: 15885326, ADORA2B||3' Proximal Enhancer:37096, PBMC:HC; 17: 16284127, UBB||Proximal Promoter:-239, PBMCnotRA; 17: 16341601, TRPV2||3' Proximal Enhancer:22746, Wholeblood:notRA; 17: 1645410, WDR81 ||3' Proximal Enhancer: 17286|3' Proximal Enhancer: 17577|3' Proximal Enhancer:25594, PBMC:notRA; 17: 1665123, SERPINFl ||Proximal Promoter:-135, Mono:OA; 17: 1665220, SERPINFl ||Proximal Promoter:-38, PBMC:HC; 17: 1683424, SERPINF1 ||3' Proximal Enhancer: 18166, Mono:OA; 17: 18150501, FLII||Exon 21 : 11554, Bcell:OA_SLE_HC; 17: 18918311, GRAP||3' Proximal Enhancer:32025, PBMC:notRA; 17:26443366, NLK||Intron 1 :73679, PBMC:OA_SLE_HC; 17:3379283, ASPA||Proximal Promoter: - 12|Intron 1 : 1880, Mono:SLE; 17:3379567, ASPA||Proximal Promoter:272|Exon 2:2164, Mono:OA_SLE_HC,Mono:SLE; 17:3629901, ITGAE||Intron 26:74636, PBMCnotRA; 17:37024042, LASPl ||Proximal Promoter:-2069, PBMC:OA_SLE_HC; 17:37042201, LASPl ||Intron 2: 16090, PBMC:HC; 17:37081875, LASP1 ||3' Proximal Enhancer:55764, Mono:OA_SLE_HC; 17:38077870, GSDMB||Distal Promoter: -4077|Distal Promoter: -2967,ORMDL3||Exon 4:6014, PBMC:SLE; 17:38081186, GSDMB||5' Proximal Enhancer:-7393|5' Proximal Enhancer:-6283,ORMDL3||Intron 1:2698, PBMC:HC; 17:39769213, KRT16||Proximal Promoter: -134, PBMC:OA; 17:40687392, NAGLU||Proximal Promoter: -558, PBMC:notRA; 17:40705708, NAGLU||3' Proximal Enhancer: 17758, PBMC:notRA; 17:41159289, IFI35||Intron 1 :548, Bcell:OA_SLE_HC,PBMC:OA; 17:41170693, IFI35||3' Proximal Enhancer: 11952, PBMC:SLE; 17:45773857, TBKBPl ||Intron 1 : 1228, PBMC:OA_SLE_HC; 17:47294967, PHOSPH01 ||3' Proximal Enhancer: 13161 , PBMC:OA; 17:47296970, PHOSPH01 ||3' Proximal Enhancer: 11158, Mono:HC,PBMC:HC; 17:47297130, PHOSPH01 ||3' Proximal Enhancer: 10998, PBMC:OA_SLE_HC; 17:47301614, PHOSPH01 ||Exon 3:6514, PBMC:HC; 17:56283364, EPX||3' Proximal Enhancer: 13276,MKSl ||Exon 18: 13302|Exon 18: 13602, PBMC:notRA; 17:57187728, SKA2||Exon 3:Exon 4:45072,TRIM37||Distal Promoter:-3462, PBMC:OA_SLE_HC; 17:59226714, BCAS3||Intron 22:Intron 23:471543, PBMC:notRA; 17:59473674, BCAS3||3' Proximal Enhancer:718503, PBMC:OA; 17:61774794, MAP3K3||3' Proximal Enhancer:74994, PBMC:SLE; 17:61959416, GH2||Proximal Promoter:-193, PBMC:notRA; 17:62294665, TEX2||Intron 1 :45988, Mono:HC; 17:6557720, TXNDC17||3' Proximal Enhancer: 13499, PBMC:notRA; 17:7197775, SLC2A4||3' Proximal Enhancer: 12722, Bcell:HC,Bcell:OA_SLE_HC,Mono:OA_SLE_HC; 17:7197813, SLC2A4||3' Proximal Enhancer: 12760, PBMC:OA_SLE_HC; 17:7527668, SAT2||3' Proximal Enhancer: 3526, PBMC:HC,PBMC:OA_SLE_HC; 17:76183602, TKl ||Proximal Promoter:-317, PBMC:OA_SLE_HC; 17:80330719, UTS2R||Proximal Promoter: -1481, PBMC:OA_SLE_HC; 17:80337729, UTS2R||3' Proximal Enhancer:5529, PBMC:HC,PBMC:notRA; 17:80393504, HEXDC||Intron 5: 17253, PBMC:HC; 17:80393595, HEXDC||Exon 6: 17344, PBMC:OA_SLE_HC; 17:80393666, HEXDCpxon 6: 17415, PBMC:HC; 17:80402548, HEXDC||3' Proximal Enhancer:26297, Bcell:OA_SLE_HC; 17:80415420, NARF||Proximal Promoter:- 1119|Proximal Promoter: -639, PBMC:HC; 17:80415469, NARF || Proximal Promoter:-1070|Proximal Promoter:-590, PBMC:HC; 18: 13824359, MC 5 R|| Proximal Promoter:- 1183, Tcell:OA_SLE_HC; 18: 19176371, ESC01 ||Intron 1 :4322, PBMC:notRA; 18:32446543, DTNA||Exon 8:Intron 8:48242|Intron 10:Intron 8:48297|Intron 7:48618|Exon 17:Intron 16: 110604|Exon 15:Exon 17: 156348|Intron 15:Intron 16:273262|Exon l l :Exon 17:Intron 16:373290, PBMC:HC; 18:60192893, ZCCHC2||Intron 1 :2236, Bcel OA SLE HC; 18:74981730, GALRl ||Exon 3 : 19723, PBMC:OA_SLE_HC; 18:8370160, PTPRM||Intron 21 :Intron 23:802847, BcelhHC; 19: 11074303, SMARCA4|| Intron l:2496|Intron 1:2706, PBMC:HC; 19:11074428, SMARCA4||Intron l:2621|Intron 1:2831, PBMC:HC; 19:12759034, MAN2Bl||Exon 21: 18557, PBMC:OA_SLE_HC; 19:14586979, PTGERl||Proximal Promoter:-805, PBMC:OA_SLE_HC,PBMC:notRA; 19: 1466162, APC2||Exon 15: 16015, Wholeblood:notRA; 19:14890139, EMR2|| Proximal Promoter:-786, Mono:SLE; 19:15342982, BRD4||3' Proximal Enhancer:48280, PBMC:OA; 19:15391832, BRD4||Proximal Promoter:-570, PBMC:HC; 19:18436975, LSM4||Distal Promoter: -2974, Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC; 19:19322527, NCAN||Proximal Promoter: -254, Wholeblood:notRA; 19:19339362, NCAN||Exon 8:16581, Mono:OA; 19: 19367084, NCAN||3' Proximal Enhancer:44303, PBMC:HC; 19:30202712, C19orfl2||Intron 1:325 l|Intron l:3740|Intron 1:3984, PBMC:notRA; 19:3771880, MATK||3' Proximal Enhancer: 14535|3' Proximal Enhancer:29930, PBMC:notRA; 19:40359249, FCGBP||Intron 33:81284, PBMC:notRA; 19:40376883, FCGBP||Exon 24:63650, PBMC:OA_SLE_HC; 19:40391320, FCGBP||Intron 17:49213, PBMC:notRA; 19:41531916, CYP2B6||3' Proximal Enhancer:34713, PBMC:OA; 19:42416271, ARHGEF1||3' Proximal Enhancer:27826|3' Proximal Enhancer:29005, PBMC:notRA; 19:4543498, LRGl||Distal Promoter:-3462, PBMC:HC; 19:45449301, APOC2|| Proximal Promoter:63,CLPTMl||5' Proximal Enhancer: -9297|5' Proximal Enhancer:-8948|5' Proximal Enhancer: -8540, Mono:OA_SLE_HC; 19:45457306, APOC2||3' Proximal Enhancer:8068,CLPTMl||Proximal Promoter:-1292|Proximal Promoter: -943 IProximal Promoter:-535, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 19:46282571, DMPK||Exon 3: 1290|Exon 4:3244, Tcel HC; 19:47839132, GPR77||Proximal Promoter:-1238, PBMC:notRA; 19:4790990, FEMlA||Proximal Promoter: -737, Mono:HC; 19:49372608, PPPlR15A||Distal Promoter:-3040, Tcell:OA_SLE_HC; 19:49921142, PTH2||3' Proximal Enhancer:5556, PBMC:HC; 19:49925720, PTH2||Exon 2:978, PBMC:OA; 19:50869007, NAPSA||Proximal Promoter:-76, PBMC:HC; 19:51327177, KLKl||Proximal Promoter:-134, Bcell:OA_SLE_HC,PBMC:HC; 19:51330299, KLKl||Distal Promoter:-3256, TcelhHC; 19:51457389, KLK6||3' Proximal Enhancer: 14658|3' Proximal Enhancer: 15540, Bcell:OA_SLE_HC; 19:51875946, NKG7|| Proximal Promoter: 14, Tcell:OA_SLE_HC; 19:54876795, LAIR11 IProximal Promoter:-74, PBMC:OA_SLE_HC; 19:54877827, LAIR1|| Proximal Promoter:- 1106, PBMC:HC; 19:55013821, LAIR2|| Proximal Promoter:- 191, PBMC:HC; 19:55014357, LAIR2||Proximal Promoter:345, PBMC:notRA; 19:55128350, LILRBl||Proximal Promoter: -278, Mono:HC; 19:55142181, LILRB11 IProximal Promoter:214|Proximal Promoter:274|Intron 2:13553, Tcel OA; 19:55385581, FCAR| IProximal Promoter:33,KIR3DL2||3' Proximal Enhancer:23684, PBMC:HC; 19:55571354, RDH13||Intron l:3231|Intron 2:9560, PBMC:notRA; 19:55573572, RDH13||Intron l:1013|Intron 2:7342, Mono:OA; 19:6424217, KHSRP||Intron 1:605, PBMCnotRA; 19:6531539, TNFSF9||Intron 1:530, PBMC:notRA; 19:9092130, MUC16||Proximal Promoter:-112, Tcell:OA_SLE_HC; 1: 101704898, SlPRlpxon 2:2594, PBMC:HC; 1:109914235, SORTl||Intron l:21744|Intron 1:26328, PBMC:HC; 1:109941060, SORTl||5' Proximal Enhancer:-5081|Proximal Promoter: -497,
Bcell:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC; 1:109941072, SORTl||5' Proximal Enhancer: - 5093|Proximal Promoter:-509, PBMC:HC; 1: 113464716, SLC16Al||Exon 3:33969|Exon 3:34259, PBMC:notRA; 1: 114355571, RSBNl ||Proximal Promoter:-501, PBMC:HC; 1:11918954, NPPB||Proximal Promoter:38, Bcell:OA_SLE_HC,Bcell:SLE; 1:12181213, TNFRSF8||Distal Promoter:-4744|Intron 8:57780, TcelhSLE; 1:12186079, TNFRSF8||Proximal Promoter: 122|Exon 11:62646, Bcell:OA_SLE_HC; 1: 14032034, PRDM2||Exon l:685|Intron 1:5300, Mono:HC; 1:147101904, BCL9||3' Proximal Enhancer:88723, PBMC:HC; 1:147246154, GJA5||Proximal Promoter: -670, PBMC:notRA; 1: 151965283, S100A10||Intron 1:1431, Tcell:OA_SLE_HC; 1:153014310, SPRR2D||Proximal Promoter:-716, PBMC:HC; 1:153321198, PGLYRP4|| Proximal Promoter:- 176, PBMC:notRA; 1:153389629, S100A7A||Intron 1:630, PBMC:OA; 1: 153533922, S100A2||Exon 3:4384, Mono:OA_SLE_HC; 1:153590243, S100A13||3' Proximal Enhancer:9281|3' Proximal Enhancer:9501|3' Proximal Enhancer:9874|3' Proximal Enhancer: 10472|3' Proximal Enhancer: 16325,
Mono:HC,PBMC:notRA,Tcell:HC; 1: 153599487, SlOOAl 3 ||Proximal Promoter:37|Proximal Promoter:257|Intron l:630|Intron 2: 1228|Intron 3:7081, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 1:153599671, SlOOAl 3 ||Proximal Promoter:-147|Proximal Promoter: 731 Proximal Promoter:446|Intron 2: 1044|Intron 3:6897, Bcell:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC,Tcell:OA_SLE_HC; 1:153599704, SlOOAl 3 ||Proximal Promoter:-180|Proximal Promoter: 401 Proximal Promoter:413|Intron 2: 101 l|Intron 3:6864, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 1:153599831, SlOOAl 3 ||Proximal Promoter: -307|Proximal Promoter:-87|Proximal Promoter:286|Intron 2:884|Intron 3:6737, Mono:HC,Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_ HC; 1:153600064, SlOOAl 3 ||Proximal Promoter:-540|Proximal Promoter:-320|Proximal Promoter:53|Exon 2:651|Intron 3:6504, PBMC:HC,PBMC:OA_SLE_HC,Tcell:HC; 1: 153600132, S100A13||Proximal Promoter:-608|Proximal Promoter:-388|Proximal Promoter:-15|Intron l:583|Intron 3:6436, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:HC,Tcell:OA_SLE_HC; 1: 153600156, SlOOAl 31 |Proximal Promoter:-632|Proximal Promoter:-412|Proximal Promoter:-39|Intron l:559|Intron 3:6412, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:HC,Tcell:OA_SLE_HC; 1: 153607617, S100A13||5' Proximal Enhancer:-8093|5' Proximal Enhancer:-7873|5' Proximal Enhancer:-7500|5' Proximal Enhancer:-6902|Proximal Promoter:- 1049, PBMC:HC; 1:156609523, BCAN||Proximal Promoter:-2216, Mono:HC,Mono:OA_SLE_HC; 1: 156624237, BCAN||3' Proximal Enhancenlntron 8:12498, Tcell:HC; 1: 156889128, PEAR1||3' Proximal Enhancer:25606, PBMC:notRA; 1: 159174728, DARC|| Proximal Promoter:-320|Exon 1:926, Bcell:SLE,Mono:OA_SLE_HC,Mono:SLE,PBMC:OA_SLE_HC,PBMC:SLE,Tcell:OA_SLE_HC;
1: 160708987, SLAMF7||Proximal Promoter:-89, PBMC:notRA; 1: 160765805, LY9||Proximal Promoter: - 122, PBMC:HC; 1:160765919, LY9||Proximal Promoter:-8, Mono:HC; 1: 16087977, FBLIMl||Distal Promoter: -3481|Distal Promoter:-3016|Intron 1:2723, PBMCnotRA; 1: 16304821, ZBTB17||Proximal Promoter: -2194, PBMC:notRA; 1:16370634, CLCNKB||Distal Promoter:-4649|Proximal Promoter:388, PBMC:notRA; 1:171156996, FM02||Intron 2:2609, PBMC:notRA; 1:171306733, FM04||Intron 9:23248, Bcell:OA; 1: 174769548, RABGAP 1 L| |Exon 1:514, PBMC:OA_SLE_HC; 1: 174843754, RABGAP 1 L| |Proximal Promoter: -901 |Proximal Promoter:231 |Intron 2:74720, PBMCSLE; 1: 174843909, RABGAP lL||Proximal Promoter:-746|Proximal Promoter:386|Intron 2:74875, PBMC:SLE; 1: 174844397, RABGAP lL||Proximal Promoter:-258|Intron l:874|Intron 2:75363,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,Tcell:SLE; 1: 174844490, RABGAP 1 L| | Proximal Promoter: - 165|Intron l:967|Intron 2:75456,
Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:SLE; 1: 17600880, PADI3||Intron 10:25288, PBMCnotRA; 1:18969652, PAX7||Intron 4:12153, Tcell:OA_SLE_HC; 1:19218007, ALDH4A1 ||Proximal Promoter:-622|Intron 1: 11286, PBMC:HC; 1:192542576, RGSl||Proximal Promoter: - 2280, Tcell:OA_SLE_HC; 1:192548609, RGSl||Exon 5:3753, Tcell:OA_SLE_HC; 1:205743344, RAB7Ll||Intron l:Intron 2: 1266, PBMC:HC,PBMC:OA_SLE_HC; 1:205743515, RAB7Ll||Intron l:Intron 2: 1095, Mono:HC; 1:207096358, FAIM3||Proximal Promoter:-1123|Proximal Promoter: -980, PBMC:HC; 1:207817630, CR1L|| Proximal Promoter:-827, PBMC:HC; 1:207849914, CRlL||Intron 1:31457, PBMC:HC; 1:2082315, PRKCZ||Exon 6:46161|Exon 6:76891|Exon 6:77230|Exon 9:100407, PBMC:HC; 1:211547951, TRAF5||Exon 1 l:28246|Exon l l:47804|Exon 11:47995, PBMC:HC; 1:223901187, CAPN2||Intron l: 1069|Intron 1:11893, PBMC:OA_SLE_HC; 1:226114565, LEFTY2||3' Proximal Enhancer: 14518, Mono:OA; 1:22919937, EPHA8||3' Proximal Enhancer:Exon 6:29934, PBMCnotRA; 1:22921120, EPHA8||3' Proximal Enhancer: Intron 7:31117, Wholeblood:notRA; 1:240774809, GREM2||Intron 1:653, PBMC:notRA; 1:242310145, PLD5||Intron 4:Intron 5:302639|Intron 6:377853, PBMC:OA_SLE_HC; 1:2437200, PLCH2||3' Proximal Enhancer:29447, PBMC:notRA; 1:243736307, AKT3||Exon 8:270277|Exon 9:270579, PBMCnotRA; 1:243877024, AKT3||Intron l: 129560|Intron 2: 129862, Mono:HC; 1:244006288, AKT3||Proximal Promoter:296|Intron 2:598, Mono:OA_SLE_HC; 1:27817404, WASF2|| Proximal Promoter:-726, PBMC:notRA; 1:33116074, RBBP4||Proximal Promoter: - 884|Proximal Promoter: -674, PBMC:notRA; 1:33160791, RBBP4||3' Proximal Enhancer:43833|3' Proximal Enhancer:44043, PBMC:HC,PBMC:OA_SLE_HC; 1:33160900, RBBP4||3' Proximal Enhancer:43942|3' Proximal Enhancer:44152, PBMC:OA_SLE_HC; 1:35250839, GJA4||5' Proximal Enhancer: - 7759,GJB3||Exon 2:2929|Exon 2:4050, Mono:OA_SLE_HC; 1:40219054, BMP8B||3' Proximal Enhancer:35479, PBMC:notRA; 1:45267345, PLK3||Exon 4: 1310, PBMC:HC; 1:58704335, DABl||Intron 1:11876, PBMC:HC; 1:61624321, NFIA||Intron 2:76342|Intron 3:76788|Intron 2:81376, Tcel HC; 1:71511514, PTGER3||Intron 1:1977, PBMC:OA_SLE_HC; 1:7834809, PER3||5' Proximal Enhancer:- 9953, PBMCnotRA; 1:7884824, PER3||Intron 15:40062, PBMC:notRA; 1:7887199, PER3||Exon 17:42437, Mono:HC; 1:7887271, PER3||Exon 17:42509, PBMC:HC,Wholeblood:notRA; 1:7887346, PER3||Exon 17:42584, PBMC:HC; 1:7887455, PER3||Exon 17:42693,
PBMC:HC,Tcell:HC,Wholeblood:notRA; 1:7887560, PER3||Exon 17:42798,
PBMC:HC,Wholeblood:notRA; 1:89829871, GBP6||Proximal Promoter:436,
PBMC:HC,PBMC:OA_SLE_HC; 1:9006680, CA6||Intron 1:759, Mono:SLE; 1:90313059, LRRC8D||Intron 2:25580|Intron 2:26487, PBMC:HC; 1:92952517, GFIl||Distal Promoter: -3161 |Proximal Promoter:-889|Proximal Promoter:-84, Tcell:OA_SLE_HC; 1:92953279, GFIl||Distal Promoter: - 3923|Proximal Promoter:- 165 l|Proximal Promoter:-846, PBMC:notRA; 20: 1918153, SIRPA||Exon 8:42328|Exon 9:42729|Exon 9:43341, PBMC:notRA; 20:19954588, RIN2||Intron 6:84379|Intron 7:87424, Bcell:OA_SLE_HC,Bcell:SLE; 20:2383390, TGM6|| Intron 7:21837, PBMC:notRA; 20:3667620, SIGLECl||Exon 21:20155, PBMC:OA; 20:36793866, TGM2||Proximal Promoter:- 166, PBMC:OA_SLE_HC; 20:3772433, CDC25B||Distal Promoter:-3967, PBMC:HC; 20:39307538, MAFB||3' Proximal Enhancer: 10338, PBMC:notRA; 20:39320005, MAFB||Proximal Promoter: -2129, Tcel OA; 20:44542136, PLTP||Distal Promoter: -2503|Proximal Promoter:- 1133, PBMC:notRA; 20:54949299, AURKA||Intron 6:Intron 7:Intron 8: 18052, PBMC:notRA; 20:981673, RSP04||Intron 1: 1234, PBMC:HC; 21:35016873, ITSNl||Intron 1:2090, PBMC:HC; 21:35889668, KCNE1||5' Proximal Enhancer: -6055, PBMC:notRA; 21:42877638, TMPRSS2||Intron l:2354|Intron 1:2447, PBMC:SLE; 21:42880448, TMPRSS211 Proximal Promoter:-456|Proximal Promoter: -363, PBMC:notRA; 21 :43619559, ABCGl ||Proximal Promoter:-362|Proximal Promoter:-239, PBMC:SLE; 21 :43824262, UBASH3A||Proximal Promoter:292, PBMC:HC; 21:44525949, U2AFl ||Intron 1 : 1739, Mono:OA; 21 :44528396, U2AFl ||Proximal Promoter: -708, Tcell:OA_SLE_HC; 21 :45575573, C21orG3||3' Proximal Enhancer:22080, PBMC:HC; 22: 18893382, PRODH||3' Proximal Enhancer:30582|3' Proximal Enhancer:30684, Mono:OA; 22: 19513106, CLDN5||Proximal Promoter:-246, BcelhOA; 22:22597965, VPREBl ||Proximal Promoter:-1234, PBMC:HC; 22:27017854, CRYBBl ||Distal Promoter: -3863, BcelhOA; 22:28191914, MNl ||Intron 1 :5572, Mono:SLE; 22:36718563, MYH9||Exon 6:65500, PBMC:notRA; 22:36960499, CACNG2||Exon 4: 138191, PBMC:notRA; 22:47081903, CERK||Exon 13:52249, PBMC:HC; 22:47082044, CERK||Exon 13:52108, PBMC:HC; 22:47135171, CERK||Proximal Promoter:- 1019, PBMC:notRA; 22:47135258, CERK||Proximal Promoter:- 1106,
PBMC:HC,PBMC:OA_SLE_HC; 22:50496499, MLC1 ||3' Proximal Enhancer:27282|3' Proximal Enhancer:27859, PBMC:notRA; 22:50524541, MLCl ||Proximal Promoter:-760|Proximal Promoter:-183, BcelhOA; 22:50625225, PANX2||3' Proximal Enhancer: 16066, Wholeblood:notRA; 22:50738550, PLXNB2||Intron 1 :7451, PBMC:notRA; 22:50747878, PLXNB2|| Proximal Promoter:- 1877, Mono:HC; 22:50965373, SC02||Proximal Promoter:- 1340|Proximal Promoter:-1339|Proximal Promoter:-799|Proximal Promoter:-505, Tcell:OA_SLE_HC; 22:50965782, SC02|| Proximal Promoter:-1749|Proximal Promoter: - 1748|Proximal Promoter:-1208|Proximal Promoter: -914, Tcell:SLE; 22:50970943, SC02||5' Proximal Enhancer:-6910|5' Proximal Enhancer:-6909|5' Proximal Enhancer:-6369|5' Proximal Enhancer:-6075, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC,Tcell:SLE; 22:50971109, SC02||5' Proximal Enhancer:-7076|5' Proximal Enhancer:-7075|5' Proximal Enhancer:-6535|5' Proximal Enhancer:-6241, PBMC:OA_SLE_HC,Tcell:SLE; 22:50971140, SC02||5' Proximal Enhancer: -7107|5' Proximal Enhancer: - 7106|5' Proximal Enhancer:-6566|5' Proximal Enhancer:-6272,
Mono:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 22:50973101, SC02||5' Proximal Enhancer:-9068|5' Proximal Enhancer:-9067|5' Proximal Enhancer:-8527|5' Proximal Enhancer:-8233, Mono:SLE,PBMC:SLE; 2: 101428924, NPAS2||5' Proximal Enhancer:-7688, PBMCnotRA; 2: 102316496, MAP4K4||Intron 2: 1959|Intron 2:2332, PBMC:HC; 2: 106055153, FHL2||Proximal Promoter:77, BcelhHC; 2: 109605518, EDAR|| Proximal Promoter:310, PBMC:SLE,Tcell:SLE; 2: 109606018, ED AR|| Proximal Promoter:-190, TcelhSLE; 2: 113404678, SLC20Al ||Exon 2: 1245, Bcell:OA_SLE_HC,Bcell:SLE; 2: 113420964, SLC20Al ||Exon 11 : 17531, Mono:OA_SLE_HC,PBMC:SLE; 2: 128052778, MAP3K2||3' Proximal Enhancer:48027, PBMC:HC; 2: 128052889, MAP3K2||3' Proximal Enhancer:47916, PBMC:HC; 2: 135214041, MGAT5||3' Proximal Enhancer:202212, PBMC:notRA; 2: 148617336, ACVR2A|| Intron 1 : 14767, BcelhHC; 2: 171676809, GADl ||Intron 2:3610, PBMC:SLE; 2: 171717400, GADl pxon 17:44201, PBMC:notRA; 2: 176954533, HOXD12||5' Proximal Enhancer: -9996, PBMC:notRA,Tcell:HC; 2: 177053568, HOXDl ||Proximal Promoter:262, PBMC:OA; 2:200321348, SATB2||Intron l : 1471 |Intron 2:8483|Intron 2: 14641, PBMC:OA; 2:200335683, SATB2||5' Proximal Enhancer:-5852|Proximal Promoter:306, PBMC:notRA; 2:202897387, FZD7||Proximal Promoter:-1922, PBMC:notRA; 2:205403360, PARD3B||5' Proximal Enhancer: -7155, PBMC:HC; 2:205546112, PARD3B||Intron 1 : 135597, PBMC:notRA; 2:206255841, PARD3B||Intron 17:Intron 18:845326, Mono:OA_SLE_HC; 2:206566025, NRP2||Intron 2: 18802, Bcell:OA_SLE_HC; 2:206599315, NRP2||Intron 7:52092, PBMC:HC; 2:209224676, PIKFYVE||3' Proximal Enhancer:93686, PBMC:OA; 2:216877276, MREG||Intron 1 : 1070, Mono:OA_SLE_HC; 2:219246070, SLCl lAl ||Proximal Promoter:-681, PBMC:notRA; 2:219671206, CYP27Al ||Intron 1 :24735, PBMC:HC; 2:220312854, SPEG||Exon 4: 13155, PBMC:OA_SLE_HC; 2:220313153, SPEG||Exon 4: 13454, PBMC:OA; 2:239337689, ASBl ||Intron 1 :2064, BcelhOA; 2:242051737, PASK||3' Proximal EnhancenExon 15:37182|Exon 16:37657, PBMC:OA_SLE_HC,PBMC:SLE; 2:242051808, PASK||3' Proximal Enhancer:Exon 15:3711 l |Exon 16:37586, Tcel HC; 2:242714049, GAL3ST2||Proximal Promoter:-2190, PBMC:notRA; 2:25142117, ADCY3||Proximal Promoter:-62, PBMC:HC; 2:26700908, OTOF|| Proximal Promoter:2|Intron 18:80658, PBMC:HC; 2:37381088, EIF2AK2||5' Proximal Enhancer: -6123 |Intron 1 :3102, Tcel SLE; 2:37383568, EIF2AK2||5' Proximal Enhancer:-8603|Intron 1 :622,
PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 2:37384523, EIF2AK2||5' Proximal Enhancer:- 9558|Proximal Promoter:-333, PBMC:SLE; 2:37384708, EIF2AK2||5' Proximal Enhancer:-9743|Proximal Promoter: -518, PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 2:37576821, QPCT||Intron 1 :5069, Bcell:OA_SLE_HC; 2:46406516, PRKCE||Intron 14:527474, PBMC:HC; 2:46523461, EPASl ||Proximal Promoter:- 1079, Tcell:OA_SLE_HC; 2:46593223, EPASl ||Intron 6:68683, PBMC:notRA; 2:54760330, SPTBNl ||Intron 2:76877, PBMC:HC; 2:60687132, BCLl lA||Exon 4:Intron 4:93501, PBMC:notRA; 2:60712421, BCLl lA||Intron 2:68212, PBMC:notRA; 2:62428082, B3GNT2|| Intron 1 :4821, PBMC:SLE; 2:62445279, B3GNT2||Intron 1 :22018, PBMC:HC; 2:65593933, SPRED2||Proximal Promoter: -21 Intron 1 :65723, PBMC:notRA; 2:65594021, SPRED2|| Proximal Promoter:-90|Intron 1 :65635, PBMC:notRA,Wholeblood:notRA; 2:65604910, SPRED2||Intron 1 :54746, Tcel SLE; 2:65640057, SPRED2||Intron 1:19599, PBMC:OA; 2:7016509, RSAD2||Proximal Promoter:-1286, BcelhOA SLE HC; 2:7017571, RSAD2||Proximal Promoter: -224, PBMC:SLE,Tcell:SLE; 2:7018020, RSAD2||Proximal Promoter:225, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 2:7018153, RSAD2||Proximal Promoter:358, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 2:74780229, DOKl||Proximal Promoter:-1282|Intron 1:4083, PBMC:OA_SLE_HC; 2:96055060, KCNIP3||3' Proximal Enhancer:42293|3' Proximal Enhancer:91989, Mono:OA_SLE_HC; 2:96809970, DUSP2||Exon 3:1209, PBMC:HC; 3: 111260756, CD96||Proximal Promoter: -169, PBMC:HC; 3: 111260783, CD96||Proximal Promoter: -142, Wholeblood:notRA; 3: 11348436, ATG7||Exon 4:34427, PBMC:notRA; 3: 119187570, POGLUTl||Proximal Promoter: - 214,TMEM39A||5' Proximal Enhancer:-5099, PBMC:notRA; 3:119499190, NR1121| Proximal Promoter: - 2366|Proximal Promoter:-140, PBMC:HC; 3:122044172, CSTA||Proximal Promoter: 162, PBMC:HC; 3: 12800816, TMEM40||Proximal Promoter:-8, Mono:OA; 3: 128964838, COPG||Distal Promoter:-3614, PBMC:OA_SLE_HC,PBMC:notRA; 3: 146258875, PLSCRl||Intron 1:3753,
Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 3: 146260954, PLSCRl||Intron 1: 1674, Bcell:OA_SLE_HC,PBMC:OA_SLE_HC,Tcell:OA_SLE_HC; 3:146263336, PLSCRl||Proximal Promoter: -708, PBMCnotRA; 3: 155200562, PLCHl||Exon 23:Exon 24: 193543|Exon 22:221435, PBMC:notRA; 3:183260375, KLHL6||Intron 1: 13124, Bcell:HC; 3:18480297, SATBl||Proximal Promoter:-32, PBMC:HC; 3:18484742, SATBl||Distal Promoter: -4477, Mono:HC; 3: 186503527, EIF4A2||Intron 4:2167, Bcell:OA_SLE_HC; 3:191048377, UTS 2D || Proximal Promoter:-52, Tcell:SLE; 3: 191048753, UTS2D||Proximal Promoter:-428, Tcell:SLE; 3:196001706, PCYT1A|| Intron 2: 12878, PBMC:HC; 3:23849114, UBE2El||Distal Promoter: -2819|Intron 2:1731, Bcell:OA_SLE_HC; 3:24535365, THRB||Intron 1:948, Bcell:SLE; 3:3097738, CNTN4||Intron 15:163840|Intron 23:817226|Intron 24:957189, Mono:OA_SLE_HC; 3:46785957, PRSS46||5' Proximal Enhancer:-8036, Bcell:HC; 3:49705435, BSN||Exon 12:113514, Bcell:HC; 3:50194470, SEMA3F||Intron 1: 1623, PBMGSLE; 3:56810151, ARHGEF31 |Proximal Promoter:-406|Intron l:25844|Intron 4:303185, Mono:OA_SLE_HC; 3:57128136, IL17RD||Exon 13:71267, Mono:HC; 3:57199524, IL17RD||Proximal Promoter:- 121, PBMC:notRA; 3:57263543, APPLl||Intron 1: 1779, PBMC:notRA; 3:58103186, FLNB||Intron 18:109060, Bcell:OA_SLE_HC; 3:58569597, FAM107A||5' Proximal Enhancer: -6106, PBMC:notRA,Tcell:HC; 3:63428305, SYNPR||Proximal Promoter: -447|Intron 2:164392, PBMC:notRA; 3:71111489, FOXPl||Intron l:2585|Intron 2:68603 |Intron 3: 182827|Intron 4:242422|Intron 6:481219|Intron 7:521415|Intron 7:521651, PBMC:OA_SLE_HC,PBMC:notRA; 3:71178485, FOXPl||Intron l: 1607|Intron 2:115831|Intron 3: 175426|Intron 5:414223 |Intron 6:454419|Intron 6:454655, PBMC:SLE; 3:71481486, FOXPl||Intron 2: 111222|Intron 3:151418|Intron 3: 151654, PBMC:OA_SLE_HC; 3:86061698, CADM2|| Intron 8:286067|Intron 8:1053566, PBMC:notRA; 4:119732131, SEC24D||Intron 6:25195, PBMC:HC; 4: 145566441, HHIP|| Proximal Promoter:-706, PBMC:notRA; 4: 145566595, HHIP|| Proximal Promoter: - 552, PBMC:notRA; 4:147573410, POU4F2||3' Proximal Enhancer: 13366, PBMC:HC; 4: 164088478, NAFl||Proximal Promoter: -405, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 4: 164088493, NAFl||Proximal Promoter:-420, Bcell:OA_SLE_HC; 4: 187628026, FATlpxon 2: 16961, BcelhHC; 4: 187630905, FATl||Exon 2: 14082, Wholeblood:notRA; 4:190862026, FRGl||Proximal Promoter:53, PBMC:SLE; 4:26585218, TBClD19||Proximal Promoter:-327, PBMC:SLE; 4:27004697, STIM2||Exon 7: 142385, PBMC:OA_SLE_HC; 4:2819614, SH3BP2|| Proximal Promoter:-926|Proximal Promoter: -297|Intron l:5669|Intron 1:24865, Wholeblood:notRA; 4:76599597, G3BP2||Proximal Promoter:-1254|Proximal Promoter:-930, PBMC:HC,PBMC:notRA; 4:76862254, NAAA||Proximal Promoter:-88, Mono:OA; 4:79473488, ANXA3||Intron 1:747, PBMC:notRA; 4:84255411, HPSE||Intron l:555|Intron l:623|Intron 2:895, PBMC:SLE; 4:84257153, HPSE||Proximal Promoter:-1187|Proximal Promoter:-1119|Proximal Promoter:-847, PBMC:HC; 4:87849250, AFF1||5' Proximal Enhancer: -6903, PBMC:HC; 4:96292858, UNC5C||Intron 1:177503, BcelhHC; 4:96470349, UNC5C||Proximal Promoter:12, BcelhOA; 4:96472269, UNC5C||Proximal Promoter:-1908, BcelhHC; 5:122375318, PPIC||Distal Promoter: -2893, PBMC:OA; 5:131543977, P4HA2||Intron 7:18958|Intron 7:Intron 8:19579, PBMC:HC; 5: 131561292, P4HA2||Intron l: 1643|Intron l:Intron 2:2264, Bcell:OA_SLE_HC; 5:131563921, P4HA211 Proximal Promoter:-986|Proximal Promoter: -365, Mono:OA; 5: 134661102, H2AFY||3' Proximal Enhancer:73826|3' Proximal Enhancer: 74475, PBMC:HC; 5:134688497, H2AFY||Intron 5:Intron 6:4643 l|Intron 6:47080, PBMC:OA_SLE_HC; 5:134780343, TIFAB||3' Proximal Enhancer:7746, Mono:HC; 5:135384080, TGFBI||Intron 6:19497, PBMC:OA_SLE_HC; 5:138861241, TMEM173||Exon 3: 1102, Tcell:OA_SLE_HC; 5: 139283199, NRG2||Intron 1:139685, PBMC:OA; 5:1394296, SLC6A3||Exon 15:51247, PBMC:HC; 5:140562562, PCDHB9|| Distal Promoter: -4330, PBMC:HC; 5: 141062490, ARAP3||Proximal Promoter: -690, PBMC:OA_SLE_HC; 5:146837147, DPYSL3||Distal Promoter: -3887|Intron 1:52472, Mono:OA_SLE_HC; 5:149546946, CDXl||Intron 1:603, PBMC:OA_SLE_HC; 5:150871546, SLC36Al||Exon 11:44384, Mono:HC; 5: 17220477, BASPl||Intron 1:2728, BcelhOA; 5:17221971, BASPl||Intron 1:4222, BcelhHC; 5:176270730, UNC5A||Intron 1:33171, Wholeblood:notRA; 5:176798049, RGS14||Intron 11:13206, PBMC:notRA; 5:176859356, GRK6||Intron 4:5670, PBMC:HC; 5:257420, SDHA||3' Proximal Enhancer:39065, PBMC:HC,PBMC:OA_SLE_HC; 5:308268, AHRR||Intron 1 :3978, PBMC:notRA; 5:369969, AHRR||Intron 3:65679, PBMC:OA; 5:491905, SLC9A3||Exon 2:32644, PBMC:HC; 5:508185, SLC9A3||Intron 1: 16364, Mono:OA; 5:607516, CEP72||Distal Promoter: -4888, Bcell:OA_SLE_HC; 5:640245, CEP72||Intron 8:27841, Mono:OA_SLE_HC,PBMC:OA_SLE_HC,PBMC:notRA,Tcell:OA_SLE_HC; 5:67535553, PIK3R1 || Intron 2:23970, Tcell:OA_SLE_HC; 5:72746811, FOXDl ||Proximal Promoter: -2459, Bcell:OA_SLE_HC; 5:76010444, F2R||Proximal Promoter: -1423, Mono:SLE; 5:76012757, F2R||Intron 1 :890, Wholeblood:notRA; 5:98108543, RGMB|| Intron 2:3545, PBMC:OA_SLE_HC; 6: 112575929, LAMA4||Proximal Promoter:-101, PBMC:OA_SLE_HC; 6: 112575966, LAMA4|| Proximal Promoter:- 138, PBMC:OA_SLE_HC; 6: 1396771, FOXF2||3' Proximal Enhancer:6703, Bcell:OA_SLE_HC,Bcell:SLE; 6: 150073879, PCMTl ||Intron 1 :3049, PBMC:HC; 6: 170554521, LOC154449||3' Proximal Enhancer: 17136, PBMC:HC,PBMC:OA_SLE_HC; 6: 170554795, LOC154449||3' Proximal Enhancer: 16862, PBMC:HC; 6: 170557102, LOC154449||3' Proximal Enhancer: 14555, PBMC:HC; 6: 170557582, LOC154449||3' Proximal Enhancer: 14075, PBMC:HC; 6: 170557757, LOC154449||3' Proximal Enhancer: 13900, PBMC:HC; 6: 170557976, LOC154449||3' Proximal Enhancer: 13681, PBMC:HC; 6: 170558063, LOC154449||3' Proximal Enhancer: 13594, PBMC:HC; 6: 170571786, LOCI 54449 Proximal Promoter: - 129, PBMC:HC; 6: 170571794, LOC154449||Proximal Promoter:- 137, PBMC:HC; 6:27368122, ZNF391 ||Exon 3: 11599, Bcel OA; 6:2888212, SERPINB9||Exon 7: 15333, PBMC:OA_SLE_HC; 6:2892150, SERPINB9||Exon 6: 11395, PBMC:notRA; 6:2892152, SERPINB9||Exon 6: 11393, PBMC:notRA; 6:2991147, NQ02||5' Proximal Enhancer:-8919, Mono:HC; 6:30036373, RNF39||3' Proximal Enhancer: 7253 Proximal Enhancer: 7255, PBMC:notRA; 6:30038712, RNF39||Exon 5:4914|Exon 4:4916, PBMC:OA_SLE_HC; 6:30039130, RNF39||Intron 4:4496|Exon 4:4498, PBMC:OA_SLE_HC; 6:30039142, RNF39||Intron 4:4484|Exon 4:4486, PBMC:OA_SLE_HC,Tcell:OA; 6:30039175, RNF39||Intron 4:4451 |Exon 4:4453, PBMC:OA_SLE_HC; 6:30039206, RNF39||Exon 4:4420|Exon 4:4422, Tcel OA; 6:30039374, RNF39||Exon 4:4252|Exon 4:4254, PBMC:OA_SLE_HC; 6:30039376, RNF39||Exon 4:4250|Exon 4:4252, PBMC:OA_SLE_HC; 6:30039380, RNF39||Exon 4:4246|Exon 4:4248, PBMC:OA_SLE_HC; 6:30039403, RNF39||Exon 4:4223|Exon 4:4225, PBMC:OA_SLE_HC; 6:30039408, RNF39||Exon 4:4218|Exon 4:4220, PBMC:OA_SLE_HC; 6:30039432, RNF39||Exon 4:4194|Exon 4:4196, PBMC:OA_SLE_HC; 6:30039435, RNF39||Exon 4:4191 |Exon 4:4193, PBMC:OA_SLE_HC; 6:30039442, RNF39||Exon 4:4184|Exon 4:4186, PBMC:OA_SLE_HC; 6:30039466, RNF39||Exon 4:4160|Exon 4:4162, PBMC:OA_SLE_HC; 6:30458586, HLA-E||Intron 3: 1404, BcelhOA SLE HC; 6:30459540, HLA-E||Intron 5:2358, BcelhOA SLE HC; 6:30690355, FLOTl ||3' Proximal Enhancer:20098, PBMC:notRA; 6:30691259, FLOTl ||3' Proximal Enhancer: 19194, PBMC:notRA; 6:30713246, FLOTl ||Distal Promoter:-2793,IER3||Proximal Promoter: -919, PBMC:notRA; 6:30720484, IER3||5' Proximal Enhancer:-8157, PBMC:HC; 6:30850581, DDR1 ||5' Proximal Enhancer:- 5883|Proximal Promoter: -2175 |Proximal Promoter: -1745 |Proximal Promoter:-1279,
PBMC:OA_SLE_HC,PBMC:SLE; 6:31096861, PSORSlCl ||Intron 2: 14254, PBMC:OA_SLE_HC; 6:31107186, CCHCR1 ||3' Proximal Enhancer: 18380|3' Proximal Enhancer: 18829, PBMC:HC,PBMC:OA_SLE_HC; 6:31510735, ATP6V1G2||3' Proximal
Enhancer:3890,DDX39B||Proximal Promoter:-483, Bcell:OA_SLE_HC; 6:31650735, LY6G5C||Distal Promoter: -2585, PBMC:HC; 6:31779020, HSPAlA||Distal Promoter:-4270, PBMC:notRA; 6:31779637, HSPAlA||Distal Promoter:-3653, PBMC:notRA; 6:31804461, C6orf48||Intron 2:Intron 3: 1769,HSPA1B||3' Proximal Enhancer:8950, PBMC:HC; 6:31838973, EHMT2||3' Proximal Enhancer:26491, PBMC:OA; 6:32033006, TNXB||Intron 18:44145, PBMC:HC,PBMC:OA_SLE_HC; 6:32057846, TNXB||Intron 4: 19305, Mono:OA_SLE_HC; 6:32159036, GPSM3||Exon 8:4264, PBMC:HC; 6:3228365, TUBB2B||Proximal Promoter:-397, TcelhOA; 6:32709158, HLA-DQA2|| Proximal Promoter: -4, PBMC:HC; 6:32711617, HLA-DQA2||Intron 1 :2455, PBMC:notRA; 6:32712979, HLA-DQA2||Exon 2:3817, Mono:OA_SLE_HC,PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE,PBMC:notRA; 6:32713827, HLA-DQA2||Exon 3:4665, Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 6:32725332, HLA-DQB2|| Intron 3:5998, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:32728862, HLA-DQB2||Intron 2:2468, PBMC:OA_SLE_HC; 6:32728951, HLA-DQB2||Intron 2:2379,
PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 6:32729118, HLA-DQB2||Intron 2:2212, PBMC:HC,PBMC:OA_SLE_HC,PBMC:SLE; 6:32729130, HLA-DQB2|| Intron 2:2200, PBMC:HC; 6:32731438, HLA-DQB2||Proximal Promoter:- 108, PBMC:notRA; 6:32732585, HLA-DQB2||Proximal Promoter:-1255, PBMCnotRA; 6:32782988, HLA-DOB||Exon 2: 1837, Mono:OA; 6:32785622, HLA- DOB||Proximal Promoter: -797, PBMC:notRA; 6:32785740, HLA-DOB||Proximal Promoter:-915, PBMC:notRA; 6:32974843, HLA-DOA|| Intron 4:2546, PBMC:OA_SLE_HC; 6:33243552, RPS18||Intron 2:3701, Bcell:OA_SLE_HC; 6:33245701, RPS18||3' Proximal Enhancer:5850, PBMC:SLE; 6:33276465, DAXX||3' Proximal Enhancer: 14328, PBMCnotRA; 6:33286244, DAXX||3' Proximal Enhancer:4549, PBMC:SLE; 6:34724741, SNRPC|| Proximal Promoter: -129, Mono:HC,Mono:OA_SLE_HC,PBMC:HC; 6:39195019, KCNK5||Intron 1:2232, PBMC:HC; 6:43022109, CUL7||Proximal Promoter: -426, PBMC:notRA; 6:44190729, SLC29Al||Proximal Promoter:-633|Proximal Promoter:-566|Intron 1:3488, PBMC:OA_SLE_HC,PBMC:SLE; 6:44217925, HSP90ABl||Intron 5:3077, PBMC:OA; 6:46703538, PLA2G7||Proximal Promoter:-387|Proximal Promoter: -108, Bcell:OA_SLE_HC; 6:7115345, RREBl||Intron l:7260|Intron 1:7516, PBMC:HC; 6:7169632, RREBl||Intron l:61547|Intron 1:61803, PBMC:HC; 6:7234581, RREBl||Intron 10:126496|Intron 10: 126752, Mono:HC; 6:88032061, GJB7||Intron 2:6935, PBMC:OA_SLE_HC; 7:101555711, CUXl||Intron l:94830|Intron l:96424|Intron 1:96528, PBMC:HC; 7:107572753, LAMBl||Exon 28:71051, PBMC:HC; 7:116138591, CAV2|| Proximal Promoter: - 1506|Proximal Promoter: -1063, PBMCnotRA; 7:127291444, SNDl||Proximal Promoter:-757, PBMC:HC,PBMC:OA_SLE_HC,PBMC:notRA; 7:127292389, SNDl||Proximal Promoter: 188, PBMC:notRA; 7: 127514192, SNDl||Intron 12:221991,
Mono:HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 7: 133451621, EXOC4||Intron 10:513799, Bcell:HC; 7: 150434077, GIMAP5||Proximal Promoter:-358, PBMC:notRA; 7:150744384, CDK5||3' Proximal Enhancer: 10668, PBMC:OA_SLE_HC; 7:150754081, CDK5||Intron 2:971, PBMC:notRA; 7:150755897, CDK5||Proximal Promoter:-845, PBMC:HC; 7: 150974554, SMARCD3||Proximal Promoter:-734|Proximal Promoter:-323, Bcel OA; 7: 151248135, PRKAG2||3' Proximal Enhancer:81209|3' Proximal Enhancer:263822|3' Proximal Enhancer:326181, Bcell:OA_SLE_HC; 7:151411526, PRKAG2|| Intron 3: 100431|Intron 3:162790, PBMC:HC; 7: 151505116, PRKAG2|| Intron l:6841|Intron 1:69200, PBMC:HC; 7: 1581583, MAFK||Exon 3: 11216, PBMC:notRA; 7: 193229, FAM20C||Proximal Promoter:261, PBMC:OA; 7:218726, FAM20C||Intron 3:25758, BcelhHC; 7:27138396, HOTAIRM 11 |Intron 1:2684, PBMC:HC; 7:2764599, GNA12||3' Proximal Enhancer: 119360, Mono:HC; 7:2769865, GNA12||Exon 4: 114094, Mono:OA,PBMC:HC; 7:2773010, GNA12||Intron 3:110949, PBMC:HC; 7:2800436, GNA12||Intron 2:83523, BcelhSLE; 7:28075371, JAZFl||Intron 1:145066, PBMC:notRA; 7:44184403, GCK||Exon 10:Exon l l: 14484|Exon 10:44619, PBMC:OA_SLE_HC; 7:44677772, OGDH||Intron 2:31652, PBMC:OA_SLE_HC; 7:50744032, GRB10||Intron 2:28966|Intron 2:56018|Intron 3: 117127, PBMC:HC,PBMC:OA_SLE_HC; 7:50850870, GRB10||Intron 1:10289, PBMC:notRA; 7:50862067, GRB10||Proximal Promoter: -908, BcelhOA SLE HC; 7:556429, PDGFA||Intron 2:3052, PBMC:SLE; 7:5568044, ACTB||Exon 4:2188, PBMC:HC; 7:5631268, FSCNl||Proximal Promoter:- 1167, Mono:OA; 7:6465799, DAGLB||Intron 4:Intron 6:21844, Mono:HC; 7:66207656, RABGEFl||Intron 1:2014, BcelhOA; 7:77827379, MAGI2|| Intron 11:1255511, PBMC:OA_SLE_HC; 7:89873891, STEAP2||3' Proximal Enhancer:30758|3' Proximal Enhancer: 32718|3' Proximal Enhancer:32892, PBMC:OA; 7:91763103, CYP51Al||Intron l:737|Intron 1:956, PBMC:HC; 7:94220697, SGCE||Intron 10:Intron 8:Intron 9:64824, Wholeblood:notRA; 7:94285642, SGCE||Proximal Promoter:- 121, Mono:OA_SLE_HC,PBMC:OA; 7:94286110, SGCE||Proximal Promoter: -589, PBMC:notRA; 7:94286473, SGCE||Proximal Promoter:-952, PBMC:notRA; 7:95226433, PDK4|| Proximal Promoter:-508, PBMC:HC; 7:96133485, FLJ42280||Proximal Promoter:-650, Bcel HC; 7:97832830, LMTK2|| Intron 11:96634, PBMC:HC; 7:98029266, BAIAP2Ll||Intron 1: 1161, PBMC:HC; 7:98029285, BAIAP2Ll||Intron 1:1142, PBMC:HC; 7:99683264, MCM7||3' Proximal Enhancer: 15116|3' Proximal Enhancer: 16163, PBMC:HC; 7:99964511, PILRA||5' Proximal Enhancer:-6556, PBMC:HC; 8:101962118, YWHAZ||Intron l:681|Intron l: 1442|Intron l:2239|Intron l:3103|Intron 1:3505, PBMC:HC; 8:103243598, RRM2B||Intron 2:7461|Intron l:Intron 2:7748, BcelhHC; 8: 103666796, KLF10||Proximal Promoter:-628|Intron 1:1187, Bcel OA; 8: 109092720, RSP02||Intron 2:3193, PBMC:HC,PBMC:OA_SLE_HC; 8:11303039, FAM167A||Intron 1:21237, Bcell:OA_SLE_HC; 8: 118890491, EXTl||Intron 1:233567, PBMC:notRA; 8: 119086762, EXTl||Intron 1:37296, PBMC:OA; 8:128805414, PVTl||Proximal Promoter:- 1364, PBMC:HC; 8: 143580823, BAIl||Intron 16:35447, PBMC:notRA; 8: 143580965, BAIl||Intron 16:35589, PBMC:notRA; 8: 143992652, CYPl lB2||Exon 9:6607, PBMCnotRA; 8: 1733369, CLN8||Exon 3:21500, PBMC:notRA; 8: 1740059, CLN8||3' Proximal Enhancer:28190, PBMCSLE; 8: 1740065, CLN8||3' Proximal Enhancer:28196, PBMC:SLE,Tcell:SLE; 8:18744446, PSD3||Intron 2: 126750, PBMC:notRA; 8:22464288, PDLIM2||3' Proximal Enhancer:26302, PBMC:SLE; 8:27352103, EPHX2|| Intron 1:3459, PBMC:notRA; 8:31883729, NRGl||Intron 1:386462, Mono:OA_SLE_HC; 8:32290932, NRGl||Intron 1:793665, PBMC:notRA; 8:53321707, ST18||Intron 2:732, Tcell:OA_SLE_HC; 8:57360738, PENK|| Proximal Promoter: -2145|Proximal Promoter:-1456, TcelhOA; 8:59572557, NSMAF||Proximal Promoter: - 591|Proximal Promoter:- 153, PBMC:notRA; 8:62568172, ASPH||3' Proximal Enhancer:Intron 3:Intron 4:34236|Intron 3:59027, Tcel OA; 8:62621327, ASPH||Intron 1:5872, Tcell:OA_SLE_HC; 8:72111329, EYAl||Exon 16:Exon 17: 157650|Exon 18:163138, PBMC:OA_SLE_HC; 8:89340205, MMP16||Proximal Promoter: -488, PBMC:OA; 9: 114688737, UGCG||Exon 5:29532, PBMC:HC; 9: 123850279, CNTRL||Proximal Promoter: -294, PBMC:HC; 9: 136397058, ADAMTSL2||Distal Promoter:-2916|Proximal Promoter: -227, PBMC:HC,PBMC:OA_SLE_HC; 9:138591683, KCNTl||Proximal Promoter: - 2347,SOHLHl||Proximal Promoter: -309, PBMC:HC; 9: 138670828, KCNTl||Intron 23:76798, PBMC:notRA; 9: 140077638, SSNA1||5' Proximal Enhancer: -5415, PBMC:OA_SLE_HC; 9:19378679, RPS6||Intron 3:1556, Bcell:OA_SLE_HC,Mono:OA_SLE_HC,PBMC:OA_SLE_HC; 9:19379118, RPS6||Intron 2:1117, BcelhHC; 9:214268, DOCK8||Proximal Promoter:-596, PBMC:HC; 9:33130375, B4GALTl||Intron 2:36981, Wholeblood:notRA; 9:73178360, TRPM3||Intron 20:Intron 21:Intron 22:305614|Intron 21:558154, PBMC:HC; 9:77704473, OSTFl||Intron 1:1076, Wholeblood:notRA; X:118709261, UBE2A||5' Proximal Enhancer:-5036|Intron 2:763, BcelhOA; X:129243062, ELF4||Intron l:1413|Intron 1:1626, Bcell:OA; X:129244732, ELF4||Proximal Promoter:-257|Proximal Promoter: -44, Wholeblood:notRA; X:129299950, AIFMl||Proximal Promoter:-89, Mono:HC; X:135579106, BRS3||3' Proximal Enhancer: 8982, Mono:OA_SLE_HC; X: 153774721, IKBKG || Proximal Promoter:-1340|Proximal Promoter:-840|Intron 1:4263, PBMC:SLE; X:47050208, UBAl||Distal Promoter:-2992|Proximal Promoter:10, Wholeblood:notRA; X:48750744, PQBP1||5' Proximal Enhancer:-5030|Distal Promoter: - 4794|Distal Promoter:-4468|Distal Promoter: -4450, PBMC:notRA; X:78622859, ITM2A||Proximal Promoter: 190, Tcel HC
Table 4
Data are listed as "DML coordinate;"
DML coordinate refers to the chromosomal coordinate (chromosome: coordinate) of the cytosine of a CpG on the + strand (University of California Santa Cruz; UCSC hgl9 genome build). Each DML coordinate is labeled according to position on the + strand for simplicity but the DML may refer to the CpG on the + and/or - strand.
10:111966094 10:117997745; 10:120282778 10:122262397; 10:122356491; 10:125117367 10:131682269 10:132883127; 10:133048930 10:133528587; 10:133949209; 10:133956824 10:133956982 10:134994186; 10:1401818; 1015038349; 10:22766861; 10:334773; 10:35894430 10:37940493; 10:42863539; 10:49348564; 10:601783; 10:63683346; 10:77165673; 10:77167091 10:79398838; 10:80757927; 10:88391658; 10:99278449; 11:11177888; 11:116371188 ; 11:1220171 11:131160689; 11:131241788; 11:133784410; 11:1750353; 11:20181911; 11:3168455; 11:33097876 11:47416886; 11:48345361; 11:49017551; 11:49914049; 11:60608291; 11:61281763; 11:6291879 11:6291927; 11:6291951; 11:6292311; 11:6292490; 11:6292511; 11:63529891; 11:660597; 11:755658 11:77118761; 11:79651476; 11:85596390; 12:113229647; 12:122012243; 12:124810173; 12:124831017 12:127226034; 12:130087444; 12:130092534; 12:130450777; 12:131387360; 12:132551483 12:132962614; 12:133022550; 12:14132940; 12:15038788; 12:2944310; 12:32675207; 12:4919081 12:72149658; 12:739980; 12:740100; 12:75780994; 12:9162872; 12:9559402; 13:100642408 13:110386267; 13:113419790; 13:113841719; 13:114741241; 13:114783503; 13:114814401 13:20703415; 13:41366576; 13:50414468; 13:53442030; 13:88329151; 13:95652307; 13:99095003 14:103862143; 14:104734272; 14:104734368; 14:105036133; 14:105332627; 14:105944942 14:105945022; 14:105945287; 14:105945685; 14:105945699; 14:106320748; 14:21199099; 14:35032169
14:61928727 14:67983484; 14:74704714; 14:76734368; 14:76873334; 14:77767735 14:86086389
14:92788580 14:98444476; 15:100672379; 15:22413307; 15:23810334; 15:25434030: 15:25441418
15:27111604 15:27902080; 15:28567519; 15:59499030; 15:61972967 15:63758958: 15:65843003
15:72567956 15:72977851; 15:77896785; 15:79725642; 15:81122346 15:89455860: 15:99975141
15:99975310 15:99975334; 15:99975470; 16:20774873; 16:221811 16:28205389; 16:3017902
16:34787597 16:420230; 16:50769852; 16:56330268; 16:57023022; 16:57023191; 16:785033
16:7855622; 16:81703901; 16:84076900; 16:84690554; 16:86231823; 16:86899685: 16:88103629
16:88547533 16:89180587; 17:1040653; 17:12562530; 17:26443366; 17:29297380: 17:35300448
17:37042201 17:38081186; 17:40169518; 17:40174494; 17:40226702 17:40489785 17:45773857
17:47297130 17:47301614; 17:48545805; 17:52977213; 17:56283364 17:72667005 17:72948349
17:74266324 17:75884327; 17:76254129; 17:77916733; 17:78549358 17:78700928: 17:78701084
17:78701257 17:80330719; 17:80337729; 17:80393504; 17:80393595 17:80393666: 17:80816851
17:80849463 17:80860250; 17:80870529; 17:80928410; 17:8777762; 18:21656374: 18:45660777
18:60985380 18:76002290; 18:77215491; 18:77236278; 18:77278806; 19:10206625 19:10206746
19:10415557 19:12876846; 19:12877000; 19:1387894; 19:1403530; 19:14142201 19:17015427
19:17514600 19:17599784; 19:17600122; 19:17721489; 19:21860753; 19:21861136; 19:3373819
19:34621907 19:35615444; 19:36643572; 19:38229377; 19:3879858; 19:48497828; 19:49636594
19:50249584 19:50869007; 19:51830634; 19:51891210; 19:52391257; 19:52391304; 19:52514445
19:52675321 19:54567279; 19:56156430; 19:58578578; 19:6424217; 19:8212675; 101313199
1:1046164; 1109941060; 1:110306507; 1:111744108; 1:1158325; 1:1164537; 1:1178245; 118427435
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170732253; 6:170732353; 6:24646782; 6:27637520; 6:28558113; 6:28641622; 6:29442830 30095174
30095195 6:30095199 30227583 30908706 31240651 31382065 31549631 6:31550090 31589196 32141882 32449961 32489555 32490350 6:32493873 32520916 32522535 32552026 32552547 32606385 6:32609130 32632106 32632108 32712979 32728951 32729118 6:32823566 32847675 33039500
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37616410 37616598 44190729 6:45295718 6:53228363; 6:55778951 6:74160206; 6:7847437; 7:107700124; 7:112062682
1121190; 7:117835958 7:124404324; 7:1245797; 7:127291444; 7:127514192; 7:129412730; 7:1315546 142428317; 7:150744384; 7:154688294; 7:155794668; 7:156740196; 7:1581583; 7:1976263; 7:2551978 2643340; 7:29606349; 7:43204506; 7:47580148; 7:50744032; 7:55516724; 7:5568044; 7:64126140 73085754; 7:76094015; 7:76139470; 7:76221076; 7:77044158; 7:93474158; 7:97663876; 7:97832830 98741636; 7:99559579; 8:107876626; 8:129985596; 8:143992652; 8:144103587; 8:144371745 145028402; 8:18744446; 8:22561893; 8:28174928; 8:37707692; 8:37773605; 8:56903623; 8:900076 101869277; 9:114688737; 9:128776861; 9:128777132; 9:136822302; 9:137515845; 9:139644102 19378679; X:140336617

Claims

WHAT IS CLAIMED IS:
1. A method of diagnosis of RA in a mammalian subject comprising the steps of: isolating DNA from a patient;
determining a methylation status of a panel of at least 3 loci of DNA from said patient; and
collectively analyzing the methylation status of the loci in the panel using a computer to ascertain a likelihood that the patient has RA.
2. The method of Claim 1, wherein said patient presents symptoms of an autoimmune disorder.
3. The method of Claim 1, wherein said panel comprises a locus of a methylation site specified in Table 2A.
4. The method of Claim 1, wherein said panel comprises a locus of a methylation site specified in Table 2B.
5. The method of any of Claims 1-4, wherein said panel comprises a locus of a methylation site specified in Table 3A.
6. The method of any of Claims 1-5, wherein said panel comprises a locus of a methylation site specified in Table 3B.
7. The method of any of Claims 1-6, wherein said panel comprises a locus of a
methylation site specified in Table 1 A.
8. The method of any of Claims 1-7, wherein said panel comprises a locus of a
methylation site specified in Table IB.
9. The method of any of Claims 1-8, wherein said panel comprises a locus of a
methylation site of Table 4
10. The method of any of Claims 1-9, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
11. The method of any of Claims 1-9, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to a sample set comprising OA methylation patterns.
12. The method of any of Claims 1-9, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
13. The method of any of Claims 1-12, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
14. The method of any of Claims 1-12, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
15. The method of any of Claims 1-12, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriatic Arthritis, Psoriasis, Reactive Arthritis, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
16. The method of any of Claims 1-12, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriatic Arthritis, Psoriasis, Reactive Arthritis,
Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
17. The method of any of Claims 1-12, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
18. The method of any of Claims 1-12, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
19. The method of any of Claims 1-18, wherein said panel excludes loci identified in a comparison of methylation patterns of DNA obtained from at least one PBMC.
20. The method of any of Claims 1-18, wherein said panel comprises a locus
identified in a comparison of methylation patterns of DNA obtained from at least one PBMC.
21. The method of any of Claims 1-18, wherein said panel excludes loci identified in a comparison of methylation patterns of DNA obtained from at least one T-Cell.
22. The method of any of Claims 1-18, wherein said panel comprises a locus
identified in a comparison of methylation patterns of DNA obtained from at least one T-Cell.
23. The method of any of Claims 1-18, wherein said panel excludes loci identified in a comparison of methylation patterns of DNA obtained from at least one B-Cell.
24. The method of any of Claims 1-18, wherein said panel comprises a locus identified in a comparison of methylation patterns of DNA obtained from at least one B-Cell.
25. The method of any of Claims 1-18, wherein said panel excludes loci identified in a comparison of methylation patterns of DNA obtained from at least one monocyte.
26. The method of any of Claims 1-18, wherein said panel comprises a locus
identified in a comparison of methylation patterns of DNA obtained from at least one monocyte.
27. The method of any of Claims 1-26, wherein the methylation status of at least 5 loci are determined.
28. The method of any of Claims 1-26, wherein the methylation status of at least 10 loci are determined.
29. The method of any of Claims 1-26, wherein the methylation status of at least 25 loci are determined.
30. The method of any of Claims 1-26, wherein the methylation status of at least 50 loci are determined
31. The method of any of Claims 1-26, wherein the methylation status of at least 200 loci are determined.
32. The method of any of Claims 1-26, wherein the methylation status of at least 250 loci are determined.
33. The method of any of Claims 1-26, wherein at least one of said loci comprises 500 bp on either side of the methylation site.
34. The method of any of Claims 1-26, wherein at least one of said loci comprises 2.5kb on either side of the methylation site.
35. The method of any of Claims 1-34, wherein said DNA is isolated from a source selected from the list comprising: free circulating DNA, DNA isolated from urine, DNA isolated from blood, DNA isolated from other body fluid, DNA isolated from other body tissue.
36. The method of any of Claims 1-34, wherein said DNA is isolated from whole blood.
37. The method of any of Claims 1-34, wherein said DNA is isolated from at least one PBMC.
38. The method of Claim 37, wherein said at least one peripheral blood mononuclear cell is selected from a group comprising: T-cells, B-cells, monocytes, Thl cells, Th2 cells, Thl7 cells, T-regs, NK cells, Bl cells, B2 cells, Ml and M2 monocytes, or dendritic cells.
39. The method of any of Claims 1-34, wherein said DNA is isolated from at least one T-Cell.
40. The method of any of Claims 1-34, wherein said DNA is isolated from at least one B-Cell.
41. The method of any of Claims 1-34, wherein said DNA is isolated from at least one monocyte.
42. The method of any of Claims 1-41, further comprising comparing said patient methylation status to that of a corresponding locus in a sample from a non-RA DNA source.
43. The method of any of Claims 1-41, further comprising comparing said patient methylation status to that of a corresponding locus in a sample from an RA DNA source.
44. The method of any of Claims 1-43, further comprising analyzing on the computer the status of one or more of the traits selected from the list comprising: SNP or gene variation status, levels of auto-antibodies such as ACPAs or rheumatoid factor, and serum proteins such as cytokine or chemokine levels or inflammatory molecules together with analyzing the methylation status of the loci in the panel.
45. A method for detecting methylation events at a panel of methylation sites, which comprises subjecting a human sample to chemical treatment that differentially affects methylated bases of said human sample, and ascertaining the extent of methylation of a panel of regions comprising at least one region of a locus of a methylation site specified in at least one of Table 2A or 2B or Table 3 A or 3B as an indicator of RA status based on said differential effect.
46. The method of Claim 45, wherein said panel comprises a locus of a methylation site specified in Table 2A.
47. The method of any of Claims 45-46, wherein said panel comprises a locus of a methylation site specified in Table 2B.
48. The method of any of Claim 45-47, wherein said panel comprises a locus of a methylation site specified in Table 3A.
49. The method of any of Claim 45-48, wherein said panel comprises a locus of a methylation site specified in Table 3B.
50. The method of any of Claim 45-49, wherein said panel comprises a locus of a methylation site specified in Table 1 A.
51. The method of any of Claim 45-50, wherein said panel comprises a locus of a methylation site specified in Table IB.
52. The method of any of Claim 45-51, wherein said panel comprises a locus of a methylation site of Table 4.
53. The method of any of Claims 45-52, wherein said treatment comprises contacting said locus with bisulfite.
54. The method of any of Claims 45-52, wherein said panel comprises at least 5 loci.
55. The method of any of Claims 45-52, wherein said panel comprises at least 10 loci.
56. The method of any of Claims 45-52, wherein said panel comprises at least 20 loci.
57. The method of any of Claims 45-52, wherein said panel comprises at least 50 loci.
58. The method of any of Claims 45-52, wherein the methylation status of at least 200 loci are determined.
59. The method of any of Claims 45-52, wherein the methylation status of at least 250 loci are determined.
60. The method of any of Claims 45-59, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
61. The method of any of Claims 45-59, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to a sample set comprising an OA sample.
62. The method of any of Claims 45-59, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
63. The method of any of Claims 45-59, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
64. The method of any of Claims 45-59, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
65. The method of any of Claims 45-59, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
66. The method of any of Claims 45-59, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
67. A method of diagnosis of RA in a mammalian subject comprising the steps of:
isolating at least one cell from a patient;
determining accumulation levels of transcripts from a panel of genes identified from said at least one cell; and
collectively analyzing the methylation status of the loci in the panel using a computer to ascertain a likelihood that the patient has RA.
68. The method of Claim 67, wherein said at least one gene of said panel is identified in Table 2A.
69. The method of any of Claims 67-68, wherein said at least one gene of said panel is identified in Table 2B.
70. The method of any of Claims 67-69, wherein said at least one gene of said panel is identified in Table 3A.
71. The method of any of Claims 67-70, wherein said at least one gene of said panel is identified in Table 3B.
72. The method of any of Claims 67-71, wherein said at least one gene of said panel is identified in Table 1 A.
73. The method of any of Claims 67-72, wherein said at least one gene of said panel is identified in Table IB.
74. The method of any of Claims 67-73, wherein said at least one gene of said panel corresponds to a methylation site which is listed in Table 4.
75. The method of any of Claims 67-74, wherein said at least one gene is within 1 kb of a methylation site.
76. The method of any of Claims 67-74, wherein said at least one gene is within 10 kb of a methylation site.
77. The method of any of Claims 67-76, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
78. The method of any of Claims 67-76, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
79. The method of any of Claims 67-76, wherein said panel excludes loci identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
80. The method of any of Claims 67-76, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
81. The method of any of Claims 67-76, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
82. The method of any of Claims 67-76, wherein said panel comprises a locus
identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
83. The method of any of Claims 67-76, wherein said transcripts are isolated from at least one PBMC.
84. The method of Claim 83, wherein said at least one peripheral blood mononuclear cell is selected from a group comprising: T-cells, B-cells, monocytes, Thl cells, Th2 cells, Thl 7 cells, T-regs, NK cells, Bl cells, B2 cells, Ml and M2 monocytes, or dendritic cells.
85. The method of any of Claims 67-74, wherein said transcripts are isolated from at least one T-Cell.
86. The method of any of Claims 67-74, wherein said transcripts are isolated from at least one B-Cell.
87. The method of any of Claims 67-74, wherein said transcripts are isolated from at least one monocyte.
88. The method of any of Claims 67-74, wherein said transcripts are isolated from whole blood.
89. The method of any of Claims 67-88, further comprising comparing said patient transcript accumulation levels to those of a corresponding locus in a sample from a non-RA transcript source.
90. The method of any of Claims 67-88, further comprising comparing said patient transcript accumulation levels to those of a corresponding locus in a sample from an RA transcript source.
91. A method for evaluating RA in a mammalian subject comprising:
Measuring the accumulation level or activity level of each of a panel of proteins in a sample of the subject, wherein each of the proteins is encoded by a gene that is identified by a methylation site in Table 1A, Table IB, Table 2 A, Table 2B, Table 3A or Table 3B; and
collectively analyzing the measured levels in the panel using a computer to ascertain a likelihood that the patient has RA.
92. The method of Claim 91, wherein said panel includes a protein encoded by a gene that is identified in Table 2A.
93. The method of any of Claims 91-92, wherein said panel includes a protein encoded by a gene that is identified in Table 2B.
94. The method of any of Claims 91-93, wherein said panel includes a protein encoded by a gene that is identified in Table 3 A.
95. The method of any of Claims 91-94, wherein said panel includes a protein encoded by a gene that is identified in Table 3B.
96. The method of any of Claims 91-95, wherein said panel includes a protein encoded by a gene that is identified in Table 1 A.
97. The method of any of Claims 91-96, wherein said panel includes a protein encoded by a gene that is identified in Table IB.
98. The method of any of Claims 91-97, wherein said panel includes a protein encoded by a gene that is identified in Table 4.
99. The method of any of Claims 91-98, wherein said panel comprises a protein
encoded by a gene identified in a comparison of methylation patterns
corresponding to RA with methylation patterns corresponding to OA.
100. The method of any of Claims 91-98, wherein said panel comprises a
protein encoded by a gene identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
101. The method of any of Claims 91-98, wherein said panel comprises a protein encoded by a gene identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
102. The method of any of Claims 91-98, wherein said panel comprises a
protein encoded by a gene identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
103. The method of any of Claims 91-97, wherein said protein is encoded by a gene within lkb of a methylation site.
104. The method of any of Claims 91-97, wherein said protein is encoded by a gene within 10 kb of a methylation site.
105. The method of any of Claims 91-104, wherein said sample comprises proteins derived from at least one PBMC of the subject.
106. The method of any of Claim 105, wherein said at least one peripheral blood mononuclear cell is selected from a group comprising: T-cells, B-cells, monocytes, Thl cells, Th2 cells, Thl 7 cells, T-regs, NK cells, Bl cells, B2 cells, and Ml and M2 monocytes or dendritic cells.
107. The method of any of Claims 91-106, wherein said sample comprises proteins derived from at least one T-cell of the subject.
108. The method of any of Claims 91-106, wherein said sample comprises proteins derived from at least one B-cell of the subject.
109. The method of any of Claims 91-106, wherein said sample comprises proteins derived from at least one monocyte of the subject.
110. The method of any of Claims 91-106, wherein said sample comprises proteins derived from whole blood.
111. The method of any of Claims 91-110, further comprising comparing said protein accumulation level or activity to that of a corresponding protein in a cell from a non-RA patient.
112. The method of any of Claims 91-110, further comprising comparing said protein accumulation level or activity to that of a corresponding protein in a cell from an RA patient.
113. The method of any of Claims 91-110, wherein the protein accumulation level or protein activity from a protein extract from a panel of proteins identified from said at least one cell is determined.
114. The method of Claim 113, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 2A, Table 2B, Table 3A, Table 3B, Table 1A, or Table IB.
115. The method of Claim 113, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 2A.
116. The method of Claim 113, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 2B.
117. The method of Claim 114, wherein said panel further comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 3 A.
118. The method of Claim 114, wherein said panel further comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 3B.
119. The method of Claim 114, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table 1A.
120. The method of Claim 114, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of loci of methylation sites specified in Table IB.
121. The method of any of Claims 114-120, wherein said panel comprises protein accumulation level or protein activity identified with at least one locus selected from the list of methylation sites in Table 4.
122. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 5 loci is determined.
123. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 10 loci is determined.
124. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 20 loci is determined.
125. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 50 loci is determined.
126. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 200 loci is determined.
127. The method of any of Claims 114-121, wherein the protein accumulation level or protein activity identified with at least 250 loci is determined.
128. The method of any of Claims 91-127, further comprising comparing said protein accumulation level or protein activity to that of a corresponding gene in a cell from a non-RA patient.
129. The method of any of Claims 91-127, further comprising comparing said protein accumulation level or protein activity to that of a corresponding gene in a cell from an RA patient.
130. A method of characterizing a potential RA disease status in a subject, comprising the steps of:
ascertaining the methylation status of a panel comprising at least 3 methylation sites in DNA from a mammalian subject, wherein said methylation sites are differentially methylated in individuals with RA;
electronically comparing in a computer values reflective of said methylation status of said panel of methylation sites with stored information reflective of methylation status of methylation sites in at least one standard population;
generating a report based on said comparison relative to said potential autoimmune disease; and
providing said report to a caregiver or to said subject;
wherein said at least 3 methylation sites are selected from the methylation sites listed in Tables 1A, IB, 2A, 2B, 3A, and 3B.
131. The method of Claim 130, wherein said panel comprises a methylation site of Table 2A.
132. The method of Claim 130, wherein said panel comprises a methylation site of Table 2B.
133. The method of Claim 130, wherein said panel comprises a methylation site of Table 3 A.
134. The method of Claim 130, wherein said panel comprises a methylation site of Table 3B.
135. The method of Claim 130, wherein said panel comprises a methylation site of Table 1A.
136. The method of Claim 130, wherein said panel comprises a methylation site of Table IB.
137. The method of any of Claims 130-136, wherein said panel comprises a methylation site of Table 4.
138. The method of any of Claims 130-137, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to OA.
139. The method of any of Claims 130-137, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to SLE.
140. The method of any of Claims 130-137, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to HC.
141. The method of any of Claims 130-137, wherein said panel comprises a locus identified in a comparison of methylation patterns corresponding to RA with methylation patterns corresponding to Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
142. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from said subject.
143. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from circulating cells of said subject comprising PBMC cells.
144. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of said subject.
145. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from T-cells of said subject.
146. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from B-cells of said subject.
147. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from monocytes of said subject.
148. The method of any of Claims 130-141, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA whole blood.
149. The method of any of Claims 130-148, wherein said laboratory analysis comprises chemical treatment of DNA extracted from said sample that differentially affects methylated and unmethylated bases.
150. The method of Claim 149, wherein said treatment comprises bisulfite treatment.
151. The method of Claim 130, wherein said laboratory analysis comprises amplification of fragments of DNA comprising loci having a differentially methylated site.
152. The method of any of Claims 130-151, wherein said panel comprises at least 5 methylation sites.
153. The method of any of Claims 130-151, wherein said panel comprises at least 10 methylation sites.
154. The method of any of Claims 130-151, wherein said panel comprises at least 20 methylation sites.
155. The method of any of Claims 130-151, wherein said panel comprises at least 50 methylation sites.
156. The method of any of Claims 130-151, wherein said panel comprises at least 200 methylation sites.
157. The method of any of Claims 130-151, wherein said panel comprises at least 250 methylation sites.
158. A method of characterizing a potential autoimmune disease in a subject, comprising the steps of:
ascertaining the methylation status of a panel comprising at least 3 differentially-methylated loci (DMLs) in DNA from a mammalian subject, wherein said DMLs are differentially methylated in individuals with said autoimmune disease;
electronically comparing in a computer values reflective of said methylation status of said panel of DMLs with stored information reflective of methylation status of DMLs in at least one standard population;
generating a report based on said comparison relative to said potential autoimmune disease; and
providing said report to a caregiver or to said subject;
wherein said at least 3 DMLs are selected from the DMLs listed in Tables 1A, IB, 2A, 2B, 3A or 3B.
159. The method of Claim 158, wherein at least one of said DMLs is listed in Table 4.
160. The method of Claim 158, wherein said DNA from a mammalian subject is derived from peripheral blood mononuclear cells (PBMCs).
161. The method of Claim 158, wherein said DNA from a mammalian subject is derived from T cells.
162. The method of Claim 158, wherein said DNA from a mammalian subject is derived from B cells.
163. The method of Claim 158, wherein said DNA from a mammalian subject is derived from monocytes.
164. The method of Claim 158, wherein said DNA from a mammalian subject is derived from whole blood.
165. The method of any of Claims 158-164, wherein said autoimmune disease is rheumatoid arthritis (RA).
166. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from PBMCs of said subject.
167. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from circulating cells of said subject comprising PBMC cells.
168. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of said subject comprising PBMC DNA.
169. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from free circulating DNA of said subject.
170. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from T-cells of said subject.
171. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from B-cells of said subject.
172. The method of any of Claims 158-164, wherein said ascertaining step comprises receiving values reflective of methylation status based on laboratory analysis of DNA from monocytes of said subject.
173. The method of any of Claims 158-172, wherein said laboratory analysis comprises chemical treatment of DNA extracted from said sample that differentially affects methylated and unmethylated bases.
174. The method of Claim 173, wherein said treatment comprises bisulfite treatment.
175. The method of any of Claims 158-172, wherein said laboratory analysis comprises amplification of fragments of DNA comprising loci having a differentially methylated site.
176. The method of Claim 175, wherein said fragments comprise 20 bp on either side of said DML.
177. The method of Claim 175, wherein said fragments comprise 40 bp on either side of said DML.
178. The method of Claim 175, wherein said fragments comprise 60 bp on either side of said DML.
179. The method of Claim 175, wherein said fragments comprise 80 bp on either side of said DML.
180. The method of Claim 175, wherein said fragments comprise 100 bp on either side of said DML.
181. The method of Claim 175, wherein said fragments comprise 500 bp on either side of said DML.
182. The method of Claim 175, wherein said fragments comprise 1 kb on either side of said DML.
183. The method of Claim 175, wherein said fragments comprise 1.5 kb on either side of said DML.
184. The method of Claim 175, wherein said fragments comprise 2 kb on either side of said DML.
185. The method of Claim 175, wherein said fragments comprise 2.5 kb on either side of said DML.
186. The method of Claim 175, wherein said fragments comprise 5 kb on either side of said DML.
187. The method of Claim 175, wherein said fragments comprise 10 kb on either side of said DML.
188. The method of any of Claims 158-187, wherein said laboratory analysis further comprises contacting said amplified DNA with a reagent that distinguishes between bisulfite-treated methylated and bisulfite-treated unmethylated DNA
189. The method of Claim 188, wherein said reagent is an oligonucleotide probe
190. The method of Claim 188, wherein said reagent is a protein that differentially binds DNA according to its methylation status.
191. The method of Claim 188, wherein said panel comprises at least 5 DML.
192. The method of Claim 188, wherein said panel comprises at least 10 DML.
193. The method of Claim 188, wherein said panel comprises at least 20 DML
194. The method of Claim 188, wherein said panel comprises at least 50 DML.
195. The method of Claim 188, wherein said panel comprises at least 200
DML.
196. The method of Claim 188, wherein said panel comprises at least 250
DML.
197. The method of any of Claims 158-196, wherein at least one said standard population comprises individuals not having said autoimmune disease.
198. The method of any of Claims 158-196, wherein at least one said standard population comprises individuals having an autoimmune disease.
199. The method of any of Claims 197-198, wherein at least one said standard population comprises individuals having said autoimmune disease.
200. The method of any of Claims 158-196, wherein the standard populations comprise individuals with RA, Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
201. The method of any of Claims 158-196, wherein said ascertaining step further comprises ascertaining values reflective of one or more additional non-DML characteristics of the subject, and wherein said electronically comparing step further comprises comparing those non-DML values with non-DML values from said one or more standard populations in said computer.
202. The method of Claim 201, wherein said non-DML values are selected from the group consisting of: SNP or gene variation status, levels of auto- antibodies such as anti-dsDNA antibodies or anti-nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels inflammatory molecules and miRNA levels.
203. A method for detecting methylation events at loci set forth in Tables 1A, IB, 2A, 2B, 3A, or 3B which comprises subjecting a sample from a human individual comprising DNA to treatment that differentially affects methylated bases of said human sample, and ascertaining the extent of methylation of a panel of loci, wherein a plurality of said loci are listed in one or more of Tables 1A, IB, 2A, 2B, 3A, or 3B.
204. The method of Claim 203, wherein at least one of said loci is listed in Table 4.
205. The method of Claim 203, wherein said sample comprises circulating
DNA.
206. The method of Claim 203, wherein said sample comprises DNA from circulating blood cells.
207. The method of Claim 203, wherein said sample comprises PBMC DNA.
208. The method of Claim 203, wherein said sample comprises B Cell DNA.
209. The method of Claim 203, wherein said sample comprises T Cell DNA.
210. The method of Claim 203, wherein said sample comprises Monocyte
DNA.
211. The method of Claim 203, wherein said sample comprises whole blood
DNA.
212. The method of Claim 203, wherein the PBMC DNA source comprises DNA selected from the list of DNA sources consisting of T-cell DNA, B-cell DNA and monocyte DNA.
213. The method of Claim 203, further comprising comparing the methylation status of the loci of said panel with methylation status indicative of RA, Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
214. The method of Claim 203, wherein said treatment comprises contacting said locus with bisulfite.
215. The method of Claim 203, wherein said panel comprises at least 5 loci.
216. The method of Claim 203, wherein said panel comprises at least 10 loci.
217. The method of Claim 203, wherein said panel comprises at least 20 loci.
218. The method of Claim 203, wherein said panel comprises at least 50 loci.
219. The method of Claim 203, wherein said panel comprises at least 200 loci.
220. The method of Claim 203, wherein said panel comprises at least 250 loci.
221. The method of Claim 203, further comprising determining the status of one or more of the traits from the individual selected from the list comprising: SNP or gene variation status, levels of auto- antibodies such as anti-dsDNA antibodies or anti- nuclear antibodies, anti-CCP, ACPAs, or RF serum proteins, cytokine or chemokine levels inflammatory molecules and miRNA levels.
222. A method of diagnosis of a disorder in a mammalian subject comprising the steps of:
isolating PBMCs from a patient;
determining an accumulation level of transcripts from at least two genes identified from said PBMCs; and
diagnosing whether the patient has a disorder based on said determination; wherein said at least two genes are genes associated with DML in Tables 1A, IB, 2A, 2B, 3A, or 3B; and
wherein said disorder is RA, Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, or Ulcerative Colitis.
223. The method of Claim 222, wherein at least one of said DML is listed in Table 4.
224. The method of Claim 222, wherein each said gene is within 20 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
225. The method of Claim 222, wherein each said gene is within 40 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
226. The method of Claim 222, wherein each said gene is within 60 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
227. The method of Claim 222, wherein each said gene is within 80 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
228. The method of Claim 222, wherein each said gene is within 100 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
229. The method of Claim 222, wherein each said gene is within 500 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
230. The method of Claim 222, wherein each said gene is within 1 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
231. The method of Claim 222, wherein each said gene is within 1.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
232. The method of Claim 222, wherein each said gene is within 2 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
233. The method of Claim 222, wherein each said gene is within 2.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
234. The method of Claim 222, wherein each said gene is within 5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
235. The method of Claim 222, wherein each said gene is within 10 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
236. The method of Claim 222, wherein said at least one PBMC comprises at least one cell selected from the list of cells consisting of T-cells, B-cells and monocytes.
237. The method of Claim 222, wherein the accumulation levels of a panel of transcripts are determined.
238. The method of Claim 222, wherein the accumulation levels of at least 5 transcripts are determined.
239. The method of Claim 222, wherein the accumulation levels of at least 10 transcripts are determined.
240. The method of Claim 222, wherein the accumulation levels of at least 20 transcripts are determined.
241. The method of Claim 222, wherein the accumulation levels of at least 50 transcripts are determined.
242. The method of Claim 222, wherein the accumulation levels of at least 200 transcripts are determined.
243. The method of Claim 222, wherein the accumulation levels of at least 250 transcripts are determined.
244. The method of Claim 222, wherein said method involves oligonucleotides to detect transcript accumulation levels.
245. The method of Claim 244, wherein each said oligonucleotides anneal within 20 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
246. The method of Claim 244, wherein each said oligonucleotides anneal within 40 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
247. The method of Claim 244, wherein each said oligonucleotides anneal within 60 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
248. The method of Claim 244, wherein each said oligonucleotides anneal within 80 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
249. The method of Claim 244, wherein each said oligonucleotides anneal within 100 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
250. The method of Claim 244244, wherein each said oligonucleotides anneal within 500 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
251. The method of Claim 244, wherein each said oligonucleotides anneal within 1 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
252. The method of Claim 244, wherein each said oligonucleotides anneal within 1.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
253. The method of Claim 244, wherein each said oligonucleotides anneal within 2 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
254. The method of Claim 244, wherein each said oligonucleotides anneal within 2.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
255. The method of Claim 244, wherein each said oligonucleotide anneals within 5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
256. The method of Claim 222, further comprising comparing said accumulation levels to those of corresponding transcripts in a non-disorder cell, wherein said disorder is RA.
257. The method of Claim 222, further comprising comparing said accumulation levels to those of a corresponding set of transcripts in a disorder cell, wherein said disorder is RA.
258. The method of any of Claims 256-257, wherein a non-disorder cell comprises a cell from an individual classified as HC, or as having at least one of OA, SLE, Ankylosing Spondylitis, Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis.
259. A method of diagnosis of a disorder in a mammalian subject comprising the steps of:
isolating at least one circulating cell from a patient;
determining a protein accumulation level or activity level of proteins from genes identified from said at least one cell; and
diagnosing whether the patient has a disorder based on said determination; wherein said genes are genes associated with DML in Tables 1A, IB, 2 A, 2B, 3A, or 3B; and
wherein said disorder is RA.
260. The method of Claim 259, wherein at least one of said DML is listed in Table 4.
261. The method of Claim 259, wherein said at least one circulating cell is a
PBMC.
262. The method of Claim 259, wherein said at least one circulating cell is a B- cell.
263. The method of Claim 259, wherein said at least one circulating cell is a T- cell.
264. The method of Claim 259, wherein said at least one circulating cell is a monocyte.
265. The method of Claim 259, wherein said at least one circulating cell is a white blood cell.
266. The method of Claim 259, wherein each said gene is within 20 bp of a DML in Tables 1 Tables 1A, IB, 2A, 2B, 3A, or 3B.
267. The method of Claim 259, wherein each said gene is within 40 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
268. The method of Claim 259, wherein each said gene is within 60 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
269. The method of Claim 259, wherein each said gene is within 80 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
270. The method of Claim 259, wherein each said gene is within 100 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
271. The method of Claim 259, wherein each said gene is within 500 bp of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
272. The method of Claim 259, wherein each said gene is within 1 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
273. The method of Claim 259, wherein each said gene is within 1.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
274. The method of Claim 259, wherein each said gene is within 2 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
275. The method of Claim 259, wherein each said gene is within 2.5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
276. The method of Claim 259, wherein each said gene is within 5 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
277. The method of Claim 259, wherein each said gene is within 10 kb of a DML in Tables 1A, IB, 2A, 2B, 3A, or 3B.
278. The method of any of Claims 259-277, wherein said DML is listed in Table 4.
279. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of a panel of proteins are determined.
280. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 5 proteins are determined.
281. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 10 proteins are determined.
282. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 20 proteins are determined.
283. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 50 proteins are determined.
284. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 200 proteins are determined.
285. The method of any of Claims 259-278, wherein the accumulation levels or activity levels of at least 250 proteins are determined.
286. The method of any of Claims 259-278, further comprising comparing said accumulation levels or activity levels to those of a corresponding protein in a non- disorder cell, wherein said disorder is RA.
287. The method of Claim 259, further comprising comparing said accumulation levels or activity levels to those of a corresponding protein in a disorder cell, wherein said disorder is RA.
288. The method of any of Claims 286-287, wherein a non-disorder cell is selected from the list comprising Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis
289. The method of Claim 259, wherein said detection comprises differential antibody binding.
290. A method for the evaluation of differential methylation in a subject comprising:
(a) determining the extent of methylation at a plurality of DNA loci selected from the loci in Tables 1A, IB, 2A, 2B, 3Aor 3B in a sample comprising PBMC DNA taken from the subject;
(b) evaluating values reflective of the extent of methylation at said loci; and
(c) providing a report based on the evaluation of step (b).
291. The method of Claim 290, wherein at least one of said loci is listed in Table 4.
292. The method of Claim 290, wherein said evaluating step comprises processing values reflective of methylation at said loci in a computer and comparing said processed values to values known to be reflective of an autoimmune disorder status.
293. The method of Claim 291, wherein the report further discusses a treatment regimen for said autoimmune disorder based on said evaluating step.
294. The method of Claim 290, wherein said loci comprise a panel of loci.
295. The method of Claim 290, wherein said loci comprise a panel of at least 5 loci.
296. The method of Claim 290, wherein said loci comprise a panel of at least 10 loci.
297. The method of Claim 290, wherein said loci comprise a panel of at least 20 loci.
298. The method of Claim 290, wherein said loci comprise a panel of at least 50 loci.
299. The method of Claim 290, wherein said loci comprise a panel of at least 200 loci.
300. The method of Claim 290, wherein said loci comprise a panel of at least 250 loci
301. A set of PCR primers capable of amplifying loci of human chromosomal DNA in a PCR reaction, wherein said loci are selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
302. The primers of Claim 301, wherein said loci comprise 20 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
303. The primers of Claim 301, wherein said loci comprise 40 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
304. The primers of Claim 301, wherein said loci comprise 60 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, 3B or 4.
305. The primers of Claim 301, wherein said loci comprise 80 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
306. The primers of Claim 301, wherein said loci comprise 100 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3 A, or 3B.
307. The primers of Claim 301, wherein said loci comprise 500 bp on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3 A, or 3B.
308. The primers of Claim 301, wherein said loci comprise lkb on either side of a methylation site selected from the DML identified in Tables 1 A, IB, 2A, 2B, 3A, or 3B.
309. The primers of Claim 301, wherein said loci comprise 1.5kb on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
310. The primers of Claim 301, wherein said loci comprise 2kb on either side of a methylation site selected from the DML identified in Tables 1 A, IB, 2A, 2B, 3A, or 3B.
311. The primers of Claim 301, wherein said loci comprise 2.5kb on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
312. The primers of Claim 301, wherein said loci comprise 5kb on either side of a methylation site selected from the DML identified in Tables 1 A, IB, 2A, 2B, 3A, or 3B.
313. The primers of Claim 301, wherein said loci comprise lOkb on either side of a methylation site selected from the DML identified in Tables 1A, IB, 2A, 2B, 3A, or 3B.
314. The primers of any of Claims 301-313, wherein at least one of said loci is listed in Table 4.
315. A kit for the diagnosis of a disorder selected from the group of disorders consisting of RA, Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis, in a mammalian subject comprising a plurality of DNA reagents, said reagents capable of distinguishing between methylated and unmethylated DNA from loci listed in at least one of Tables 1A, IB, 2A, 2B, 3 A, and 3B upon subjecting said DNA to a treatment that differentially affects methylated bases.
316. The kit of Claim 315, wherein at least one of said loci is listed in Table 4.
317. The kit of Claim 315, wherein said reagents comprise oligonucleotides.
318. The kit of Claim 315, wherein said treatment is a chemical modification.
319. The kit of Claim 315, wherein said treatment comprises bisulfite mapping.
320. The kit of Claim 315, wherein said treatment comprises bisulfite sequencing.
321. The kit of Claim 315, wherein said kit comprises a plurality of different reagents, each capable of distinguishing between methylated and unmethylated DNA at a respective locus listed in at least one of Tables 1A, IB, 2A, 2B, 3A, or 3B
322. The kit of Claim 321, wherein said locus is listed in Table 4.
323. An isolated DNA molecule having a sequence spanning a DML of Tables 1A, IB, 2A, 2B, 3A, or 3B, wherein DNA at said DML has been chemically modified as a result of the presence of methylation at said DML, resulting in a detectable moiety reflective of methylation at said DML.
324. The isolated DNA molecule of Claim 323, wherein said locus is listed in Table 4.
325. The isolated DNA molecule of Claim 323, wherein said DNA molecule has a sequence which anticipates the sequence of the vicinity of a DML of Tables 1A, IB, 2A, 2B, 3A, or 3B upon chemical modification to identify methylation status, wherein said modified form is an expected product of a reaction whereby an isolated DNA molecule of Claim 323 having a methylation signature characteristic of a disorder selected from the list of disorders consisting of RA, Ankylosing Spondylitis, Crohn's Disease, HC, Multiple Sclerosis, OA, Psoriasis, Psoriatic Arthritis, Reactive Arthritis, SLE, Spondyloarthropathy, Type I Diabetes, and Ulcerative Colitis, in DNA isolated from blood is subjected to treatment that differentially affects methylated bases.
326. The isolated DNA molecule of Claim 323, wherein said DNA isolated from blood is isolated from whole blood.
327. The isolated DNA molecule of Claim 323, wherein said DNA isolated from blood is isolated from at least one PBMC cell.
328. The isolated DNA molecule of Claim 323, wherein said PBMC is a T-cell, a B-cell or a monocyte.
329. The isolated DNA molecule of Claim 323, wherein said treatment comprises contacting said isolated DNA molecule with bisulfite.
330. The isolated DNA molecule of Claim 323, wherein said molecule comprises at least 14 bases.
331. A panel of different DNA molecules comprising molecules of Claims 323-
330.
332. The panel of Claim 331, wherein said treatment comprises contacting said molecule with bisulfite.
333. The panel of Claim 331, comprising at least 5 different DNA molecules.
334. The panel of Claim 331, comprising at least 10 different DNA molecules.
335. The panel of Claim 331, comprising at least 20 different DNA molecules.
336. The panel of Claim 331 , comprising at least 50 different DNA molecules.
337. The panel of Claim 331, comprising at least 200 different DNA molecules
338. The panel of Claim 331, comprising at least 250 different DNA molecules
339. A method for developing an assay for the detection of a methylation profile comprising the steps of:
selecting a plurality of DML from the DML listed in Tables 1A, IB, 2A, 2B, 3A, or 3B;
analyzing with a computer the extent of methylation at said loci; and ascertaining a methylation pattern at said loci that correlates with a positive diagnosis indicative of a status of an autoimmune disorder selected from the list comprising RA Crohn's Disease, Multiple Sclerosis, Psoriasis, Psoriatic Arthritis, SLE, Type I Diabetes, or Ulcerative Colitis.
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'Human Gene LBX1 (uc001ksx.3) Description and Page Index. Homo Sapiens Ladybird Homeobox 1 (LBX1), mRNA. Transcript (Including UTRs) Position: chr10:102,986,733-102,988,717.', [Online] 14 June 2013, Retrieved from the Internet: <URL:http://genome.ucsc.edu/index.html.> [retrieved on 2014-02-19] *
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