WO2006053955A2

WO2006053955A2 - Method and kit for detecting a risk of essential arterial hypertension

Info

Publication number: WO2006053955A2
Application number: PCT/FI2005/050429
Authority: WO
Inventors: Jukka T. Salonen; Juha-Matti Aalto; Ricardo Fuentes; Outi Kontkanen; Mia Pirskanen; Pekka Uimari
Original assignee: Oy Jurilab Ltd
Priority date: 2004-11-19
Filing date: 2005-11-21
Publication date: 2006-05-26
Also published as: WO2006053955A3; EP1824996A2; CA2587979A1; AU2005305765A1

Abstract

Genes, SNP markers and haplotypes of susceptibility or predisposition to hypertension (HT) are disclosed. Methods for diagnosis, prediction of clinical course and efficacy of treatments for HT using polymorphisms in the HT risk genes are also disclosed. The genes, gene products and agents of the invention are also useful for monitoring the effectiveness of prevention and treatment of HT. Kits are also provided for the diagnosis, selecting treatment and assessing prognosis of HT.

Description

Method and kit for detecting a risk of essential arterial hypertension

BACKGROUND OF THE INVENTION

Field of the Invention

The present invention relates generally to the field of diagnosis of cardiovascular diseases (CVD) such as arterial hypertension (HT). More particularly, it provides a method of diagnosing or detecting a predisposition or propensity or susceptibility for HT. Specifically, the invention focuses on a method that comprises the steps of providing a biological sample from the subject to be tested and detecting the presence or absence of one or several genomic single nucleotide polymorphism (SNP) markers in the biological sample. Furthermore, the invention utilizes both genetic and phenotypic information as well as information obtained by questionnaires to construct a score that provides the probability of developing HT. In addition, the invention provides a kit to perform the method. The kit can be used to set an etiology- based diagnosis of HT for targeting of treatment and preventive interventions such as dietary advice, as well as stratification of the subject in clinical trials testing drugs and other interventions.

Description of Related Art

Public health significance of CVD and HT Cardiovascular Diseases (CVD) (ICD/10 codes 100-199, Q20-Q28) include ischemic

(coronary) heart disease (IHD, CHD), hypertensive diseases, cerebrovascular disease (stroke) and rheumatic fever/rheumatic heart disease, among others (AHA, 2004). HT (ICD/10 110- 115) is defined as systolic pressure of 140 mm Hg or higher, or diastolic pressure of 90 mm Hg or higher, or taking antihypertensive medicine (AHA, 2004). Apart from being a CVD itself, HT is a risk factor for other CVD, such as IHD, stroke and congestive heart failure (CHF). About half of those people who have a first heart attack and two thirds of those who have a first stroke, have blood pressure (BP) higher than 160/95 mm Hg. HT precedes the development of CHF in 91% of cases (AHA, 2004). Of patients with HT, 90-95% have essential HT in which the underlying cause remains unknown. Essential HT refers to a lasting increase in BP with heterogeneous genetic and environmental causes. Its prevalence rises with age irrespective of the type of BP measurement and the operational thresholds used for diagnosis. HT aggregates with other cardiovascular risk factors such as abdominal obesity, dyslipidaemia, glucose intolerance, hyperinsulinaemia and hyperuricaemia, possibly because of a common underlying cause (Salonen JT et al, 1981, 1998, Staessen JA et al, 2003).

In 2001 an estimated 16.6 million - or one-third of total global deaths - resulted from the various forms of CVD (7.2 million due to HT, 5.5 million to cerebrovascular disease, and an additional 3.9 million to hypertensive and other heart conditions). At least 20 million people survive heart attacks and strokes every year, a significant proportion of them requiring costly clinical care, putting a huge burden on long-term care resources. It is necessary to recognize that CVDs are devastating to men, women and children (AHA, 2004). Around 80% of all CVD deaths worldwide took place in developing, low and middle-income countries. It is estimated that by 2010, CVD will be the leading cause of death in both developed and developing countries. The rise in CVDs reflects a significant change in dietary habits, physical activity levels, and tobacco consumption worldwide as a result of industrialization, urbanization, economic development and food market globalization (WHO, 2004). This emphasizes the role of relatively modern environmental or behavioral risk factors. However, ethnic differences in the incidence and prevalence of CVD and the enrichment of CVD in families suggest that heritable risk factors play a major role. In terms of disability measured in disability-adjusted life years (DALYs) CVD caused 9.7% of global DALYs, 20.4% of DALYs in developed countries and 8.3% of DALYs in the developing countries. HT caused 1.4% of global DALYs, 4.7% of DALYs in developed countries and 0.9% of DALYs in the developing countries (Murray CJL and Lopez AD, 1997).

On the basis of data from the NHANES III study (1988-1994), it is estimated that in 2001, 64.4 million Americans were affected by some form of CVD, which corresponds to a prevalence of 22.6% (21.5% for males, 22.4% for females). Of these, 50 million had HT (20% prevalence). Of those with HT, 30% do not know they have HT; 34% are on medication and have HT controlled; 25% are on medication but do not have their HT under control; and 11% are not on medication (AHA, 2004). HT is also a public health problem in developing countries where prevalences of 10% or higher are common and it is frequently associated with low levels of awareness, treatment and control (Fuentes RM et al, 2000). The cost of CVD in the United States in 2004 was estimated at $368.4 billion ($133.2 billion for HT, $53.6 billion for stroke, $55.5 billion for hypertensive disease). This figure includes health expenditures (direct costs) and lost productivity resulting from morbidity and mortality (indirect costs) (AHA, 2004). Pathophysiology of essential HT

The pressure required to move blood through the circulatory bed is provided by the pumping action of the heart [cardiac output (CO)] and the tone of the arteries [peripheral resistance (PR)]. Each of these primary determinants of BP is, in turn, determined by the interaction of a complex series of iactors.

Factors affecting cardiac output

An increased CO has been found in some young, borderline hypertensives who may display a hyperkinetic circulation. If it is responsible for HT, the increase in CO could logically arise in two ways: either from an increase in fluid volume (preload) or from an increase in contractility from neural stimulation of the heart. However, even if it is involved in the initiation of HT, the increased CO probably does not persist. The typical hemodynamic finding in established HT is an elevated PR and normal CO (Cowley AW, 1992).

Although an increased heart rate may not simply be a reflection of a hyperdynamic circulation or an indicator of increased sympathetic activity, multiple epidemiologic surveys have shown that an elevated heart rate is an independent predictor of the development of HT (Palatini P and Julius S, 1999).

Left ventricular hypertrophy has generally been considered a compensatory mechanism to an increased vascular resistance. However, it could also reflect a primary response to repeated neural stimulation and, thereby, could be an initiating mechanism for HT (Julius S et al., 1991c) as well as an amplifier of CO that reinforces the elevation of BP from arterial stiffening (Segers P et al., 2000). Another mechanism that could induce HT by increasing CO would be an increased circulating fluid volume (preload). However, in most studies, subjects with high BP have a lower blood volume and total exchangeable sodium than normal subjects (Harrap SB et al., 2000). Even without an expanded total volume, blood may be redistributed so that more is in the central or cardiopulmonary section because of greater peripheral vasoconstriction (Schobel HP et al., 1993). Venous return to the heart would thereby be increased and could mediate an increased CO.

Excess sodium intake induces HT by increasing fluid volume and preload, thereby increasing CO (Chobanian AV and Hill M, 2000). Both experimental data (Tobian L, 1991) and epidemiologic evidence (Stamler J et al., 1997) support a close association between HT and a high sodium-potassium ratio in humans. Because almost everyone in industrialized societies ingests a high-sodium diet, the fact that only about half will develop HT suggests a variable degree of BP sensitivity to sodium (Weinberger MH, 1996). In healthy people, when BP increases, renal excretion of sodium and water increases, shrinking fluid volume and returning the BP to normal - this phenomenon is pressure- natriuresis. On the basis of animal experiments and computer models, the regulation of body fluid volume by the kidneys is considered to be the dominant mechanism for the long-term control of BP (Guyton AC 1961, 1992). Therefore, if HT develops, something must be wrong with the pressure-natriuresis control mechanism; otherwise the BP would return to normal (Cowley AW and Roman RJ, 1996). In patients with primary HT a resetting of the pressure- sodium excretion curve prevents the return of BP to normal (Palmer BF, 2001). The shift in pressure-natriuresis requires increased BP to maintain fluid balance. The pressure-natriuresis relationship can be modified by neural and humoral factors including the renin-angiotensin system (RAS), sympathetic nervous activity, atrial natriuretic factor, metabolites of arachidonic acid, and intrarenal nitric oxide (Moreno C et al., 2001; Majid DS et al., 2001). The major modifier is likely to be theRAS (Hall JE et al., 1999; van Paassen P et al., 2000), with an increase in renal sodium reabsorption occurring at concentrations of Angiotensin II much below those needed for peripheral vasoconstriction. Angiotensin II acts not only on vascular smooth muscle and the adrenal cortex but also within the heart, kidneys, and central and autonomic nervous systems. These actions amplify its volume-retaining and vasoconstrictive effects on the peripheral vascular system, thus affecting both CO and PR. Furthermore, Angiotensin II induces cell growth and hypertrophy independent of its effect on BP (Su EJ et al., 1998). Moreover, Angiotensin II appears to induce an inflammatory response in vascular smooth muscle cells (Kranzhδfer R et al., 1999), with activation of nuclear factor k-B (Luft FC, 2001) and adhesion molecule-1 expression (Tummala PE et al., 1999), which may serve as direct links to atherosclerosis.

Stress may activate the sympathetic nervous system (SNS) directly; and SNS overactivity, in turn, may interact with high sodium intake, the RAS, and insulin resistance, among other possible mechanisms. Considerable evidence supports increased SNS activity in early HT (Esler M et al., 2001) and, even more impressively, in the still-normotensive offspring of hypertensive parents, of whom a large number are likely to develop HT. Whatever the specific role of SNS activity in the pathogenesis of HT, it appears to be involved in the increased cardiovascular morbidity and mortality that afflicts hypertensive patients during the early morning hours. Epinephrine levels begin to increase after awakening and norepinephrine rises sharply on standing (Dodt C et al., 1997). As a consequence of the increased SNS activity, BP rises suddenly and markedly, and this rise is at least partly responsible for the increase in sudden death, heart attack, and stroke during the early morning hours. Increased sympathetic activity is probably also responsible for the increased heart rate present in many hypertensives that was previously noted to be associated with increased cardiovascular mortality.

Factors affecting peripheral resistance HT is maintained by increased PR, largely due to decreased arterial lumen size or radius.

According to Poiseuille's law, vascular resistance is positively related to both the viscosity of blood and the length of the arterial system, and negatively related to the third power of the luminal radius. Because neither viscosity nor length is altered much if at all, and because small changes in the luminal radius can have a major effect, it is apparent that the increased vascular resistance seen in established HT must reflect changes in the calibre of the small resistance arteries and arterioles (Folkow B et al., 1970). Because of the increased wall thickness-lumen diameter ratio, higher wall stress and intraluminal pressure develop when resistance vessels are stimulated. In HT, small arteries undergo functional, structural and mechanical changes, resulting in reduced lumen size and increased peripheral resistance (Mulvany MJ, 2002; Intengan HD and Schiffrin EL. 2001). Functional alterations include enhanced reactivity or impaired relaxation, and reflect changes in excitation-contraction coupling, altered electrical properties of vascular smooth muscle cells, or endothelial dysfunction (Johns DG et al, 2000; Feldman RD and Gros R, 1998). Major structural changes include remodelling due to increased cell growth, extracellular matrix deposition and inflammation (Mulvany MJ, 2002; Intengan HD and Schiffrin EL, 2001; Brasier AR, 2002). Vascular smooth muscle cells are central to these events and play a fundamental role in the dynamic processes underlying the alterations that occur in HT.

Vascular changes in HT are associated with humoral and mechanical factors that modulate signalling events, resulting in abnormal function and growth of cellular components of the media (Touyz RM, 2000; Roller A, 2002). The humoral factors that regulate arteries in HT include vasoconstrictor agents such as angiotensin II, endothelin-1, catecholamines and vasopressin; vasodilator agents such as nitric oxide, endothelium-derived hyperpolarizing factor and natriuretic peptides; growth factors such as insulin- like growth factor- 1, platelet- derived growth factor (PDGF), epidermal growth factor (EGF) and basic fibroblast growth factor; and cytokines such as transforming growth factor- [beta], tumour necrosis factor and interleukins (Touyz RM, 2000). Mechanical factors that influence the vasculature in HT include shear stress, wall stress and the direct actions of pressure itself (Touyz RM, 2000; Ko Her A, 2002). In addition to these factors, there is growing evidence that reactive oxygen species (ROS) that act as intercellular and intracellular signalling molecules, regulate vascular tone and structure (Wilcox CS, 2002; Berry C et al, 2001).

A recent advance in the field of angiotensin II signalling was the demonstration that, in addition to its vasoconstrictor properties, angiotensin II has potent mitogenic-like and proinflammatory- like characteristics. These actions are mediated through phosphorylation of both nonreceptor tyrosine kinases and receptor tyrosine kinases (Touyz RM, 2003). It is also becoming increasingly apparent that many signalling events that underlie abnormal vascular function in HT are influenced by changes in intracellular redox status. In particular, increased bioavailability of ROS stimulates growth-signalling pathways, induces expression of proinflammatory genes, alters contraction-excitation coupling and impairs endothelial function (Touyz RM, 2003).

In concert with the various functional and structural changes that are responsible for HT, the arteries become stiffer or less elastic. Vascular stiffness progressively increases with age (Slotwiner DJ et al., 2001) and is responsible for the progressive increase in systolic as compared to diastolic pressure, leading to the typical increase of pulse pressure that is now recognized to be the major determinant of cardiovascular risk (Beltran A et al., 2001). Measures of stiffness and elasticity have been shown to be an independent predictor of the development of HT (Liao D et al., 1999) and a marker of cardiovascular risk in those with HT (Blacher J et al., 1999). Changes in the physical characteristics of the large arteries reflected in the BP pulse contour alter not only BP and pulse pressure, but also cardiac work and performance.

The complexity of pathophysiologic mechanisms that lead to BP elevation is such that selective, mechanistically based antihypertensive treatment is rarely possible in any hypertensive patient. HT is highly prevalent among middle-aged and elderly persons, and the success rate in controlling BP in these individuals is poor. Current treatment guidelines generally recommend a generic approach to treating HT, with little emphasis on selecting therapy on the basis of the underlying pathophysiology of the elevated BP (Chobanian AV et al, 2003; ESH/ESC, 2003). With increased recognition of specific causes, it may be possible to develop therapies selective for distinct pathophysiologic mechanisms with fewer adverse effects, resulting in more effective BP reduction. The use of powerful new techniques of genetics, genomics, and proteomics, integrated with systems physiology and population studies, will make more selective and effective approaches to treating and even preventing HT possible in the coming decades (Oparil S et al, 2003).

Essential HT: a polygenic disease

Nuclear family studies show greater similarity in BP within families than between families, with heritability estimates ranging between 0.20 and 0.46 (Fuentes RM, 2003). Twin studies document greater concordance of BP in monozygotic than dizygotic twins, giving the highest heritability estimates between 0.48 and 0.64 (Fuentes RM, 2003). Adoption studies demonstrate greater concordance of BP among biological siblings than adoptive siblings living in the same household, estimating heritability between 0.45 and 0.61 (Fuentes RM, 2003).

Single genes can have major effects on BP, accounting for the rare Mendelian forms of high and low BP (Lifton RP et al, 2001). Although identifiable single-gene mutations account for only a small percentage of HT cases, studying these rare disorders may elucidate pathophysiologic mechanisms that predispose to more common forms of HT and may suggest novel therapeutic approaches (Lifton RP et al, 2001). Mutations in 10 genes that cause

Mendelian forms of human HT and 9 genes that cause hypotension have been described to date (Lifton RP et al, 2001; Wilson FH et al, 2001). These mutations affect BP by altering renal salt handling, reinforcing the hypothesis that the development of HT depends on genetically determined renal dysfunction with resultant salt and water retention (Guyton AC, 1991). Importantly, all the monogenic HT syndromes identified to date are caused by defects resulting in renal salt retention, whereas all the low BP syndromes share a common mechanism of excess renal sodium loss (Hopkins PN and Hunt SC, 2003).

The best studied monogenic cause of HT is the Liddle syndrome, a rare but clinically important disorder in which constitutive activation of the epithelial sodium channel predisposes to severe, treatment-resistant HT (Shimkets RA et al, 1994). Epithelial sodium channel activation has been traced to mutations in the beta or gamma subunits of the channel, resulting in inappropriate sodium retention at the renal collecting duct level. Patients with the Liddle syndrome typically display volume-dependent, low-renin, and low-aldosterone HT.

In most cases, HT results from a complex interaction of genetic, environmental, and demographic factors. Improved techniques of genetic analysis, especially candidate gene association studies and genome wide linkage analysis (genome wide scan, GWS), have enabled a search for genes that contribute to the development of primary HT in the population.

Thus far, the candidate gene approach has provided more examples than the linkage approach of gene variants that appear to affect BP. Reasonable candidate genes to consider include genes related to physiological systems known to be involved in the control of BP and genes known to affect BP in mouse models. To date more than 80 candidate genes have been evaluated for HT (Fuentes RM, 2004, unpublished review). However, the association with HT of only three genes have been widely replicated: angiotensinogen precursor (AGT), adducin 1 (ADDl) and guanine nucleotide-binding protein, beta-3 subunit (GNB3) (Hopkins PN and Hunt SC, 2003). Gene-environment interactions affecting HT treatment have been shown between AGT, ADDl and salt intake reduction (Hunt SC et al, 1998; Hunt SC et al, 1999; Cusi D et al. 1997), and between ADDl, GNB3 and diuretic treatment (Cusi D et al. 1997; Turner ST et al, 2001). Gene-gene interactions affecting HT risk development have been shown between ADDl and the ACE gene I/D polymorphisms (Staessen JA et al, 2001). Lessons learned from the studies of candidate genes to date include the shortcomings that result from the limited statistical power of many studies, expected variation from one population to another, the need for better phenotyping of study subjects, the relatively small effect of the genes studied on population prevalence of HT, and the lack of sufficient certainty of consequences of any genes studied thus far to make treatment recommendations based on genotype (Hopkins PN and Hunt SC, 2003).

To date more than 30 GWS studies have been reported to identify loci for BP/HT (Fuentes RM, 2004, unpublished review). Some studies utilized families, others affected or dissimilar sibling pairs. Linked loci with at least indicative LOD scores to BP/HT have been observed on every chromosome. Perhaps most striking is the lack of consistently linked loci. Koivukoski L et al, 2004 found evidence of susceptibility regions for BP/HT on chromosomes 2pl2-q22.1 and 3pl4.1-ql2.3 that had modest or non-significant linkage in each individual study when applying the genome-search meta-analysis method (GSMA) to nine published genome-wide scans of BP (n = 5) and HT (n = 4) from Caucasian populations. This may serve to illustrate the heterogeneity of human HT as well as the potential shortcomings of attempting to compare studies using different methodologies.

Opportunity for population genetics Previous medical research concerning the genetic etiology of HT has been based to a large extent on retrospective case-control and family studies in humans and studies in genetically modified animals. As recognized only recently, retrospective case-control studies are prone to survival and selection biases, and they have produced a myriad of biased findings concerning a large number of candidate genes. A commonly used approach is to compare gene expression between affected and unaffected persons. Gene expression studies, which are mostly cross- sectional, cannot however separate cause and consequence. Findings from animal models concerning HT cannot be generalised to humans, as the pathophysiology in humans is unique. The unsuitability of the animal studies is the main reason why genetic epidemiologic studies are the most important means in the clarification of genetic etiologies of human diseases.

Prospective cohort studies in humans overcome these problems. Developments in GWS and sequencing technology and methods of data analysis render possible the attempt to identify liability genes in complex, multifactorial traits, and to dissect the role of genetic predisposition and environment/life style factors in these disorders with new precision. Genetic and environmental effects vary over the life span, and only longitudinal studies in genetically informative data sets permit the study of such effects. A major advantage of population genetics approaches in disease gene discovery over other methodologies is that it will yield diagnostic markers that are valid in humans. The identification of genes causing major public health problems such as HT is now enabled by the following recent advances in molecular biology, population genetics and bioinformatics: 1. the availability of new genotyping platforms that will dramatically lower operating costs and increase throughputs; 2. the application of genome scans using dense marker maps; 3. data analysis using new powerful statistical methods testing for linkage disequilibrium using haplotype sharing analysis, and 4. the recognition that a smaller number of genetic markers than previously thought is sufficient for genome scans in genetically homogeneous populations.

Traditional GWS using microsatellite markers with linkage analyses have not been successful in finding genes causing common diseases. The failure has in part been due to too small a number of genetic markers used in GWS, and in part due to too heterogeneous study populations. With the advancements of the human genome project and genotyping technology, the first dense marker maps have recently become available for mapping the entire human genome. The microarrays used by Jurilab include probes for over 100,000 single nucleotide polymorphism (SNP) markers. These SNPs form a marker map covering, for the first time, the entire genome tightly enough for the discovery of most disease genes causing HT.

Genetic homogeneity of the East Finland founder population

Finns descend from two human immigration waves occurring about 4,000 and 2,000 years ago. Both Y-chromosomal haplotypes and mitochondrial sequences show low genetic diversity among Finns compared with other European populations and confirm the long¬ standing isolation of Finland (Sajantila A et al, 1996). During King Gustavus of Vasa (1523— 1560) over 400 years ago, internal migrations created regional subisolates, the late settlements (Peltonen L et al, 1999). The most isolated of these are the East Finns.

The East Finnish population is the most genetically-homogenous population isolate known that is large enough for effective gene discovery program. The reasons for homogeneity are: the young age of the population (fewer generations); the small number of founders; long-term geographical isolation; and population bottlenecks because of wars, famine and fatal disease epidemics.

Owing to the genetic homogeneity of the East Finland population, there are fewer mutations in important disease predisposing genes and the affected individuals share a similar genetic background. Because of the stronger linkage disequilibrium (LD), fewer SNPs and fewer subjects are needed for GWS than in other populations.

SUMMARY OF THE INVENTION

The present invention relates to single nucleotide polymorphism (SNP) markers, combinations of such markers and haplotypes associated with altered risk of HT, and genes associated with HT within or close to which said markers or haplotypes are located. Said SNP markers may be associated either with increased HT risk or reduced HT risk i.e. protective of HT. The "prediction" or risk implies here that the risk is either increased or reduced.

Thus, the present invention provides individual SNP markers associated with HT and combinations of SNP markers and haplotypes in genetic regions associated with HT, genes previously known in the art, but not known to be associated with HT, methods of estimating susceptibility or predisposition of an individual to HT, as well as methods for prediction of clinical course and efficacy of treatments for HT using polymorphisms in the HT risk genes. Accordingly, the present invention provides novel methods and compositions based on the disclosed HT associated SNP markers, combinations of SNP markers, haplotypes and genes.

The invention further relates to a method for estimating susceptibility or predisposition of an individual to HT comprising the detection of the presence of SNP markers and haplotypes, or an alteration in expression of an HT risk gene set forth in tables 2 through 8, as well as alterations in the polypeptides encoded by the said HT risk genes. The alterations may be quantitative, qualitative, or both.

The invention yet further relates to a method for estimating susceptibility or predisposition of an individual to HT. The method for estimating susceptibility or predisposition of an individual to HT is comprised of detecting the presence of at-risk haplotypes in an individual's nucleic acid.

The invention further relates to a kit for estimating susceptibility to HT in an individual comprising wholly or in part: amplification reagents for amplifying nucleic acid fragments containing SNP markers, detection reagents for genotyping SNP markers and interpretation software for data analysis and risk assessment.

In one aspect, the invention relates to methods of diagnosing a predisposition to HT. The methods of diagnosing a predisposition to HT in an individual include detecting the presence of SNP markers predicting HT, as well as detecting alterations in expression of genes which are associated with said markers. The alterations in expression can be quantitative, qualitative, or both.

A further object of the present invention is a method of identifying the risk of HT by detecting SNP markers in a biological sample of the subject. The information obtained from this method can be combined with other information concerning an individual, e.g. results from blood measurements, clinical examination and questionnaires. The blood measurements include but are not restricted to the determination of plasma or serum cholesterol and high- density lipoprotein cholesterol. The information to be collected by questionnaire includes information concerning gender, age, family and medical history such as the family history of HT and diabetes. Clinical information collected by examination includes e.g. information concerning height, weight, hip and waist circumference, systolic and diastolic BP, and heart rate.

The methods of the invention allow the accurate diagnosis of HT at or before disease onset, thus reducing or minimizing the debilitating effects of HT. The method can be applied in persons who are free of clinical symptoms and signs of HT, in those who already have clinical HT, in those who have a family history of HT, or in those who have an elevated level or levels of risk factors of HT. The invention further provides a method of diagnosing susceptibility to HT in an individual. This method comprises screening for at-risk haplotypes that predict HT that are more frequently present in an individual susceptible to HT, compared to the frequency of its presence in the general population, wherein the presence of an at-risk haplotype is indicative of a susceptibility to HT. The "at-risk haplotype" may also be associated with a reduced rather than increased risk of HT. An "at-risk haplotype" is intended to embrace one or a combination of haplotypes described herein over the markers that show high correlation to HT. Kits for diagnosing susceptibility to HT in an individual are also disclosed.

Those skilled in the art will readily recognize that the analysis of the nucleotides present in one or several of the SNP markers of this invention in an individual's nucleic acid can be done by any method or technique capable of determining nucleotides present in a polymorphic site. As it is obvious in the art the nucleotides present in SNP markers can be determined from either nucleic acid strand or from both strands. The major application of the current invention involves prediction of those at higher risk of developing HT. Diagnostic tests that define genetic factors contributing to HT might be used together with or independent of the known clinical risk factors to define an individual's risk relative to the general population. Better means for identifying those individuals at risk of HT should lead to better preventive and treatment regimens, including more aggressive management of the current clinical risk factors for sequelae of HT such as cigarette smoking, hypercholesterolemia, elevated LDL cholesterol, low HDL cholesterol, HT and elevated BP, diabetes mellitus, glucose intolerance, insulin resistance and the metabolic syndrome, obesity, lack of physical activity, and inflammatory components as reflected by increased C-reactive protein levels or other inflammatory markers. Information on genetic risk may be used by physicians to help convince particular patients to adjust life style (e.g. to stop smoking, reduce caloric intake, to increase exercise). Finally, preventive measures aimed at lowering blood pressure such as reduction of weight, intake of salt and alcohol, can be both better motivated to the patients and selected on the basis of the molecular subdiagnosis of HT. A further object of the invention is to provide a method for the selection of human subjects for studies testing antihypertensive effects of drugs.

Another object of the invention is a method for the selection of subjects for clinical trials testing antihypertensive drugs.

Still another object of the invention is to provide a method for prediction of clinical course and efficacy of treatments for HT using polymorphisms in the HT risk genes. The genes, gene products and agents of the invention are also useful for treating HT, for monitoring the effectiveness of the treatment, and for drug development. Kits are also provided for the diagnosis, treatment and prognosis of HT. DETAILED DESCRIPTION OF THE INVENTION

Representative Target Population

An individual at risk of HT is an individual who has at least one risk factor of HT, such as family history of HT, central or other type of obesity, lack of physical activity, high sodium intake, high intake of saturated fats, low intake of potassium and/or magnesium, low HDL cholesterol, diabetes mellitus, glucose intolerance, insulin resistance and the metabolic syndrome, elevated inflammatory marker, and an at-risk allele or haplotype with one or several HT risk SNP markers.

In another embodiment of the invention, an individual who is at risk of HT is an individual who has a risk- increasing allele in an HT risk gene, in which the presence of the polymorphism is indicative of a susceptibility to HT. The term "gene," as used herein, refers to an entirety containing all regulatory elements located both upstream and downstream as well as within of a polypeptide encoding sequence, 5' and 3' untranslated regions of mRNA and the entire polypeptide encoding sequence including all exon and intron sequences (also alternatively spliced exons and introns) of a gene.

Assessment for At-Risk Alleles and At-Risk Haplotypes

The genetic markers are particular "alleles" at "polymorphic sites" associated with HT. A nucleotide position at which more than one sequence is possible in a population, is referred to herein as a "polymorphic site". Where a polymorphic site is a single nucleotide in length, the site is referred to as a SNP. For example, if at a particular chromosomal location, one member of a population has an adenine and another member of the population has a thymine at the same position, then this position is a polymorphic site, and, more specifically, the polymorphic site is a SNP. Polymorphic sites may be several nucleotides in length due to insertions, deletions, conversions or translocations. Each version of the sequence with respect to the polymorphic site is referred to herein as an "allele" of the polymorphic site. Thus, in the previous example, the SNP allows for both an adenine allele and a thymine allele. Typically, a reference nucleotide sequence is referred to for a particular gene. Alleles that differ from the reference are referred to as "variant" alleles. The polypeptide encoded by the reference nucleotide sequence is the "reference" polypeptide with a particular reference amino acid sequence, and polypeptides encoded by variant alleles are referred to as "variant" polypeptides with variant amino acid sequences.

Nucleotide sequence variants can result in changes affecting the properties of a polypeptide. These sequence differences, when compared to a reference nucleotide sequence, include insertions, deletions, conversions and substitutions: e.g. an insertion, a deletion or a conversion may result in a frame shift generating an altered polypeptide; a substitution of at least one nucleotide may result in a premature stop codon, aminoacid change or abnormal mRNA splicing; the deletion of several nucleotides, resulting in a deletion of one or more amino acids encoded by the nucleotides; the insertion of several nucleotides, such as by unequal recombination or gene conversion, resulting in an interruption of the coding sequence of a reading frame; duplication of all or a part of a sequence; transposition; or a rearrangement of a nucleotide sequence, as described in detail above. Such sequence changes alter the polypeptide encoded by an HT susceptibility gene. For example, a nucleotide change in a gene resulting in a change in corresponding polypeptide aminoacid sequence can alter the physiological properties of a polypeptide resulting in a polypeptide having altered biological activity/iunction, distribution or stability.

Alternatively, nucleotide sequence variants can result in changes affecting transcription of a gene or translation of it's mRNA. A polymorphic site located in a regulatory region of a gene may result in altered transcription of a gene e.g. due to altered tissue specifity, altered transcription rate or altered response to transcription iactors. A polymorphic site located in a region corresponding to the mRNA of a gene may result in altered translation of the mRNA e.g. by inducing stable secondary structures to the mRNA and affecting the stability of the mRNA. Such sequence changes may alter the expression of an HT susceptibility gene. A "haplotype," as described herein, refers to any combination of genetic markers ("alleles"), such as those set forth in tables 3, 4, 5, 7 and 8. A haplotype can comprise two or more alleles.

As it is recognized by those skilled in the art, the same haplotype can be described differently by determining the haplotype defining alleles from different strands e.g. the haplotype rs2221511, rs4940595, rsl522723, rsl395266 (A T C C) described in this invention is the same as haplotype rs2221511, rs4940595, rsl522723, rsl395266 (T A G G) in which the alleles are determined from the other strand or haplotype rs2221511, rs4940595, rsl522723, rsl 395266 (T T C C), in which the first allele is determined from the other strand. The haplotypes described herein, e.g. having markers such as those shown in tables 3, 4, 5, 7 and 8, are found more frequently in individuals with HT than in individuals without HT. Therefore, these haplotypes have predictive value for detecting HT or a susceptibility to HT in an individual. Therefore, detecting haplotypes can be accomplished by methods known in the art for detecting sequences at polymorphic sites.

It is understood that the HT associated at-risk alleles and at-risk haplotypes described in this invention may be associated with other "polymorphic sites" located in HT associated genes of this invention. These other HT associated polymorphic sites may be either equally useful as genetic markers or even more useful as causative variations explaining the observed association of the at-risk alleles and at-risk haplotypes of this invention to HT.

In certain methods described herein, an individual who is at risk of HT is an individual in whom an at-risk allele or an at-risk haplotype is identified. In one embodiment, the at-risk allele or the at-risk haplotype is one that confers a significant risk of HT. In one embodiment, significance associated with an allele or a haplotype is measured by an odds ratio. In a further embodiment, the significance is measured by a percentage. In one embodiment, a significant risk is measured as an odds ratio of at least about 1.2, including but not limited to: 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0, 4.0, 5.0, 10.0, 15.0, 20.0, 25.0, 30.0 and 40.0. In a further embodiment, a significant increase or reduction in risk is at least about 20%, including but not limited to about 25%, 30%, 35%, 40%, 45%,

50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% and 98%. In a further embodiment, a significant increase in risk is at least about 50%. It is understood however, that identifying whether a risk is medically significant may also depend on a variety of iactors, including the specific disease, the allele or the haplotype, and often, environmental factors. An at-risk haplotype in, or comprising portions of, the HT risk gene, is one where the haplotype is more frequently present in an individual at risk of HT (affected), compared to the frequency of its presence in a healthy individual (control), and wherein the presence of the haplotype is indicative of HT or susceptibility to HT.

In a preferred embodiment, the method comprises assessing in an individual the presence or frequency of SNPs in, comprising portions of, an HT risk gene, wherein an excess or higher frequency of the SNPs compared to healthy control individuals is indicative that the individual has HT, or is susceptible to HT. See, for example, tables 3, 4, 5, 7 and 8 for SNPs that can form haplotypes that can be used as screening tools. These SNP markers can be identified in at-risk haploptypes. For example, an at-risk haplotype can include microsatellite markers and/or SNPs such as those set forth in tables 3, 4, 5, 7 and 8. The presence of the haplotype is indicative of HT, or a susceptibility to HT, and therefore is indicative of an individual who falls within a target population for the treatment methods described herein.

Consequently, the method of the invention is particularly directed to the detection of one or several of the SNP markers defining the following at-risk haplotypes indicative of HT: 1) rs4845303 (A/T) (SEQ ID NO: 980), rs6428195 (C/G) (SEQ ID NO: 1030) and rsl935659 (A/G) (SEQ ID NO: 637) defining the haplotype ACG;

2) rsl997454 (A/G) (SEQ ID NO: 656), rs2139502 (A/G) (SEQ ID NO: 709) and rsl519991 (A/C) (SEQ ID NO: 542) defining the haplotype AGC;

3) rsl521409 (A/G) (SEQ ID NO: 544), rslO511365 (C/T) (SEQ ID NO: 316) and rslO511366 (C/T) (SEQ ID NO: 317) defining the haplotype ACT;

4) rs7679959 (C/G) (SEQ ID NO: 1178), rslO517338 (C/G) (SEQ ID NO: 381) and rs959297 (A/T) (SEQ ID NO: 1338) defining the haplotype CGA;

5) rs2278677 (A/G) (SEQ ID NO: 749), rs3886091 (C/G) (SEQ ID NO: 899), rsl998167 (A/G) (SEQ ID NO: 657), rsl998168 (A/G) (SEQ ID NO: 658) and rs2235280 (A/G) (SEQ ID NO: 740) defining the haplotype GCAGG;

6) rsl0521062 (A/C) (SEQ ID NO: 404), rslO512296 (A/G) (SEQ ID NO: 331), rsl924001 (C/G) (SEQ ID NO: 633) and rs2417359 (A/G) (SEQ ID NO: 784) defining the haplotype AACG;

7) rsl0508933 (C/G) (SEQ ID NO: 289), rsl0509071 (A/G) (SEQ ID NO: 295) and rsl0490967 (A/G) (SEQ ID NO: 94) defining the haplotype GGA;

8) rsl0508771 (A/T) (SEQ ID NO: 286), rs3006608 (C/T) (SEQ ID NO: 854), rsl0508773 (C/T) (SEQ ID NO: 287) and rs950132 (C/T) (SEQ ID NO: 1325) defining the haplotype TCCC;

9) rsl386486 (C/T) (SEQ ID NO: 472), rsl386485 (A/C) (SEQ ID NO: 471), rsl386483 (A/G) (SEQ ID NO: 470) and rs7977245 (C/T) (SEQ ID NO: 1212) defining the haplotype

CAGT;

10) rs276002 (A/G) (SEQ ID NO: 814) and rs274460 (A/G) (SEQ ID NO: 810) defining the haplotype AA;

11) rsl245383 (A/G) (SEQ ID NO: 430), rs2133829 (C/T) (SEQ ID NO: 707), rs2173738 (C/T) (SEQ ID NO: 722), rs2050528 (C/T) (SEQ ID NO: 677) and rs202970 (C/T) (SEQ ID

NO: 671) defining the haplotype GCTTC;

12) rsl395266 (C/T) (SEQ ID NO: 476), rs931850 (A/G) (SEQ ID NO: 1303) and rsl522722 (C/T) (SEQ ID NO: 547) defining the haplotype TAC; 13) rs2221511 (A/G) (SEQ ID NO: 733), rs4940595 (G/T) (SEQ ID NO: 986), rsl522723 (OT) (SEQ ID NO: 548) and rs 1395266 (OT) (SEQ ID NO: 476) defining the haplotype ATCC;

14) rs2825555 (A/G) (SEQ ID NO: 819), rs2825583 (OT) (SEQ ID NO: 820), rs2825601 (A/G) (SEQ ID NO: 821), rs2825610 (G/T) (SEQ ID NO: 822) and rsl489734 (A/G) (SEQ ID NO: 532) defining the haplotype ATGGA

Monitoring Progress of Treatment

The current invention also pertains to methods of monitoring the effectiveness of a treatment of HT on the expression (e.g. relative or absolute expression) of one or more HT risk genes. The HT susceptibility gene mRNA, the polypeptide it is encoding, or the biological activity of the encoded polypeptide can be measured in a sample of peripheral blood or cells derived therefrom. An assessment of the levels of expression or biological activity of the polypeptide can be made before and during treatment with HT therapeutic agents.

Alternatively the effectiveness of a treatment of HT can be followed by monitoring biological networks and/or metabolic pathways related to one or several polypeptides encoded by HT risk genes listed in table 6. Monitoring biological networks and/or metabolic pathways can be done e.g. by measuring one or several polypeptides from plasma proteome and/or by measuring one or several metabolites from plasma metabolome before and during treatment. Effectiveness of a treatment is evaluated by comparing observed changes in biological networks and or metabolic pathways following treatment with HT therapeutic agents to the data available from healthy subjects.

For example, in one embodiment of the invention, an individual who is a member of the target population can be assessed for response to treatment with an HT inhibitor, by examining the HT risk gene encoding polypeptide biological activity or absolute and/or relative levels of HT risk gene encoding polypeptide or mRNA in peripheral blood in general or specific cell subfractions or combination of cell subfractions.

In addition, variations such as haplotypes or mutations within or near (within one to hundreds of kb) the HT risk gene may be used to identify individuals who are at higher risk for HT to increase the power and efficiency of clinical trials for pharmaceutical agents to prevent or treat HT or its complications. The haplotypes and other variations may be used to exclude or fractionate patients in a clinical trial who are likely to have involvement of another pathway in their HT in order to enrich patients who have pathways involved that are relevant regarding to the treatment tested and boost the power and sensitivity of the clinical trial. Such variations may be used as a pharmacogenetic test to guide selection of pharmaceutical agents for individuals.

Primers, probes and nucleic acid molecules "Probes" or "primers" are oligonucleotides that hybridize in a base-specific manner to a complementary strand of nucleic acid molecules. "Base specific manner" means that the two sequences must have a degree of nucleotide complementarity sufficient for the primer or probe to hybridize. Accordingly, the primer or probe sequence is not required to be perfectly complementary to the sequence of the template. Non-complementary bases or modified bases can be interspersed into the primer or probe, provided that base substitutions do not inhibit hybridization. The nucleic acid template may also include "nonspecific priming sequences" or "nonspecific sequences" to which the primer or probe has varying degrees of complementarity. Such probes and primers include polypeptide nucleic acids (Nielsen PE et al, 1991).

A probe or primer comprises a region of nucleic acid that hybridizes to at least about 15, for example about 20-25, and in certain embodiments about 40, 50, or 75 consecutive nucleotides of a nucleic acid of the invention, such as a nucleic acid comprising a contiguous nucleic acid sequence.

In preferred embodiments, a probe or primer comprises 100 or fewer nucleotides, in certain embodiments, from 6 to 50 nucleotides, for example, from 12 to 30 nucleotides. In other embodiments, the probe or primer is at least 70% identical to the contiguous nucleic acid sequence or to the complement of the contiguous nucleotide sequence, for example, at least 80% identical, in certain embodiments at least 90% identical, and in other embodiments at least 95% identical, or even capable of selectively hybridizing to the contiguous nucleic acid sequence or to the complement of the contiguous nucleotide sequence. Often, the probe or primer further comprises a label, e.g. radioisotope, fluorescent compound, enzyme, or enzyme co-factor.

Antisense nucleic acid molecules of the invention can be designed using the nucleotide sequences available e.g. in GenBank database for HT associated genes of table 6 as well as nucleotide sequences containing polymorphic sites listed in tables 2 to 5 and 7 to 11. Antisense oligonucleotides can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid molecule (e.g. an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g. phosphorothioate derivatives and acridine substituted nucleotides can be used. Alternatively, the antisense nucleic acid molecule can be produced biologically using an expression vector into which a nucleic acid molecule has been subcloned in an antisense orientation (i.e. RNA transcribed from the inserted nucleic acid molecule will be of an antisense orientation to a target nucleic acid of interest). The nucleic acid sequences of the HT associated genes of table 6 described in this invention can also be used to compare with endogenous DNA sequences in patients to identify genetic disorders (e.g. a predisposition for, or susceptibility to HT), and as probes, such as to hybridize and discover related DNA sequences or to extract known sequences from a sample. The nucleic acid sequences can further be used to derive primers for genetic fingerprinting, to raise anti-polypeptide antibodies using DNA immunization techniques, and as an antigen to raise anti-DNA antibodies or elicit immune responses. Portions or fragments of the nucleotide sequences identified herein (and the corresponding complete gene sequences) can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and thus locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. Additionally, the nucleotide sequences of the invention can be used to identify and express recombinant polypeptides for analysis, characterization or therapeutic use, or as markers for tissues in which the corresponding polypeptide is expressed, either constitutively, during tissue differentiation, or in diseased states. The nucleic acid sequences can additionally be used as reagents in the screening and/or diagnostic assays described herein, and can also be included as components of kits (e.g. reagent kits) for use in the screening and/or diagnostic assays described herein.

Polyclonal and monoclonal antibodies

Polyclonal and/or monoclonal antibodies that specifically bind one form of the gene product but not to the other form of the gene product are also provided. Antibodies are also provided that bind a portion of either the variant or the reference gene product that contains the polymorphic site or sites. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e. molecules that contain an antigen binding site that specifically binds an antigen. A molecule that specifically binds to a polypeptide of the invention is a molecule that binds to that polypeptide or a fragment thereof, but does not substantially bind other molecules in a sample, e.g. a biological sample, which naturally contains the polypeptide. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab') fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind to a polypeptide of the invention. The term "monoclonal antibody" or "monoclonal antibody composition" as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of a polypeptide of the invention. A monoclonal antibody composition thus typically displays a single binding affinity for a particular polypeptide of the invention with which it immunoreacts. Polyclonal antibodies can be prepared as known by those skilled in the art by immunizing a suitable subject with a desired immunogen, e.g. a polypeptide of the invention or fragment thereof. The antibody titer in the immunized subject can be monitored over time by standard techniques such as with an enzyme linked immunosorbent assay (ELISA) using immobilized polypeptide. If desired, the antibody molecules directed against the polypeptide can be isolated from the mammal (e.g. from blood) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction. At an appropriate time after immunization, e.g. when the antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique (Kohler G and Milstein C, 1975), the human B cell hybridoma technique (Kozbor D et al, 1982), the EBV-hybridoma technique (Cole SP et al, 1994), or trioma techniques (Hering S et al, 1988). To produce a hybridoma an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with an immunogen as described above, and the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds a polypeptide of the invention.

Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating a monoclonal antibody to a polypeptide of the invention (Bierer B et al, 2002). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods that would also be useful.

As an alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal antibody to a polypeptide of the invention can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g. an antibody phage display library) with the polypeptide to thereby isolate immunoglobulin library members that bind the polypeptide (Hayashi N et al, 1995; Hay BN et al, 1992; Huse WD et al, 1989; Griffiths AD et al, 1993). Kits for generating and screening phage display libraries are commercially available. Additionally, recombinant antibodies, such as chimeric and humanized monoclonal antibodies comprising both human and nonhuman portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art.

In general, antibodies of the invention (e.g. a monoclonal antibody) can be used to isolate a polypeptide of the invention by standard techniques such as affinity chromatography or immunoprecipitation. A polypeptide-specific antibody can facilitate the purification of natural polypeptide from cells and of recombinantly produced polypeptide expressed in host cells. Moreover, an antibody specific for a polypeptide of the invention can be used to detect the polypeptide (e.g. in a cellular lysate, cell supernatant, or tissue sample) in order to evaluate the abundance and pattern of expression of the polypeptide. Antibodies can be used diagnostically to monitor protein levels in tissue such as blood as part of a test predicting the susceptibility to HT or as part of a clinical testing procedure, e.g. to determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, and acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include I, ¹³¹1, ³⁵S and ³H.

Diagnostic Assays The probes, primers and antibodies described herein can be used in methods of diagnosis of HT or diagnosis of a susceptibility to HT, as well as in kits useful for the diagnosis of HT or susceptibility to HT, or to a disease or condition associated with HT.

In one embodiment of the invention, diagnosis of HT or susceptibility to HT (or diagnosis of or susceptibility to a disease or condition associated with HT), is made by detecting one or several of at-risk alleles or at-risk haplotypes or a combination of at-risk alleles and at-risk haplotypes described in this invention in the subject's nucleic acid as described herein.

In one embodiment of the invention, diagnosis of HT or susceptibility to HT (or diagnosis of or susceptibility to a disease or condition associated with HT) is made by detecting one or several polymorphic sites that are associated with at-risk alleles and/or at-risk haplotypes described in this invention, in the subject's nucleic acid. Diagnostically, the most useful polymorphic sites are those altering the polypeptide structure of an HT associated gene due to a frame shift; due to a premature stop codon, due to an aminoacid change or due to abnormal mRNA splicing. Nucleotide changes in a gene resulting in a change in corresponding polypeptide aminoacid sequence in many case alter the physiological properties of a polypeptide by resulting in a polypeptide having altered biological activity/iunction, distribution or stability. Other diagnostically useful polymorphic sites are those affecting transcription of an HT associated gene or translation of it's mRNA due to altered tissue specifity, altered transcription rate, altered response to physiological status, altered translation efficiency of the mRNA and altered stability of the mRNA. The presence of nucleotide sequence variants altering the polypeptide structure of HT associated genes or altering the expression of HT associated genes is diagnostic for susceptibility to HT. For diagnostic applications, there may be informative polymorphisms for prediction of disease risk that are in linkage disequilibrium with the functional polymorphism. Such a functional polymorphism may alter splicing sites, affect the stability or transport of mRNA, or otherwise affect the transcription or translation of the nucleic acid. The presence of nucleotide sequence variants associated with functional polymorphism is diagnostic for susceptibility to HT.

While we have genotyped and included a limited number of example SNP markers in the experimental section, any functional, regulatory or other mutation or alteration described above in any of the HT risk genes identified herein is expected to predict the risk of HT.

In diagnostic assays determination of the nucleotides present in one or several of the HT associated SNP markers of this invention, as well as polymorphic sites associated with HT associated SNP markers of this invention, in an individual's nucleic acid can be done by any method or technique which can accurately determine nucleotides present in a polymorphic site. Numerous suitable methods have been described in the art (Kwok P-Y, 2001 ; Syvanen A-C, 2001). These methods include, but are not limited to, hybridization assays, ligation assays, primer extension assays, enzymatic cleavage assays, chemical cleavage assays and any combinations of these assays. The assays may or may not include PCR, solid phase step, modified oligonucleotides, labeled probes or labeled nucleotides, and the assay may be multiplex or singleplex. As it is obvious in the art the nucleotides present in polymorphic site can be determined from one nucleic acid strand or from both strands.

In another embodiment of the invention, diagnosis of a susceptibility to HT can also be made by examining transcription of one or several HT associated genes. Alterations in transcription can be analyzed by a variety of methods as described in the art, including e.g. hybridization methods, enzymatic cleavage assays, RT-PCR assays and microarrays. A test sample from an individual is collected and the alterations in the transcription of HT associated genes are assessed from the RNA present in the sample. Altered transcription is diagnostic for a susceptibility to HT.

In another embodiment of the invention, diagnosis of a susceptibility to HT can also be made by examining expression and/or structure and/or function of an HT susceptibility polypeptide. A test sample from an individual is assessed for the presence of an alteration in the expression and/or an alteration in structure and/or function of the polypeptide encoded by an HT risk gene, or for the presence of a particular polypeptide variant (e.g. an isoform) encoded by an HT risk gene. An alteration in expression of a polypeptide encoded by an HT risk gene can be for example, an alteration in the quantitative polypeptide expression (i.e. the amount of polypeptide produced); an alteration in the structure and/or function of a polypeptide encoded by an HT risk gene is an alteration in the qualitative polypeptide expression (e.g. expression of a mutant HT susceptibility polypeptide or of a different splicing variant or isoform). In a preferred embodiment, detection of a particular splicing variant encoded by an HT risk gene, or a particular pattern of splicing variants makes diagnosis of the disease or condition associated with HT or a susceptibility to a disease or condition associated with HT possible. Alterations in expression and/or structure and/or function of an HT susceptibility polypeptide can be determined by various methods known in the art e.g. by assays based on chromatography, spectroscopy, colorimetry, electrophoresis, isoelectric focusing, specific cleavage, immunologic techniques and measurement of biological activity as well as combinations of different assays. An "alteration" in the polypeptide expression or composition, as used herein, refers to an alteration in expression or composition in a test sample, as compared with the expression or composition of polypeptide by an HT risk gene in a control sample. A control sample is a sample that corresponds to the test sample (i.e. is from the same type of cells), and is from an individual who is not affected by HT. An alteration in the expression or composition of the polypeptide in the test sample, as compared with the control sample, is indicative of a susceptibility to HT.

Western blotting analysis using an antibody as described above that specifically binds to a polypeptide encoded by a mutant HT risk gene, or an antibody that specifically binds to a polypeptide encoded by a nonmutant gene, or an antibody that specifically binds to a particular splicing variant encoded by an HT risk gene, can be used to identify the presence in a test sample of a particular splicing variant or isoform, or of a polypeptide encoded by a polymorphic or mutant HT risk gene, or the absence in a test sample of a particular splicing variant or isoform, or of a polypeptide encoded by a nonpolymorphic or nonmutant gene. The presence of a polypeptide encoded by a polymorphic or mutant gene, or the absence of a polypeptide encoded by a nonpolymorphic or nonmutant gene, is diagnostic for susceptibility to HT, as is the presence (or absence) of particular splicing variants encoded by an HT risk gene.

In one embodiment of this method, the level or amount of polypeptide encoded by an HT risk gene in a test sample is compared with the level or amount of the polypeptide encoded by an HT risk gene in a control sample. A level or amount of the polypeptide in the test sample that is higher or lower than the level or amount of the polypeptide in the control sample, such that the difference is statistically significant, is indicative of an alteration in the expression of the polypeptide encoded by an HT risk gene, and is diagnostic for susceptibility to HT. Alternatively, the composition of the polypeptide encoded by an HT risk gene in a test sample is compared with the composition of the polypeptide encoded by an HT risk gene in a control sample (e.g. the presence of different splicing variants). A difference in the composition of the polypeptide in the test sample, as compared with the composition of the polypeptide in the control sample, is diagnostic for susceptibility to HT. In another embodiment, both the level or amount, and the composition of the polypeptide can be assessed in the test sample and in the control sample. A difference in the amount or level of the polypeptide in the test sample compared to the control sample; a difference in composition in the test sample compared to the control sample; or both a difference in the amount or level, and a difference in the composition, is indicative of susceptibility to HT.

In another embodiment, assessment of the splicing variant or isoform(s) of a polypeptide encoded by a polymorphic or mutant HT risk gene can be performed. The assessment can be performed directly (e.g. by examining the polypeptide itself), or indirectly (e.g. by examining the mRNA encoding the polypeptide, e.g. by mRNA profiling). For example, probes or primers as described herein can be used to determine which splicing variants or isoforms are encoded by an HT risk gene mRNA, using standard methods.

The presence in a test sample of a particular splicing variant(s) or isoform(s) associated with HT or risk of HT, or the absence in a test sample of a particular splicing variant(s) or isoform(s) not associated with HT or risk of HT, is diagnostic for a disease or condition associated with an HT risk gene or susceptibility to a disease or condition associated with an HT risk gene. Similarly, the absence in a test sample of a particular splicing variant(s) or isoform(s) associated with HT or risk of HT, or the presence in a test sample of a particular splicing variant(s) or isoform(s) not associated with HT or risk of HT, is diagnostic for the absence of disease or condition associated with an HT risk gene or susceptibility to a disease or condition associated with an HT risk gene.

The invention further pertains to a method for the diagnosis and identification of susceptibility to HT in an individual by identifying an at-risk allele or an at-risk haplotype in an HT risk gene. In one embodiment, the at-risk allele or the at-risk haplotype is an allele or haplotype for which the presence of the haplotype increases the risk of HT significantly. Although it is to be understood that identifying whether a risk is significant may depend on a variety of factors, including the specific disease, the haplotype, and often, environmental factors, the significance may be measured by an odds ratio or a percentage. In a further embodiment, the significance is measured by a percentage. In one embodiment, a significant risk is measured as an odds ratio of 0.8 or less or at least about 1.2, including but not limited to: 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.5, 3.0, 4.0, 5.0, 10.0, 15.0, 20.0, 25.0, 30.0 and 40.0. In a further embodiment an odds ratio of at least 1.2 is significant. In a further embodiment, an odds ratio of at least about 1.5 is significant. In a further embodiment a significant increase or decrease in risk is at least about 1.7. In a further embodiment, a significant increase in risk is at least about 20%, including but not limited to about 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% and 98%. In a further embodiment a significant increase or reduction in risk is at least about 50%. It is understood, however, that identifying whether a risk is medically significant may also depend on a variety of iactors, including the specific disease, the allele or the haplotype, and often, environmental factors.

The invention also pertains to methods of diagnosing HT or susceptibility to HT in an individual, comprising screening for an at-risk haplotype in the HT risk gene that is more frequently present in an individual susceptible to HT (affected), compared to the frequency of its presence in a healthy individual (control), wherein the presence of the haplotype is indicative of HT or susceptibility to HT. See tables 3, 4, 6, 7 and 8 for SNP markers that comprise haplotypes that can be used as screening tools. SNP markers from these lists represent at-risk haplotypes and can be used to design diagnostic tests for determining susceptibility to HT.

Kits (e.g. reagent kits) useful in the methods of diagnosis comprise components useful in any of the methods described herein, including for example, PCR primers, hybridization probes or primers as described herein (e.g. labeled probes or primers), reagents for genotyping SNP markers, reagents for detection of labeled molecules, restriction enzymes (e.g. for RFLP analysis), allele-specific oligonucleotides, DNA polymerases, RNA polymerases, marker enzymes, antibodies which bind to altered or to nonaltered (native) HT susceptibility polypeptide, means for amplification of nucleic acids comprising one or several HT risk genes, or means for analyzing the nucleic acid sequence of one or several HT risk genes or for analyzing the amino acid sequence of one or several HT susceptibility polypeptides, etc. In one embodiment, a kit for diagnosing susceptibility to HT can comprise primers for nucleic acid amplification of a region in an HT risk gene comprising an at-risk haplotype that is more frequently present in an individual susceptible to HT. The primers can be designed using portions of the nucleic acids flanking SNPs that are indicative of HT.

This invention is based on the principle that one or a small number of genotypings are performed and the sequence variations to be typed are selected on the basis of their ability to predict HT. For this reason any method to genotype sequence variations in a genomic DNA sample can be used.

Thus, the detection method of the invention may further comprise a step of combining information concerning age, gender, the family history of HT, diabetes and hypercholesterolemia, and the medical history concerning CVD or diabetes of the subject with the results obtained from step b) of the method (see claim 1) for confirming the indication obtained from the detection step. Said information may also concern hypercholesterolemia in the family, smoking status, HT in the family, history of CVD, obesity in the family, and waist-to-hip circumference ratio (cm/cm)

The detection method of the invention may also further comprise a step determining blood, serum or plasma cholesterol, HDL cholesterol, LDL cholesterol, triglyceride, apolipoprotein B and AI, fibrinogen, ferritin, transferrin receptor, C-reactive protein, serum or plasma insulin concentration.

The score that predicts the probability of HT may be calculated using a multivariate failure time model or a logistic regression equation. The results from the further steps of the method as described above render possible a step of calculating the probability of developing HT using a logistic regression equation as follows.

Probability of HT = 1/[1 + e (-(-a + Σ(bi*Xi))], where e is Napier's constant, Xi are variables related to HT, bi are coefficients of these variables in the logistic function, and a is the constant term in the logistic iunction, and wherein a and bi are preferably determined in the population in which the method is to be used, and Xi are prefereably selected among the variables that have been measured in the population in which the method is to be used. Preferable values for bi are between -20 and 20; and for i between 0 (zero) and 100,000. A negative coefficient bi implies that the marker is risk-reducing and a positive coefficient implies that the marker is risk- increasing.

Xi are binary variables that can have values or are coded as 0 (zero) or 1 (one) such as SNP markers. The model may additionally include any interaction (product) or terms of any variables Xi, e.g. biXi. An algorithm is developed for combining the information to yield a simple prediction of HT as percentage of risk in one year, two years, five years, 10 years or 20 years.

Alternative statistical models are failure-time models such as the Cox's proportional hazards' model, other iterative models and neural networking models.

The test can be applied to test the risk of developing HT in both healthy persons, as a screening or predisposition test, and high-risk persons (who have e.g. family history of HT, central or other type of obesity, lack of physical activity, high sodium intake, high intake of saturated fats, low intake of potassium and/or magnesium, low HDL cholesterol, diabetes mellitus, glucose intolerance, insulin resistance and the metabolic syndrome, elevated inflammatory marker, or any combination of these or an elevated level of any other risk factor for HT). The method can be used in the prediction and early diagnosis of HT in adult persons, stratification and selection of subjects in clinical trials, and/or stratification and selection of persons for intensified preventive and curative interventions. The aim is to reduce the cost of clinical drug trials and health care.

Pharmaceutical Compositions

The present invention also pertains to pharmaceutical compositions comprising agents described herein, particularly nucleotides in HT risk genes, and/or comprising other splicing variants encoded by HT risk genes; and/or an agent that alters (e.g. enhances or inhibits) HT risk gene expression or HT susceptibility gene polypeptide activity as described herein. For instance, a polypeptide, protein (e.g. a receptor), an agent that alters an HT risk gene expression, or an HT susceptibility polypeptide binding agent or binding partner, fragment, fusion protein or prodrug thereof, or a nucleotide or nucleic acid construct (vector) comprising a nucleotide of the present invention, or an agent that alters HT susceptibility gene polypeptide activity, can be formulated with a physiologically acceptable carrier or excipient to prepare a pharmaceutical composition. The carrier and composition can be sterile. The formulation should suit the mode of administration. In a preferred embodiment pharmaceutical compositions comprise an agent or agents reversing, at least partially, HT associated changes in biological networks and/or metabolic pathways related to the HT associated genes of this invention (Table 6).

Suitable pharmaceutically acceptable carriers include but are not limited to water, salt solutions (e.g. NaCl), saline, buffered saline, alcohols, glycerol, ethanol, gum arabic, vegetable oils, benzyl alcohols, polyethylene glycols, gelatin, carbohydrates such as lactose, amylose or starch, dextrose, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oil, fatty acid esters, hydroxymethylcellulose, polyvinyl pyrolidone, etc., as well as combinations thereof. The pharmaceutical preparations can, if desired, be mixed with auxiliary agents, e.g. lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, flavoring and/or aromatic substances and the like that do not deleteriously react with the active agents.

The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulation can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, polyvinyl pyrolidone, sodium saccharine, cellulose, magnesium carbonate, etc.

Methods of introduction of these compositions include, but are not limited to, intradermal, intramuscular, intraperitoneal, intraocular, intravenous, subcutaneous, topical, oral and intranasal. Other suitable methods of introduction can also include gene therapy (as described below), rechargeable or biodegradable devices, particle acceleration devices ("gene guns") and slow release polymeric devices. The pharmaceutical compositions of this invention can also be administered as part of a combinatorial therapy with other agents.

The composition can be formulated in accordance with the routine procedures as a pharmaceutical composition adapted for administration to human beings. For example, compositions for intravenous administration are typically solutions in sterile isotonic aqueous buffer. Where necessary, the composition may also include a solubilizing agent and a local anesthetic to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water, saline or dextrose/water. Where the composition is administered by injection, an ampule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.

For topical application, nonsprayable forms, viscous to semi-solid or solid forms comprising a carrier compatible with topical application and having a dynamic viscosity preferably greater than water, can be employed. Suitable formulations include but are not limited to solutions, suspensions, emulsions, creams, ointments, powders, enemas, lotions, sols, liniments, salves, aerosols, etc., which are, if desired, sterilized or mixed with auxiliary agents, e.g. preservatives, stabilizers, wetting agents, buffers or salts for influencing osmotic pressure, etc. The agent may be incorporated into a cosmetic formulation. For topical application, sprayable aerosol preparations wherein the active ingredient, preferably in combination with a solid or liquid inert carrier material, is packaged in a squeeze bottle or in admixture with a pressurized volatile, normally gaseous propellant, e.g. pressurized air, are also suitable.

Agents described herein can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.

The agents are administered in a therapeutically effective amount. The amount of agents which will be therapeutically effective in the treatment of a particular disorder or condition will depend on the nature of the disorder or condition, and can be determined by standard clinical techniques. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration, and the severity of the symptoms of HT, and should be decided according to the judgment of a practitioner and each patient's circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.

Methods of Therapy

The present invention encompasses methods of treatment (prophylactic and/or therapeutic) for HT or a susceptibility to HT, such as individuals in the target populations described herein, using an HT therapeutic agent. An "HT therapeutic agent" is an agent that alters (e.g. enhances or inhibits) HT risk affecting polypeptide (enzymatic activity or quantity) and/or an HT risk gene expression, as described herein (e.g. an agonist or antagonist). HT therapeutic agents can alter an HT susceptibility polypeptide activity or nucleic acid expression by a variety of means, for example, by providing additional HT susceptibility polypeptide or by upregulating the transcription or translation of the HT risk gene; by altering posttranslational processing of the HT susceptibility polypeptide; by altering transcription of an HT risk gene splicing variants; or by interfering with an HT susceptibility polypeptide activity (e.g. by binding to an HT susceptibility polypeptide); or by downregulating the transcription or translation of the HT risk gene, or by inhibiting or enhancing the elimination of an HT susceptibility polypeptide.

In particular, the invention relates to methods of treatment for HT or susceptibility to HT (for example, for individuals in an at-risk population such as those described herein); as well as to methods of treatment for manifestations and subtypes of HT. Representative HT therapeutic agents include the following: nucleic acids or fragments or derivatives thereof described herein, particularly nucleotides encoding the polypeptides described herein and vectors comprising such nucleic acids (e.g. a gene, cDNA, and/or mRNA, double-stranded interfering RNA, a nucleic acid encoding an HT susceptibility polypeptide or active fragment or derivative thereof, or an oligonucleotide; for examples see tables 2 through 8; other polypeptides (e.g. HT susceptibility receptors); HT susceptibility polypeptide binding agents; peptidomimetics; fusion proteins or prodrugs thereof, antibodies (e.g. an antibody to a mutant HT susceptibility polypeptide, or an antibody to a non-mutant HT susceptibility polypeptide, or an antibody to a particular splicing variant encoded by an HT risk gene, as described above); ribozymes; other small molecules; and other agents that alter (e.g. inhibit or antagonize) an HT risk gene expression or polypeptide activity or that regulate transcription of an HT risk gene splicing variants (e.g. agents that affect which splicing variants are expressed, or that affect the amount of each splicing variant that is expressed); and other reagents that alter (e.g. induce or agonize) an HT risk gene expression or polypeptide activity or that regulate transcription of an HT risk gene splicing variants (e.g. agents that affect which splicing variants are expressed or that affect the amount of each splicing variant that is expressed).

More than one HT therapeutic agent can be used concurrently, if desired.

The HT therapeutic agent that is a nucleic acid is used in the treatment of HT. The term, "treatment" as used herein, refers not only to ameliorating symptoms associated with the disease, but also preventing or delaying the onset of the disease and also lessening the severity or frequency of symptoms of the disease, preventing or delaying the occurrence of a second episode of the disease or condition; and/or also lessening the severity or frequency of symptoms of the disease or condition. In the case of atherosclerosis, "treatment" also refers to a minimization or reversal of the development of plaques. The therapy is designed to alter (e.g. inhibit or enhance), replace or supplement activity of an HT polypeptide in an individual. For example, an HT therapeutic agent can be administered in order to upregulate or increase the expression or availability of an HT risk gene or of specific splicing variants of an HT susceptibility, gene or, conversely, to downregulate or decrease the expression or availability of an HT risk gene or specific splicing variants of an HT risk gene. Upregulation or increasing expression or availability of a native HT risk gene or of a particular splicing variant could interfere with or compensate for the expression or activity of a defective gene or another splicing variant; downregulation or decreasing expression or availability of a native HT risk gene or of a particular splicing variant could minimize the expression or activity of a defective gene or the particular splicing variant and thereby minimize the impact of the defective gene or the particular splicing variant. The HT therapeutic agent(s) are administered in a therapeutically effective amount (i.e. an amount that is sufficient to treat the disease, e.g. by ameliorating symptoms associated with the disease, preventing or delaying the onset of the disease, and/or also lessening the severity or frequency of symptoms of the disease). The amount which will be therapeutically effective in the treatment of a particular individual's disorder or condition will depend on the symptoms and severity of the disease and can be determined by standard clinical techniques. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the formulation will also depend on the route of administration and the severity of the disease or disorder, and should be decided according to the judgment of a practitioner and each patient's circumstances. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems.

In one embodiment, a nucleic acid of the invention (e.g. a nucleic acid encoding an HT susceptibility polypeptide set forth in table 6 optionally comprising at least one polymorphism shown in tables 2 through 11 ; or another nucleic acid that encodes an HT susceptibility polypeptide or a splicing variant, derivative or fragment thereof, can be used, either alone or in a pharmaceutical composition as described above. For example, an HT risk gene or a cDNA encoding an HT susceptibility polypeptide, either by itself or included within a vector, can be introduced into cells (either in vitro or in vivo) such that the cells produce native HT susceptibility polypeptide. If necessary, cells that have been transformed with the gene or cDNA or a vector comprising the gene or cDNA can be introduced (or re-introduced) into an individual affected with the disease. Thus, cells that in nature lack a native HT risk gene expression and activity, or have mutant HT risk gene expression and activity, or have expression of a disease-associated HT risk gene splicing variant, can be engineered to express an HT susceptibility polypeptide or an active fragment of an HT susceptibility polypeptide (or a different variant of an HT susceptibility polypeptide). In a preferred embodiment, nucleic acid encoding an HT susceptibility polypeptide, or an active fragment or derivative thereof, can be introduced into an expression vector, such as a viral vector, and the vector can be introduced into appropriate cells in an animal. Other gene transfer systems including viral and nonviral transfer systems can be used. Alternatively, nonviral gene transfer methods such as calcium phosphate coprecipitation, mechanical techniques (e.g. microinjection); membrane fusion-mediated transfer via liposomes; or direct DNA uptake, can also be used.

Alternatively, in another embodiment of the invention, a nucleic acid of the invention; a nucleic acid complementary to a nucleic acid of the invention; or a portion of such a nucleic acid (e.g. an oligonucleotide as described below) can be used in "antisense" therapy in which a nucleic acid (e.g. an oligonucleotide) that specifically hybridizes to the mRNA and/or genomic DNA of an HT risk gene is administered or generated in situ. The antisense nucleic acid that specifically hybridizes to the mRNA and/or DNA inhibits expression of the HT susceptibility polypeptide, e.g. by inhibiting translation and/or transcription. Binding of the antisense nucleic acid can be by conventional base pair complementarity, or for example in the case of binding to DNA duplexes, through specific interaction in the major groove of the double helix.

An antisense construct of the present invention can be delivered, for example, as an expression plasmid as described above. When the plasmid is transcribed in the cell it produces RNA that is complementary to a portion of the mRNA and/or DNA which encodes an HT susceptibility polypeptide. Alternatively, the antisense construct can be an oligonucleotide probe that is generated ex vivo and introduced into cells; it then inhibits expression by hybridizing with the mRNA and/or genomic DNA of an HT risk gene. In one embodiment, the oligonucleotide probes are modified oligonucleotides that are resistant to endogenous nucleases, e.g. exonucleases and/or endonucleases, thereby rendering them stable in vivo. Exemplary nucleic acid molecules for use as antisense oligonucleotides are phosphoramidate, phosphothioate and methylphosphonate analogs of DNA. Additionally, general approaches to constructing oligomers useful in antisense therapy are also described by van der Krol AR et al, 1988 and Stein CA and Cohen JS, 1988. With respect to antisense DNA, oligodeoxyribonucleotides derived from the translation initiation site, e.g. between the -10 and +10 regions of an HT risk gene sequence, are preferred.

To perform antisense therapy, oligonucleotides (mRNA, cDNA or DNA) are designed that are complementary to the mRNA encoding an HT susceptibility polypeptide. The antisense oligonucleotides bind to HT susceptibility mRNA transcripts and prevent translation. Absolute complementarity, although preferred, is not required. A sequence "complementary" to a portion of an RNA, as referred to herein, indicates that a sequence has sufficient complementarity to be able to hybridize with the RNA forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid, as described in detail above. Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA it may contain and still form a stable duplex (or triplex, as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures.

The oligonucleotides used in antisense therapy can be DNA, RNA, or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotides can be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule, hybridization, etc. The oligonucleotides can include other appended groups such as peptides (e.g. for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (Letsinger RL et al, 1989; Lemaitre M et al, 1987) or the blood-brain barrier (Jaeger LB and Banks WA, 2004), or hybridization- triggered cleavage agents (van der Krol AR et al, 1988) or intercalating agents. (Zon G, 1988). To this end, the oligonucleotide may be conjugated to another molecule (e.g. a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent).

The antisense molecules are delivered to cells that express an HT risk gene in vivo. A number of methods can be used for delivering antisense DNA or RNA to cells; e.g. antisense molecules can be injected directly into the tissue site, or modified antisense molecules, designed to target the desired cells (e.g. antisense linked to peptides or antibodies that specifically bind receptors or antigens expressed on the target cell surface) can be administered systematically. Alternatively, in a preferred embodiment, a recombinant DNA construct is utilized in which the antisense oligonucleotide is placed under the control of a strong promoter (e.g. pol III or pol II). The use of such a construct to transfect target cells in the patient results in the transcription of sufficient amounts of single stranded RNAs that will form complementary base pairs with the endogenous HT risk gene transcripts and thereby prevent translation of the HT susceptibility mRNA. For example, a vector can be introduced in vivo such that it is taken up by a cell and directs the transcription of an antisense RNA. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art and described above. For example, a plasmid, cosmid, YAC or viral vector can be used to prepare the recombinant DNA construct that can be introduced directly into the tissue site. Alternatively, viral vectors can be used which selectively infect the desired tissue, in which case administration may be accomplished by another route (e.g. systemically).

An endogenous HT risk gene expression can be also reduced by inactivating or "knocking out" an HT risk gene or its promoter using targeted homologous recombination (Smithies O et al, 1985; Thomas KR and Capecchi MR, 1987; Thompson S et al, 1989). For example, a mutant, non-iunctional HT risk gene (or a completely unrelated DNA sequence) flanked by DNA homologous to the endogenous HT risk gene (either the coding regions or regulatory regions of an HT risk gene) can be used, with or without a selectable marker and/or a negative selectable marker, to transfect cells that express an HT risk gene in vivo. Insertion of the

DNA construct, via targeted homologous recombination, results in inactivation of the HT risk gene. The recombinant DNA constructs can be directly administered or targeted to the required site in vivo using appropriate vectors, as described above. Alternatively, expression of nonmutant HT risk gene can be increased using a similar method: targeted homologous recombination can be used to insert a DNA construct comprising a nonmutant, functional HT risk gene (e.g. any gene shown in table 6 that may optionally comprise at least one polymorphism shown in tables 2 through 11), or a portion thereof, in place of a mutant HT risk gene in the cell as described above. In another embodiment, targeted homologous recombination can be used to insert a DNA construct comprising a nucleic acid that encodes an HT susceptibility polypeptide variant that differs from that present in the cell.

Alternatively, an endogenous HT risk gene expression can be reduced by targeting deoxyribonucleotide sequences complementary to the regulatory region of an HT risk gene (i.e. the HT risk gene promoter and/or enhancers) to form triple helical structures that prevent transcription of an HT risk gene in target cells in the body (Helene C, 1991 ; Helene C et al, 1992; Maher LJ, 1992). Likewise, the antisense constructs described herein can be used in the manipulation of tissue, by antagonizing the normal biological activity of one of the HT proteins, e.g. tissue differentiation both in vivo and for ex vivo tissue cultures. Furthermore, the anti-sense techniques (e.g. microinjection of antisense molecules, or transfection with plasmids whose transcripts are anti-sense with regard to an HT mRNA or gene sequence) can be used to investigate the role of an HT risk gene in developmental events, as well as the normal cellular function of an HT risk gene in adult tissue. Such techniques can be utilized in cell culture, but can also be used in the creation of transgenic animals. In yet another embodiment of the invention, other HT therapeutic agents as described herein can also be used in the treatment or prevention of HT. The therapeutic agents can be delivered in a composition, as described above, or by themshelves. They can be administered systemically, or can be targeted to a particular tissue. The therapeutic agents can be produced by a variety of means including chemical synthesis; recombinant production; in vivo production, e.g. a transgenic animal (Meade H et al, 1990) and can be isolated using standard means such as those described herein.

A combination of any of the above methods of treatment (e.g. administration of non-mutant HT susceptibility polypeptide in conjunction with antisense therapy targeting mutant HT susceptibility mRNA; administration of a first splicing variant encoded by an HT risk gene in conjunction with antisense therapy targeting a second splicing encoded by an HT risk gene), can also be used.

The invention will be further described by the following nonlimiting examples. The teachings of all publications cited herein are incorporated herein by reference in their entirety.

EXPERIMENTAL SECTION

East Finnish HT Patients and Phcnotypc Characterization

The subjects were participants of the Kuopio Ischaemic Heart Disease Risk Factor Study (KIHD), which is an ongoing prospective population-based study designed to investigate risk factors for chronic diseases, including HT and CVD, in middle-aged men (Salonen JT 1988, Salonen JT et al 1998, 1999, Tuomainen T-P et al 1999). The study population was a random age-stratified sample of men living in Eastern Finland who were 42, 48, 54 or 60 years old at baseline examinations in 1984-1989. A total of 2682 men were examined during 1984-89. The male cohort was complemented by a random population sample of 920 women first examined during 1998-2001, at the time of the 11-year follow up of the male cohort. The recruitment and examination of the subjects has been described previously in detail (Salonen JT, 1988). The University of Kuopio Research Ethics Committee approved the study. All participants gave their written informed consent.

The analyses are based on logistic modeling in a case-control set of 81 cases with HT (SBP 140 mmHg or more or DBP 90 mmHg or more or antihypertensive medication) and HT in either sibling or parent, and 82 controls who had neither HT nor family history of HT, both from the KIHD cohort. Three of the subjects (two cases, one control) were women, 160 were men. Thirty-eight of the 81 cases had antihypertensive medication at the time of BP measurements in the KIHD baseline examination.

HT was defined as either systolic BP (SBP) >140 mmHg or diastolic BP (DBP) >90 mmHg or antihypertensive medication. Both BPs were measured in the morning by a nurse with a random-zero mercury sphygmomanometer. The measuring protocol included three measurements in supine, one in standing and two in sitting position with 5 -minutes intervals. The mean of all six measurements were used as SBP and DBP (Salonen JT et al, 1998). The family history of HT was defined positive, if either father, the mother or a sibling of the study subject had reported a history or prevalent hypertension. Table 1. Selected characteristics of the cases and controls

Hypertensive cases (n=81) Normotensive controls (n=82)

Mean Min Max Mean Min Max

Age (years) 54.6 42.1 71.9 54.6 42.2 61.1

Cigarettes/day 5.3 0 40 7.4 0 40

S-Cholesterol (mmoi/L) 6.2 3.8 9.1 6.0 3.2 8.7

S-HDL-Chol (mmol/L) 1.21 0.82 2.15 1.34 0.76 2.77

B-GluCOSe (mmol/L) 5.13 3.3 12.6 4.55 3.5 5.9

S-Insulin (U/L) 14.7 4.7 59.6 9.33 1.7 22.5

Mean SBP (mmHg) 140.0 110.0 182.33 124.5 99.0 148.33

Mean DBP (mmHg) 92.1 63.3 122.3 81.3 66.0 94.3

In table 1 selected characteristics of the cases and controls are summarized. Age and tobacco smoking were recorded on a self-administered questionnaire checked by an interviewer. Fasting blood glucose was measured using a glucose dehydrogenase method after precipitation of proteins by trichloroacetic acid. Serum insulin was determined with a Novo Biolabs radioimmunoassay kit (Novo Nordisk). HDL fractions were separated from fresh serum by combined ultracentrifugation and precipitation. The cholesterol contents of lipoprotein fractions and serum triglycerides were measured enzymatically. Fibrinogen was measured based on the clotting of diluted plasma with excess thrombin.

Adulthood socioeconomical status (SES) is an index comprised of measures of education, occupation, income and material living conditions. The scale is inverse, low score corresponding to high SES. These data have been collected by a self administered questionnaire.

Serum ferritin was assessed with a commercial double antibody radioimmunoassay (Amersham International, Amersham, UK). Lipoproteins, including high density lipoprotein (HDL) and low density lipoprotein (LDL), were separated from fresh serum samples by ultracentrifugation followed by direct very low density lipoprotein (VLDL) removal and LDL precipitation (Salonen et al 1991). Cholesterol concentration was then determined enzymically. Serum C-reactive protein was measured by a commercial high-sensitive immunometric assay (Immulite High Sensitivity CR Assay, DPC, Los Angeles).

Genomic DNA isolation and quality testing

High molecular weight genomic DNA samples were extracted from frozen venous whole blood using standard methods, and dissolved in standard TE buffer. The quantity and purity of each DNA sample was evaluated by measuring the absorbance at 260 and 280 nm and integrity of isolated DNA samples was evaluated with 0.9% agarose gel electrophoresis and Ethidiumbromide staining. A sample was qualified for genome wide scan (GWS) analysis if the A260/A280 ratio was >1.7 and the average size of isolated DNA was over 20 kb in agarose gel electrophoresis. Before GWS, analysis samples were diluted to a concentration of 50 ng/μl in reduced EDTA TE buffer (TEKnova). Genome-Wide Scan

Genotyping of SNP markers was performed using the technology access version of Affymetrix GeneChip® human mapping 100k system. The assay consisted of two arrays, Xba and Hind, which were used to genotype over 126,000 SNP markers from each DNA sample. The assays were performed according to the instructions provided by the manufacturer. A total of 250 ng of genomic DNA was used for each individual assay. The DNA sample was digested with either Xba I or Hind III enzyme (New England Bio labs, NEB) in the mixture of NE Buffer 2 (1 x; NEB), bovine serum albumin (1 x; NEB), and either Xba I or Hind III (0,5 U/ μl; NEB) for 2h at +37°C followed by enzyme inactivation for 20 min at +70°C. Xba I or Hind III adapters were then ligated to the digested DNA samples by adding Xba or Hind III adapter (0,25 μM, Affymetrix), T4 DNA ligase buffer (1 x; NEB), and T4 DNA ligase (250 U; NEB). Ligation reactions were allowed to proceed for 2h at +16°C followed by 20 min incubation at +70°C. Each ligated DNA sample was diluted with 75 μl of molecular biology- grade water (BioWhittaker Molecular Applications/Cambrex).

Diluted ligated DNA samples were subjected to four identical 100 μl volume polymerase chain reactions (PCR) by implementing a 10 μl aliquot of DNA sample with Pfx Amplification Buffer (1 x; Invitrogen), PCR Enhancer (1 x; Invitrogen), MgSO₄ (1 mM; Invitrogen), dNTP (300 μM each; Takara), PCR primer (1 μM; Affymetrix), and Pfx Polymerase (0,05 U/μl; Invitrogen). The PCR was allowed to proceed for 3 min at +94°C, followed by 30 cycles of 15 sec at +94°C, 30 sec at +60°C, 60 sec at +68°C, and finally for the final extension for 7 min at +68°C. The performance of the PCR was checked by standard 2% agarose gel electrophoresis in 1 x TBE buffer for Ih at 120V. PCR products were purified according to the Affymetrix manual using MinElute 96 UF PCR Purification kit (Qiagen) by combining all four PCR products of an individual sample into the same purification reaction. The purified PCR products were eluted with 40 μl of EB buffer (Qiagen), and the yields of the products were measured at the absorbance 260 nm. A total of 40 μg of each PCR product was then subjected to fragmentation reaction consisting of 0.2 U/μl fragmentation reagent (Affymetrix) in Ix Fragmentation Buffer. The fragmentation reaction was allowed to proceed for 35 min at +37°C followed by 15 min incubation at +95°C for enzyme inactivation. Completeness of fragmentation was checked by running an aliquot of each fragmented PCR product in 4% agarose 1 x TBE (BMA Reliant precast) for 30-45 min at 120V.

Fragmented PCR products were then labeled using 1 x Terminal Deoxinucleotidyl Transferase (TdT) buffer (Affymetrix), GeneChip DNA Labeling Reagent (0.214 mM; Affymetrix), and TdT (1,5 U/μl; Affymetrix) for 2h at +37°C followed by 15 min at +95°C. Labeled DNA samples were combined with hybridization buffer consisting of 0.056 M MES solution (Sigma), 5% DMSO (Sigma), 2.5 x Denhardt's solution (Sigma), 5.77 mM EDTA (Ambion), 0.115 mg/ml Herring Sperm DNA (Promega), 1 x Oligonucleotide Control reagent (Affymetrix), 11.5 μg/ml Human CoM (Invitrogen), 0.0115% Tween-20 (Pierce), and 2.69 M Tetramethyl Ammonium Chloride (Sigma). DNA-hybridization buffer mix was denatured for 10 min at +95°C, cooled on ice for 10 sec and incubated for 2 min at +48°C prior to hybridization onto corresponding Xba or Hind GeneChip® array. Hybridization was completed at +48°C for 16-18 h at 60 rpm in an Affymetrix GeneChip Hybridization Oven. Following hybridization, the arrays were stained and washed in GeneChip Fluidics Station 450 according to fluidics station protocol Mappingl0Kvl_450 as recommended by the manufacturer. Arrays were scanned with GeneChip 3000 Scanner and the genotype calls for each of the SNP markers on the array were generated using Affymetrix Genotyping Tools (GTT) software. The confidence score in SNP calling algorithm was adjusted to 0.20.

Initial SNP selection for statistical analysis

Prior to the statistical analysis, SNP quality was assessed on the basis of three values: the call rate (CR), minor allele frequency (MAF), and Hardy- Weinberg equilibrium (H-W). The CR is the proportion of samples genotyped successfully. It does not take into account whether the genotypes are correct or not. The call rate was calculated as: CR = number of samples with successful genotype call / total number of samples. The MAF is the frequency of the allele that is less frequent in the study sample. MAF was calculated as: MAF = min(p , q), where p is frequency of the SNP allele 'A' and q is frequency of the SNP allele 'B'; p = (number of samples with "AA"-genotype + 0.5*number of samples with "AB"-genotype) / total number of samples with successful genotype call; q = 1 - p. SNPs that are homozygous (MAF=O) cannot be used in genetic analysis and were thus discarded. H-W equilibrium is tested for controls. The test is based on the standard Chi-square test of goodness of fit. The observed genotype distribution is compared with the expected genotype distribution under H-W equilibrium. For two alleles this distribution is p², 2pq, and q² for genotypes 'AA', 'AB' and 'BB', respectively. If the SNP is not in H-W equilibrium it can be due to genotyping error or some unknown population dynamics (e.g. random drift, selection).

Only the SNPs that had CR > 50%, MAF > 1%, and were in H-W equilibrium (Chi-square test statistic < 23.93) were used in the statistical analysis. A total of 107,895 SNPs fulfilled the above criteria and were included in the statistical analysis.

Statistical Methods

Single SNP analysis

Differences in allele distributions between cases and controls were screened for all 107,895 SNPs. The screening was carried out using the standard Chi-square independence test with 1 df (allele distribution, 2x2 table). SNPs that gave a P-value less than 0.005 (Chi-square distribution with 1 df of 7.88 or more) were considered as statistically significant and selected for further analysis. There were 529 SNPs that fulfilled this criterium.

Haplotype analysis

The data set was analyzed with a haplotype pattern mining algorithm either with HPM-G software (Sevon P et al, 2004) or with HPM software (Toivonen HT et al, 2000). For HPM software, genotypes must be phase known to determine which alleles come from the mother and which from the father. Without family data, phases must be estimated based on population data. We used HaploRec-program (Eronen L et al, 2004) to estimate the phases. HPM-G and HPM are very fast and can handle a large number of SNPs in a single run

The difference between HPM and HPM-G is that HPM-G can use phase unknown genotypic data and HPM uses phase known (or estimated by HaploRec or similar program) data. HPM- G finds all haplotype patterns that fit the genotype configuration. For phase-known data HPM finds all haplotype patterns that are in concordance with the phase configuration. The length of the haplotype patterns can vary. As an example, if there are four SNPs and an individual has alleles A T for SNPl, C C for SNP2, C G for SNP3, and A C for SNP4, then HPM-G considers haplotype patterns (of length 4 SNPs): ACCA, TCGC, TCCA, ACGC, ACGA, TCCC, TCGA, ACCC. HPM considers only haplotype patterns that are in concordance with the estimated phase (done by HaploRec). If the estimated phase is ACGA (from the mother/lather) and TCCC (from the father/mother) then HPM considers only two patterns (of length 4 SNPs): ACGA and TCCC. A SNP is scored based on the number of times it is included in a haplotype pattern that differs between cases and controls (a threshold Chi-square value can be selected by the user). Significance of the score values is tested based on permutation tests.

Several parameters can be modified in the HPM-G and HPM programs including the Chi- square threshold value (-x), the maximum haplotype pattern length (-1), the maximum number of wildcards that can be included in a haplotype pattern (-w), and the number of permutation tests in order to estimate the P-value (-p). Wildcards allow gaps in haplotypes. The HPM-G program was run with the following parameter settings: haplotype analysis with 5 SNPs (-x9 -15 -wl -plOOOO). HaploRec+ HPM was run with the following parameter settings: haplotype analysis with 5 SNPs (-x9 -15 -wl -plOOOO). HPM-G analysis was based on the order of the SNP given in dbSNP122 and HaploRec+HPM was based on the order of the SNP given in dbSNP123. Based on 10,000 replicates (-plOOOO) in the HPM-G analyses 570 SNPs were significant at P-value less than 0.005 and 642 SNPs were significant in the HPM analysis.

Definition of terms used in the haplotype analysis results The term "haplotype genomic region" or "haplotype region" refers to a genomic region that has been found significant in the haplotype analysis (HPM, HPMG or similar statistical method/program). The haplotype region is defined as lOOKbp up/downstream from the physical position of the first/last SNP that was included in the statistical analysis (haplotype analysis) and was found statistically significant. This region is given in base pairs based on the given genome build e.g. SNP physical position (base pair position) according to NCBI Human Genome Build 35.

The term "haplotype" as described herein, refers to any combination of alleles e.g. A T C C that is found in the given genetic markers e.g rs2221511, rs4940595, rsl522723, rsl395266. A defined haplotype gives the name of the genetic markers (dbSNP rs-id for the SNPs) and the alleles. As it is recognized by those skilled in the art, the same haplotype can be described differently by determining alleles from different strands e.g. the haplotype rs2221511, rs4940595, rsl522723, rsl395266 (A T C C) is the same as haplotype rs2221511, rs4940595, rsl522723, rsl395266 (T A G G) in which the alleles are determined from the other strand, or haplotype rs2221511, rs4940595, rsl522723, rsl395266 (T T C C), in which the first allele is determined from the other strand.

The haplotypes described herein, e.g. having markers such as those shown in tables 3, 4, 5, 7 and 8, are found more frequently in individuals with HT than in individuals without HT. Therefore, these haplotypes have predictive value for detecting HT or a susceptibility to HT in an individual. Therefore, detecting haplotypes can be accomplished by methods known in the art for detecting sequences at polymorphic sites.

It is understood that the HT associated at-risk alleles and at-risk haplotypes described in this invention may be associated with other "polymorphic sites" located in HT associated genes of this invention. These other HT associated polymorphic sites may be either equally useful as genetic markers or even more useful as causative variations explaining the observed association of at-risk alleles and at-risk haplotypes of this invention to HT. Multivariate modeling

For modeling for hypertension as a binary outcome, the 734 strongest predicting SNP markers from the individual SNP analysis and 14 strongest haplotypes from the HPM analysis were tested for entry to the model. These were recoded as 0, if homozygote of the major allele, 1, if heterozygote and 2, if homozygote of the minor allele. A multivariate binary logistic iunction regression analysis was used to: a) Find the SNPs that were most predictive of HT and b) Construct a multivariate model that predicted HT the strongest. A forward step-up model construction was used with p- value to enter of 0.01 and p- value to exclude from the model of 0.02. The predictivity of the models was estimated by two methods: the Nagelkerke R square and the reclassification of the subjects to cases and controls on the basis of the logistic model contracted. The predicted probability used as cut-off was 0.5. A data reduction analysis was carried out by step-down and step-up logistic modeling.

Multivariate least-squares linear regression modeling was used to identify the SNP markers that were most strongly associated with the mean systolic and diastolic blood pressure as quantitative traits. A forward step-up model construction was used with p-value to enter of 0.001 and p-value to exclude from the model of 0.005.

The statistical software used was SPSS for Windows, version 11.5.

Results

In table 2 are summarized the characteristics of the SNP markers with the strongest association with HT in the individual marker analysis (n = 529). SNP identification numbers are according to NCBI dbSNP database build 124. Physical positions of SNP markers are according to NCBI Human Genome Build 35. Gene locus as reported by NCBI dbSNP database build 124. SNP flanking sequence provided by Affymetrix "csv" commercial access Human Mapping IOOK array annotation files. In table 3 are summarized the characteristics of the haplotype genomic regions with the strongest association with HT in the HPM-G analysis with 5 SNPs. SNP identification numbers are according to NCBI dbSNP database build 124. Physical positions of SNP markers are according to NCBI Human Genome Build 35. Associated genes are those genes positioned within lOOKbp up/downstream from the physical position of the SNPs bordering the haplotype genomic region found using NCBI Map Viewer, based on NCBI Human

Genome Build 35. SNP flanking sequence provided by Affymetrix "csv" commercial access Human Mapping IOOK array annotation files.

In table 4 are summarized the characteristics of the haplotype genomic regions with the strongest association with HT in the HaploRec + HPM analysis with 5 SNPs. SNP identification numbers are according to NCBI dbSNP database build 124. Physical positions of SNP markers are according to NCBI Human Genome Build 35. Associated genes are those genes positioned within lOOKbp up/downstream from the physical position of the SNPs bordering the haplotype genomic region found using NCBI Map Viewer, based on NCBI Human Genome Build 35. SNP flanking sequence provided by Affymetrix "csv" commercial access Human Mapping IOOK array annotation files.

In table 5 are listed haplotype blocks with the strongest association with HT based on HaploRec + HPM analysis (n = 14). SNP identification numbers are according to NCBI dbSNP database build 124.

In table 6 are listed all genes found associated with HT according to point wise and haplotype analyses (n = 722). Names of genes are according to HUGO Gene Nomenclature Committee (HGNC).

In table 7 are listed the SNP-markers and haplotypes that best predicted risk of familial HT in a multivariate logistic model. SNP identification numbers are according to NCBI dbSNP database build 124. The 8-variable model predicts 91.4% of familial HT correctly. The statistics are based on 81 KIHD participants who were hypertensive in the KIHD baseline examination (SBP 140 mmHg or more or DBP 90 mmHg or more or antihypertensive medication) and either sibling or parent had HT and 82 KIHD participants who neither had HT at KIHD baseline nor had family history of HT. The controls were matched according to age. In table 8 are listed the SNP-markers, haplotypes and phenotypic data that best predicted risk of iamilial HT in a multivariate logistic model. SNP identification numbers are according to NCBI dbSNP database build 124. The 12-variable model, including two haplotypes, five SNP markers and two phenotypic variables, predicted 87.1% of familial HT correctly. The strongest loci pinpointed by the multivariate logistic models were SERPINs B3, B4, B7 and BI l and EPCl, ORl J4 and LOC401406, 439953, 441550 and 441551.

Table 9 presents a multivariate linear regression model of the strongest SNPs predicting the mean systolic and diastolic BP. Tables 10 and 11 show the means and standard deviations of the mean systolic (Table 10) and diastolic (Table 11) BP in the genotypes of the strongest SNP markers, which predicted BP the strongest in both the univariate single-SNP, haplotype and multivariate analyses. The rank order of markers is according to the strength of association with the diastolic BP. The strongest pinpointed genes concerning BP as quantitative trait were SERPINS B3, B7 and Bl 1, A100A7, S100A6, FARSl, SPOCK3, and TLLl.

Implications and Conclusions

We have found 1365 SNP markers associated with the risk of HT and/or blood pressure in a population-based set of familial cases and healthy controls without family history. Of these, 529 were identified in the analysis of individual SNPs and 1080 in haplotype pattern mining or haplotype analysis. Of the 1365 markers, 244 predicted HT in both types of statistical analysis. We further identified SNP markers, which predict in a multivariate logistic model virtually fully the development of HT. The results of the point wise and haplotype analyses identified a total of 722 genes associated with HT, of which 330 genes had at least one of the 1365 SNP markers physically linked to the gene. Thus, we have discovered a total of 722 HT genes, in which any genetic markers can be used to predict HT, and thus these markers can be used as part of molecular diagnostic tests of HT predisposition. In addition, we have disclosed a set of 1365 SNP markers which are predictive of HT. The markers can also be used as part of pharmacogenetic tests predicting the efficacy and adverse reactions of antihypertensive agents and compounds. The genes discovered are also targets to new therapies of HT, such as drugs. Other therapies are molecular, including gene transfer. The new genes can also be used to develop and produce new transgenic animals for studies of antihypertensive agents and compounds.

While this invention has been particularly shown and described with reference to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention as defined by the appended claims.

Table 2. SNP markers with the strongest association with HT in the individual marker analysis (n = 529) .

d G S C A A M A O I b e e h 1 1 i 1 d I

S n q r 1 1 n 1 d I

N e U O e e O e s I

P e m 1 1 r 1

1 n O e e e r I r O C S A a I

S C e O A B 1 X t I

U m 1 2 i I

I S I e e o I

D D 1 e rsl395266 SERPINBIl 476 18 C T C 20.29 0.23 rs931850 None 1303 18 A G G 18.10 0.27 rsl386483 TPH2 470 12 A G A 17.88 2.61 rsl386485 TPH2 471 12 A C C 17.80 2.84 rsl0506395 None 246 12 C T T 17.04 0.29 rsl410425 None 491 13 C T T 16.89 0.11 rsl0500913 None 186 11 A G A 16.68 3.02 rsl935659 None 637 1 A G G 16.53 0.36 rsl318392 ORlJ4 438 9 A G G 15.69 2.50 rs6428195 None 1030 1 C G C 15.39 0.39 rs7112382 None 1105 11 A G A 15.28 2.64 rs2469828 None 792 17 C T T 14.97 4.59 rsl386486 TPH2 472 12 C T T 14.87 2.46 rsl0513404 NT 008470 343 9 C T C 14.74 0.32 rslO515283 None 356 5 C T C 14.55 5.73 rsl884389 None 618 20 C T T 14.21 2.66 rsl0494019 None 124 1 A T T 14.03 0.33 rs4756190 None 965 11 A G G 14.03 2.38 rslO517655 PDGFC 387 4 A G G 13.88 10.16 rsll57122 GABRAl 417 5 C T C 13.83 0.22 rs668498 FBXOl8 1058 10 C T T 13.74 2.60 rs473232 COL24A1 959 1 C T C 13.72 0.34 rsl986902 None 653 1 A G A 13.72 2.83 rs627777 LOC388458 1026 18 C T T 13.70 0.41 rs9315991 None 1294 13 G T T 13.68 4.55 rs9299552 PCDH15 1267 10 C T T 13.66 0.39 rs868299 None 1233 15 C T C 13.65 2.37 rs4845303 None 980 1 A T T 13.59 2.64 rs6935462 None 1082 6 A T A 13.51 6.29 rs7536312 None 1161 1 A G A 13.26 0.30 rs7521497 None 1159 1 C T T 13.25 2.86 rs270454 None 805 4 A G A 13.20 0.36 rsl374038 None 465 5 A C C 13.03 3.56 rs3213829 ANK3 869 10 G T G 12.94 2.30 rsl0494628 None 128 1 C T C 12.86 0.43 rs2885625 LOC145497 839 14 A G G 12.82 0.29 rs2476847 SEC5L1 793 6 C T T 12.77 2.26 rsl521409 None 544 3 A G G 12.77 9.50 rs274460 None 810 12 A G G 12.72 0.35 rsl0483354 STRN3 21 14 A C A 12.62 0.00 rs5957594 None 1010 X G T G 12.61 0.00 rsl394380 None 475 12 A G G 12.59 0.37 rsl391130 None 473 12 A G G 12.58 0.36 rsl842328 None 609 12 C T C 12.56 0.34 rs387619 None 898 11 A G A 12.56 2.22 rs9291304 GABRBl 1259 4 A G A 12.53 0.06 rslO514437 WWOX 349 16 C T T 12.53 5.88 rs2209672 None 730 10 A G A 12.49 2.26 rsl912914 None 628 1 A G G 12.45 0.41 rs2416472 None 781 5 A G G 12.44 0.42 rsl837426 None 607 2 A G G 12.44 0.43 rs301748 USH2A 855 1 A G A 12.31 0.00 rsl335311 None 447 10 C G C 12.31 2.29 rslO499961 None 175 7 C T C 12.27 3.24 rsl866565 None 616 2 C T T 12.25 0.40 rs2060688 None 682 8 C T T 12.23 0.35 rs951573 UTRN 1328 6 A G G 12.20 2.22 rs572166 None 1008 18 A G G 12.17 2.32 rsl0493787 COL24A1 122 1 C G C 12.17 0.32 rslO514689 None 352 3 A G G 12.15 2.86 rsl0494663 None 134 1 A G A 12.14 0.29 rsl997454 None 656 2 A G G 12.12 0.31 rsl0499538 DNAHIl 171 7 A G A 12.00 0.06 rs474106 COL24A1 961 1 A G A 11.96 0.35 rs916853 None 1240 7 C T T 11.93 0.29 rsl0492479 None 112 13 A G G 11.91 0.24 rs4680266 KCNABl 955 3 C T C 11.83 2.18 rs4691246 None 956 4 C T C 11.82 2.36 rs9289965 KCNABl 1257 3 C G C 11.82 2.17 rslO519989 MGC14798 397 15 A C A 11.82 0.07 rsl0485822 SNPH 49 20 C G C 11.82 3.90 rs9298688 None 1266 9 C T T 11.81 0.39 rs892271 None 1236 12 A G G 11.81 0.11 rs29800 None 849 5 A C C 11.71 0.38 rsl598978 None 575 12 A G A 11.70 2.22 rsl0494659 None 130 1 C T C 11.69 0.27 rslO515461 None 362 5 A G A 11.68 0.28 rs9283795 CMYA5 1248 5 C T T 11.67 3.39 rs503208 None 989 11 C G G 11.66 2.32 rsl578704 None 568 1 A G A 11.63 0.43 rs715732 None 1114 8 C G G 11.60 0.24 rs6469061 None 1038 8 C T T 11.53 0.00 rsl578705 None 569 1 A G G 11.51 0.45 rs716193 NPAS3 1117 14 G T T 11.49 2.28 rs9328130 None 1314 6 C T C 11.46 3.37 rsl487275 TPH2 531 12 A C C 11.45 2.20 rslO488914 None 76 4 A G A 11.42 0.11 rsl521770 None 545 8 C T C 11.42 0.44 rs6976996 CNTNAP2 1089 7 A G A 11.42 2.34 rsll73476 None 424 5 G T G 11.40 2.16 rslO486619 None 58 7 C T C 11.31 2.55 rs2105233 None 696 1 A G G 11.31 2.89 rs921382 None 1243 8 C G C 11.28 0.35 rsl452356 FLJ31810 513 9 C T C 11.25 2.16 rs956316 None 1336 7 C T C 11.25 0.43 rs7524749 SSBP3 1160 1 C T T 11.22 3.11 rsl913157 None 630 3 C G G 11.22 0.44 rsl0499668 PKDlLl 172 7 A G G 11.21 2.13 rsl614336 None 582 5 A C A 11.18 2.17 rs477862 COL24A1 972 1 C T T 11.14 0.39 rsl912941 None 629 1 C T C 11.13 0.44 rs2198044 None 729 8 A G A 11.09 0.38 rs7156058 None 1113 14 A C A 11.09 2.90 rslO511192 LOC152225 314 3 C T T 11.09 2.57 rsl0507107 EB-I 257 12 C G C 11.07 0.40 rsl0505140 None 238 8 A G A 11.04 0.35 rs6601146 None 1054 5 G T G 11.04 2.33 rs2861215 None 832 2 C T C 11.03 2.19 rsl0482862 None 19 21 A G G 11.03 3.19 rsl75741 None 592 X G T T 11.02 0.00 rs964888 None 1344 6 C T C 11.02 2.16 rsl649882 SPlOO 586 2 G T T 10.89 0.34 rs8047401 CDYL2 1221 16 C T T 10.84 0.41 rs2048506 None 674 4 C T T 10.84 2.12 rsl409367 None 490 1 C T C 10.79 0.00 rs8010717 LOC388001 1217 14 C T C 10.76 2.14 rs792762 None 1206 17 A C A 10.74 2.11 rs2175550 None 724 1 A G G 10.70 0.46 rsl391533 None 474 11 C T C 10.70 2.11 rs3856852 None 897 3 A G A 10.70 0.12 rsll60054 None 419 8 A G G 10.66 0.46 rsl882233 None 617 2 A T T 10.63 2.10 rs536617 FAT3 1001 11 C T C 10.63 2.09 rsl0488849 None 73 4 C T C 10.62 2.49 rs666899 None 1055 11 A G G 10.61 0.39 rsl376089 None 468 4 A G A 10.60 13.87 rs475553 None 964 3 C T T 10.59 0.07 rsl408356 None 486 10 A G G 10.58 3.43 rslll3983 MTHFS 413 15 G T T 10.57 2.09 rsl512828 None 538 3 A C C 10.57 0.46 rs6746500 None 1062 2 C T T 10.56 2.33 rsl430692 None 506 2 A C C 10.55 3.09 rsl0270433 None 11 7 A T A 10.51 0.24 rslO489134 None 81 1 C G C 10.47 6.23 rsl580964 None 570 12 C T T 10.47 2.08 rs2849597 PARK2 828 6 A G G 10.45 0.00 rs2279120 MATN2 751 8 C T T 10.44 5.27 rs9300909 None 1269 13 A G G 10.41 2.39 rsl281590 None 434 1 A G A 10.40 2.61 rs2417359 None 784 9 A G G 10.37 2.06 rslO484614 STXIl 35 6 C T T 10.37 3.44 rsl0491030 None 95 10 C T C 10.34 2.06 rs605627 None 1015 7 C T T 10.33 2.28 rs2222186 None 735 2 C T T 10.28 2.74 rs2121956 None 705 1 C T T 10.25 2.11 rsl0495082 None 137 1 C T C 10.25 0.47 rs9288697 ACVRl 1256 2 A C A 10.25 0.29 rs9304252 None 1277 18 A T A 10.25 4.15 rs438418 None 936 5 A G G 10.24 0.29 rsl865290 None 615 18 A T T 10.23 4.18 rsl944404 RIT2 639 18 C T C 10.21 0.35 rsl0504127 None 226 8 A G A 10.20 0.00 rsl0504596 None 228 8 C T T 10.19 0.00 rs2372643 EB-I 768 12 A G A 10.19 2.07 rsl0502283 LOC338661 202 11 C T T 10.18 0.32 rs9308066 None 1281 4 A G G 10.17 7.97 rs9321214 None 1306 6 C T C 10.15 0.40 rsl0501504 None 199 11 C T C 10.15 2.61 rsl0513802 DGKG 346 3 A T T 10.14 0.20 rs9290835 None 1258 3 A T A 10.13 2.21 rs9287120 None 1251 1 C G C 10.13 0.26 rsl0515406 None 360 5 A G G 10.12 3.40 rs2429555 None 785 17 C G C 10.11 3.81 rsl0494664 None 135 1 A C C 10.09 0.34 rs6961386 HIC 1085 7 C T T 10.07 0.26 rsl978503 None 649 18 A G G 10.06 2.85 rs3847653 None 894 12 C G C 10.03 2.41 rsl0502667 KIAA1328 209 18 C G G 10.02 0.38 rsl0502582 None 206 18 A T T 10.01 2.05 rs730694 LOC401406 1149 7 C T C 10.00 2.18 rsl0486935 None 59 7 A G A 10.00 0.31 rs9323707 LOC400234 1312 14 A G A 10.00 0.31 rs723107 None 1138 8 A G A 9.98 13.22 rsl281611 None 435 1 C T T 9.98 2.52 rs956274 None 1335 5 A C A 9.97 0.41 rs7777049 None 1190 7 A G A 9.96 2.13 rslO517654 PDGFC 386 4 G T T 9.96 5.09 rslO515622 LOC255187 364 5 G T G 9.96 2.65 rsl0510664 LOC389105 311 3 C G G 9.95 3.44 rs2173802 NPAS3 723 14 A G A 9.95 0.34 rsl423485 ADAMTS12 503 5 A G A 9.95 5.08 rs4131804 RGS7 923 1 G T T 9.91 2.45 rsl0508220 None 272 10 A G G 9.90 2.04 rs2192947 None 728 2 A G G 9.90 2.05 rsl0492232 None 109 12 C T C 9.88 3.77 rs383096 None 892 5 A G A 9.86 13.08 rs701665 None 1098 6 C T C 9.85 2.30 rs256825 SGCD 799 5 C T T 9.83 2.18 rs6879659 None 1074 5 C T T 9.80 2.81 rsl0496096 COMMDl 140 2 C G G 9.80 0.44 rsl0508229 None 274 10 A G G 9.79 0.31 rs8089921 NETOl 1223 18 C T C 9.79 2.05 rs7081811 CACNB2 1101 10 A G G 9.78 0.43 rs420350 None 929 6 A C A 9.77 2.05 rs8007568 NPAS3 1214 14 C G C 9.75 0.28 rs2381194 None 773 9 C T T 9.74 0.34 rs9741 PSD3 1350 8 C T C 9.72 0.43 rsl514471 LOC152225 540 3 A G G 9.71 2.40 rslO512853 None 339 5 C T C 9.71 0.08 rs895800 None 1237 1 A T A 9.70 0.48 rs542873 DABl 1002 1 A G A 9.69 0.49 rslO515314 None 357 5 C T C 9.66 0.13 rsl0508223 None 273 10 C T C 9.66 2.05 rs6990997 ZFPM2 1091 8 C T C 9.64 0.30 rs6832042 None 1071 4 A G G 9.63 0.45 rs2089918 None 694 1 A G A 9.60 2.87 rs2113030 None 700 5 A G G 9.59 0.13 rslO515942 A0X2 371 2 A G A 9.59 2.68 rsl827309 None 600 21 A G G 9.58 2.14 rs741283 MY03B 1154 2 G T T 9.58 0.29 rsl0499728 None 174 7 A G A 9.58 0.46 rslO41778 None 18 21 A G G 9.57 2.18 rsl446255 None 510 9 C T T 9.57 0.23 rsl0485601 TMC2 44 20 A G A 9.57 0.35 rs2077833 None 689 12 A G A 9.56 0.45 rsl29752 FBLNl 437 22 A G A 9.56 0.08 rs293443 None 847 4 C T C 9.56 0.36 rs285790 None 829 8 C T C 9.55 0.08 rsl0270360 LOC401406 10 7 A G G 9.55 2.04 rsl0513702 None 345 3 A G G 9.50 2.03 rsl0497952 ERBB4 159 2 C T T 9.49 2.29 rsl0516740 None 378 4 A G G 9.49 0.00 rsl529647 None 550 7 A G G 9.48 2.95 rsl362828 None 458 3 C G C 9.48 2.06 rs6981960 None 1090 8 C T T 9.48 2.33 rsl992906 None 655 5 A G G 9.46 7.64 rsl928326 None 635 1 C T C 9.42 2.06 rs607872 None 1017 7 C G C 9.42 2.19 rs953160 None 1330 7 A G G 9.42 0.46 rs360559 CRISP2 877 6 G T T 9.40 2.09 rslO488631 None 68 7 C T C 9.39 0.25 rs4719652 None 958 7 C T T 9.39 0.49 rsl0520170 None 398 2 C T C 9.39 2.54 rslO511824 FLJ31810 323 9 A G A 9.38 2.92 rsl0501243 None 190 11 A G A 9.38 0.21 rs8092610 None 1225 18 C T T 9.38 0.21 rsl513120 LOC152225 539 3 C T C 9.38 2.20 rs9316871 None 1298 13 C T C 9.37 2.36 rsl0501242 None 189 11 A G A 9.37 0.21 rslO516731 None 377 4 A G A 9.37 0.00 rs3906713 None 904 7 A T A 9.36 4.31 rs997661 KIAA1328 1362 18 C T T 9.36 0.39 rs2089273 None 693 4 A T A 9.34 0.39 rs960791 LOC389938 1339 10 A T T 9.34 2.11 rs7176436 ADAMlO 1122 15 A G G 9.34 0.38 rslO512731 LOC389285 338 5 C G C 9.33 2.55 rs4775086 ADAMlO 970 15 C T T 9.31 0.48 rs4086865 None 913 11 C T T 9.29 0.17 rsl0506726 None 253 12 A G A 9.29 0.29 rsl0490758 None 93 2 C G G 9.29 0.43 rsl0488777 None 71 11 C T C 9.29 3.92 rs4884068 None 984 13 C G G 9.28 2.15 rs802296 TCBAl 1220 6 A G A 9.28 2.17 rs572241 FAT3 1009 11 C T C 9.27 2.00 rs2168792 None 721 19 C G C 9.26 0.00 rs344924 LOC391046 872 1 A G G 9.25 2.74 rsl438048 PDEIlA 508 2 A C A 9.25 2.78 rs716376 None 1118 5 A G G 9.24 2.53 rsl0488747 LOC260340 69 11 C G C 9.22 0.45 rsl0490757 None 92 2 C T C 9.21 0.44 rs3897770 None 901 12 A C A 9.21 2.29 rsl544774 None 554 5 G T T 9.20 0.21 rsl0509035 None 293 10 G T G 9.19 0.49 rs6586445 None 1052 1 A C C 9.18 2.01 rs2091169 None 695 2 A G G 9.17 1.98 rs2164857 PDEIlA 719 2 A C C 9.16 2.47 rs9308440 XM_372814 1282 1 G T T 9.16 3.12 rsl550740 None 557 12 C T C 9.14 0.08 rs237112 None 767 6 C T T 9.14 2.46 rs2416863 NT 008470 782 9 C T T 9.13 0.26 rsl331772 None 445 13 A G G 9.13 0.35 rsl363522 LOC255187 460 5 C T T 9.12 2.81 rs422621 None 930 21 C T C 9.12 0.48 rs6972578 OSBPL3 1087 7 C T C 9.09 2.19 rsl0503506 None 220 8 C T C 9.09 0.36 rs747334 None 1156 10 A G G 9.08 1.97 rs342818 None 871 1 C T C 9.08 2.12 rs824848 None 1230 5 A G A 9.08 2.06 rsl0483100 DGCR2 20 22 C T C 9.07 3.38 rsl548348 NUMAl 555 11 C T T 9.07 12.23 rsl0502666 KIAA1328 208 18 C T C 9.07 0.40 rsl0502671 KIAA1328 210 18 C T T 9.07 0.40 rs2514288 None 796 11 C T C 9.07 0.46 rs9320728 None 1305 6 C T C 9.06 0.45 rsl0512709 None 337 5 A G A 9.06 2.02 rsl0498935 C6orfl57 167 6 A T T 9.06 2.96 rsl0484484 None 33 6 A G G 9.05 2.73 rsl411270 LOC138882 492 9 C G G 9.05 0.45 rs8010105 LOC388001 1216 14 A G A 9.04 1.99 rs9379628 None 1319 6 C T C 9. 04 5.75 rsl0505797 None 240 12 A G A 9. 03 0.00 rs2152634 None 714 9 C T T 9. 03 0.00 rs4766492 VPS29 968 12 A G A 9. 03 1.96 rs7085103 MY03A 1102 10 C T C 9. 03 2.02 rs2373717 None 771 11 A T T 9. 01 2.12 rs997418 None 1361 10 A G A 9. 01 0.50 rs951232 None 1327 4 C T T 9. 01 0.48 rs927348 SLC35F1 1246 6 A G G 9. 00 1.96 rsl497763 SCHIPl 533 3 C G G 8. 99 4.83 rsl0507130 DRIM 258 12 A G A 8. 98 0.34 rs2871869 None 838 1 A G A 8. 97 0.37 rsl370656 PDEIlA 463 2 A C A 8. 97 2.59 rslO512117 None 326 9 A T A 8. 97 0.50 rsl346671 None 454 11 A T T 8. 96 2.32 rs970604 DNAHIl 1348 7 A G A 8. 95 2.12 rsl959429 None 644 14 C T T 8. 92 3.07 rs4814909 None 975 20 C T T 8. 92 0.08 rsl405589 LOC402640 484 7 A G A 8. 92 0.00 rs7069564 None 1100 10 C T T 8. 92 0.31 rs891255 None 1235 2 C T T 8. 91 2.04 rs4519041 NY-BR-I 943 10 A C A 8. 91 12.03 rslO512241 None 329 9 C T T 8. 90 2.00 rs987312 None 1354 10 A G A 8. 89 2.12 rs2000112 None 660 9 C T T 8. 87 0.43 rs721599 None 1136 1 C G G 8. 86 2.03 rs948159 LOC390263 1322 11 C T C 8. 86 0.39 rsl0502774 None 213 18 G T G 8. 86 3.19 rs717293 None 1120 16 C T T 8. 85 0.50 rs2070513 None 686 21 G T T 8. 83 2.34 rsl0508731 MPP7 285 10 C T C 8. 82 2.10 rs3169160 ARRDC4 864 15 A G A 8. 81 3.38 rs3934674 None 906 4 A G A 8. 79 0.36 rs2750452 None 811 6 C G C 8. 79 2.11 rsl0521300 None 406 16 C T T 8. 78 11.87 rsl0521301 None 407 16 G T T 8. 78 11.87 rs305218 PRKCL2 858 1 C T T 8. 78 11.87 rs724417 None 1141 12 G T G 8. 78 3.85 rs9283603 None 1247 3 A G A 8. 77 2.18 rsll81875 FLJ32825 427 1 A G G 8. 77 0.28 rs4600228 None 950 11 A G A 8. 77 2.10 rsl928322 None 634 1 A G A 8. 76 2.01 rs3846211 None 893 3 A G A 8. 76 2.01 rs9332453 None 1317 9 A G A 8. 76 0.49 rslO511366 None 317 3 C T C 8. 75 7.16 rs2177520 DNAHIl 725 7 C G C 8. 74 2.10 rs2319248 None 759 4 C T T 8. 74 0.50 rsl893814 None 622 11 C T T 8. 73 2.17 rs2892734 FARPl 841 13 A G G 8. 72 1.96 rs6799641 None 1067 3 A T A 8. 72 2.56 rs2017712 None 665 21 A G G 8. 71 2.05 rsl489734 None 532 21 A G A 8. 71 0.51 rsl2654 LOC401255 432 6 C T C 8. 70 0.30 rsl969025 LOC391858 645 5 A G G 8. 70 0.47 rs382190 None 889 5 A G A 8. 68 0.08 rsl0511049 None 313 3 A G G 8. 67 0.30 rsl581413 FLJ12604 571 3 A G G 8. 67 1.96 rsl0497893 CRYGEPl 156 2 A C A 8. 66 0.51 rs2217110 C18orflO 732 18 A G G 8. 64 0.41 rs7667905 LOC339979 1176 4 A G A 8. 63 2.24 rsl0502700 None 211 18 A G A 8.63 0.24 rs4627439 None 951 18 G T T 8.63 0.24 rs251470 FLJ10904 797 5 G T T 8.63 1.96 rsl0507224 LOC390359 262 12 C T T 8.63 0.46 rs543224 None 1003 18 C T T 8.63 0.46 rs2241748 ARL4 742 7 A G A 8.62 5.48 rs2263356 None 746 9 C T T 8.62 2.33 rs935661 PRKCE 1318 2 G T T 8.61 1.97 rs2183024 None 727 9 C G C 8.61 0.38 rslO495321 SIPA1L2 138 1 A G G 8.61 4.64 rs994214 None 1357 2 C T C 8.61 1.95 rsl0507505 None 265 13 C T C 8.61 2.29 rsl0490387 LOC130576 90 2 C T T 8.61 3.30 rs361161 None 878 4 A G G 8.60 2.35 rs2394081 None 776 10 A G A 8.60 7.07 rs719639 C6orfl57 1128 6 G T G 8.59 2.18 rsl744510 None 591 6 A T A 8.59 0.45 rsl860752 None 612 7 C G C 8.58 0.48 rs2357761 None 763 6 C G G 8.58 0.48 rsl0516708 None 376 4 C T T 8.57 1.96 rslO499381 PHF14 169 7 C T T 8.57 0.39 rslO511318 None 315 3 C G C 8.56 2.71 rs3964705 LOC390561 907 15 A G G 8.56 0.43 rslO487921 None 62 7 A G A 8.56 0.38 rsl0512097 None 325 9 C T T 8.56 2.80 rsl0485602 TMC2 45 20 C T C 8.54 0.37 rs3751877 RRN3 882 16 A G G 8.54 2.72 rsl0485608 None 47 20 A G G 8.54 2.94 rs2060850 FLJ31810 683 9 A G G 8.54 1.94 rsll20712 None 416 7 C T C 8.53 1.95 rs6864370 None 1072 5 C T T 8.53 0.42 rsl0508410 LOC389938 276 10 C G G 8.53 0.09 rsl0509281 CTNNA3 298 10 C T C 8.53 0.09 rsl904641 CTNNA3 626 10 A C C 8.53 0.09 rs4102401 RRM2B 914 8 C T C 8.53 0.09 rs4404874 None 937 8 A G A 8.52 0.48 rslO496213 REGL 145 2 A C C 8.52 3.48 rsl0500296 GRLFl 180 19 C G G 8.52 0.00 rsl403105 FLJ12604 482 3 A G G 8.51 1.95 rs4129499 None 919 8 A C A 8.50 0.18 rs2252646 None 745 12 A G G 8.49 0.50 rsl61912 None 583 3 A G G 8.49 2.03 rsl0484683 None 39 6 A G G 8.49 11.67 rs802279 TCBAl 1219 6 C G C 8.48 2.40 rs6592456 NUMAl 1053 11 C T C 8.47 5.41 rs9301083 None 1273 13 A G A 8.47 1.94 rs2241443 DGKI 741 7 C T C 8.46 2.05 rslO512918 None 340 5 A G G 8.46 2.64 rsl402319 None 481 12 C T C 8.45 2.02 rsl0520415 FLJ13110 400 2 C T C 8.44 0.49 rsl0503122 None 217 18 C T T 8.44 0.22 rs966118 ASAHl 1345 8 C T T 8.43 2.02 rslO491771 None 99 9 A G A 8.43 0.51 rslO37124 ARNT2 15 15 C T T 8.43 0.32 rslO513473 None 344 9 C T T 8.42 2.39 rsl0508171 None 271 13 A G A 8.42 1.96 rslO518928 MEIS2 394 15 C T C 8.42 0.45 rsl0508412 LOC389938 278 10 C T T 8.42 1.93 rs2439538 TBC1D7 787 6 A G G 8.42 1.93 rs950171 pp9099 1326 15 C G G 8.41 1.95 rslO512629 TRAD 334 3 A T A 8.41 2.35 rs3731572 LTBPl 880 2 C T C 8.41 0.00 rslO516839 None 379 4 A C C 8.40 0.42 rs2888378 EB-I 840 12 A G A 8.40 1.92 rs4762559 EB-I 967 12 C T T 8.39 1.92 rslO491747 None 97 9 A G G 8.39 2.01 rsl561365 None 560 5 A T A 8.38 2.64 rsl0485603 TMC2 46 20 A G G 8.38 0.36 rslO519536 KIAA0882 396 4 C T T 8.36 0.42 rs4336940 None 934 10 A G G 8.36 0.51 rs964664 BAI3 1343 6 A G A 8.36 2.06 rs7908118 None 1202 10 C T T 8.35 0.50 rslO515457 KIAA1061 361 5 C T C 8.35 2.27 rsl0484858 BPAGl 40 6 C T C 8.35 0.46 rsl998570 None 659 13 A G A 8.35 2.00 rs6969674 HDAC9 1086 7 A C A 8.35 0.32 rs7763613 None 1187 6 A G G 8.35 1.91 rsl0498789 None 165 6 A G A 8.34 1.99 rsl0503493 SGCZ 219 8 G T T 8.34 3.44 rsl0503869 RBPMS 225 8 C T C 8.33 5.36 rsl0507223 LOC390359 261 12 C G G 8.32 0.46 rs9295562 LOC389370 1261 6 C T T 8.32 2.14 rsl0504702 None 230 8 A G A 8.32 0.19 rslO484126 None 31 14 C T T 8.32 5.34 rsl0487982 None 64 1 A C C 8.32 2.27 rsl498767 None 535 16 C T C 8.31 2.10 rs923312 None 1245 11 A G A 8.31 0.19 rslO515934 GORASP2 370 2 A G A 8.31 2.18 rs4073846 MAST2 911 1 C T C 8.31 1.92 rsl0485760 None 48 20 C T C 8.31 0.00 rsl407508 None 485 9 A G G 8.30 0.00 rsl455780 SIAT8B 517 15 A G A 8.30 1.91 rs4669134 None 953 2 A G A 8.30 0.49 rs2369942 None 765 12 A G A 8.30 1.96 rs2274154 None 748 6 C T T 8.29 2.78 rs6808403 None 1068 3 A G A 8.28 2.51 rs438405 RCLl 935 9 A C C 8.27 0.22 rslO515512 NDFIPl 363 5 C T C 8.25 3.69 rslll6163 LOC400019 414 12 A G G 8.24 0.35 rs340978 None 870 11 A C C 8.24 2.32 rsl0509071 None 295 10 A G A 8.23 2.18 rs719548 TLKl 1127 2 A G A 8.21 2.28 rs6490721 None 1042 13 G T G 8.21 0.00 rsl0498018 None 161 2 A G A 8.21 2.60 rsl0503837 None 224 8 C G G 8.21 3.67 rsl335310 None 446 10 C T C 8.20 2.02 rsl0489505 None 84 1 C G C 8.20 11.33 rs2008927 None 662 5 C T T 8.20 1.97 rs2160836 None 716 3 A C C 8.20 2.00 rs2298457 NUMAl 757 11 C T T 8.19 4.52 rsl0508230 None 275 10 A G A 8.18 0.40 rsl0496800 None 147 2 A G A 8.18 2.40 rsl0520676 NTRK3 402 15 A G A 8.18 2.40 rs2901383 None 846 4 C T C 8.17 0.51 rs731693 GORASP2 1151 2 C T T 8.17 2.09 rs4976621 None 988 5 C T C 8.16 0.41 rsl398868 FAFl 478 1 C T C 8.16 2.44 rsl59347 None 574 20 C T C 8.14 2.04 rsl0500474 None 181 16 A G A 8.14 0.37 rs4131886 LHCGR 924 2 A C C 8.13 2.46 rs770163 NAV3 1179 12 C T C 8.13 1.99 rsl947032 CTNNA2 640 2 A G A 8.12 2.21 rs2297139 LOC400758 754 1 A G G 8.12 0.37 rsl573219 NTRK2 563 9 C T T 8.12 2.32 rsl0508139 None 270 13 C T T 8.10 0.00 rs3774258 MRPL47 886 3 C T C 8.10 0.00 rs9312054 None 1284 4 C T C 8.10 0.00 rsl0486445 OSBPL3 55 7 C T C 8.10 2.33 rs974059 None 1349 3 A G A 8.09 0.52 rsl0484595 None 34 6 C T C 8.09 0.43 rsl0491806 ECM2 100 9 C T C 8.09 2.85 rs2861427 None 834 1 G T G 8.09 0.50 rs508544 None 991 2 C T C 8.08 2.10 rslO493731 None 121 1 A G A 8.08 3.98 rs2900362 None 844 12 A C C 8.07 0.35 rs7905537 None 1201 10 G T G 8.07 0.47 rs2270861 DRIM 747 12 C T C 8.07 0.37 rsl857706 FSHR 610 2 C T T 8.07 0.40 rs6461373 None 1035 7 G T T 8.07 2.02 rs6534623 None 1045 4 G T T 8.06 0.49 rs2414768 None 780 15 A T T 8.06 0.40 rs8092873 None 1226 18 A G G 8.05 2.92 rs2981196 None 850 8 A C C 8.05 2.34 rs9312682 LOC255130 1285 4 C T T 8.04 0.47 rsll73085 None 423 9 A G G 8.04 0.43 rsl834476 UNQ739 606 7 A T T 8.03 0.32 rs7007471 None 1094 8 A G A 8.03 0.38 rs9301082 None 1272 13 C T T 8.02 1.90 rs362492 ANK2 879 4 A G G 8.02 0.38 rs2248815 ITSNl 744 21 C T C 8.02 2.82 rs2725653 None 808 A C C 8.01 0.09 rs3770688 LANCLl 885 2 C T T 8.01 0.38 rs7720796 None 1182 5 A G A 8.01 0.28 rsl0500943 GAS2 187 11 A C A 8.00 1.99 rs7975812 None 1211 12 C G G 8.00 2.27 rsl0502526 None 204 18 A G A 7.98 2.13 rs7763189 None 1186 6 A G A 7.98 2.64 rsl0498017 None 160 2 A T A 7.98 2.58 rsl0517087 None 380 4 C T T 7.97 0.39 rs4125962 None 915 2 C T C 7.96 2.52 rsl519956 None 541 12 C T T 7.96 0.48 rsl0508904 C10orf64 288 10 G T G 7.96 1.98 rs445607 CTNND2 940 5 A G A 7.95 0.45 rs627069 MGC29875 1024 1 C G G 7.94 2.12 rsl0493583 SIAT7C 120 1 C T C 7.94 1.91 rs720884 C6orf65 1134 6 C T C 7.94 2.22 rs6972736 OSBPL3 1088 7 C T T 7.93 2.11 rsl357194 None 457 6 C T C 7.93 0.43 rsl906923 None 627 5 C G G 7.92 0.40 rs633198 PROCR 1027 20 A G G 7.92 1.89 rs997285 RASGRFl 1360 15 A C A 7.91 2.30 rslO497919 None 158 2 C T C 7.91 0.45 rsl430242 None 505 2 A G G 7.90 1.95 rsl0275635 None 12 7 A G A 7.90 0.00 rsl0492406 None 110 13 C T C 7.90 0.00 rsl0503636 EFA6R 221 8 C T T 7.90 1.88 rsl354348 None 456 3 A C C 7.89 0.15 rs3212220 IL12B 868 5 A C A 7.89 2.34 rs9315132 None 1290 13 C T T 7.89 0.37 rsl458088 None 519 11 C G G 7.88 1.99 dbSNP_rs_ID: SNP identification number in NCBI dbSNP database Gene locus: Gene locus as reported by NCBI dbSNP database build 124 Sequence_ID: Sequence identification number

Allele A: Alternate SNP allele or its complementary nucleotide in the position indicated by dbSNP RS ID and basepair position Allele B: Alternate SNP allele or its complementary nucleotide in the position indicated by dbSNP RS ID and basepair position Minor Allele: SNP allele or its complementary nucleotide that is less common in the control population Allele_X2: Chi-squared test based on allele frequencies

Table 3. Haplotype genomic regions with the strongest association with HT in the haplotype sharing analysis (HPM-G) with 5 SNPs. d G S |A|A P C P S E E G b e e |1 1 h O t n X e

S n q U 1 V r S a d t n

N e u Ie e a O i r e e

P e |1 1 1 m t t n

1 n Ie e U O i S C r O c I e S O i O

S C e |A B O n O n

U I m n t

I S I I e e

D D I n I t rslO489134 None 81 C G 0.0033 1 L 1322203 4222203 4444135 221932 None rslO489133 None 80 C T 0.0043 1 ⁱ 1344135 rsl0493327 APG4C 119 C T 0.0041 1 f 52673762 62573762 62828733 254971 APG4C rsl413242 None 498 C T 0.0034 1 < 52701781 rs998096 None 1364 A C 0.0029 1 < 52701822 rs7512480 None 1158 C T 0.0038 1 < 52728733 rs787493 LOC391046 1199 C G 0.002 1 f 57455635 67355635 67627512 271877 GADD45A rs344924 LOC391046 872 A G 0.0002 1 < 57475369 GNGl2 rsl408956 None 489 C T 0.0001 1 < 57506979 LOC391046 rs344935 None 873 C T 0.0006 1 < 57507779 rs647008 None 1039 C T 0.0008 1 < 57514855 rs675327 None 1064 G T 0.0023 1 < 57527512 rs2596268 LOC399701 802 A T 0.0046 1 ] L42748636 142648636 142853825 205189 MGC8902 rsl0494238 None 125 C T 0.0028 1 ] L42751002 LOC399701 rs3124683 None 862 A G 0.0021 1 ] L42753825

SEC22L1 rsl858232 CAPON 611 A G 0.0038 159491215 159391215 159591215 200000 CAPON

LOC284680 EAT2 rsl577567 None 566 A G 0.0047 163876348 163776348 164007533 231185 LOC116123 rsl577566 None 565 A G 0.0032 163876551 POGK

rs484666 None 981 A T 0.0026 1 163907533 rsl415678 None 501 A G 0.0039 1 165841708 165741708 165946218 204510 DPT rsl0489358 None 82 A G 0.003 1 165842250 rs726055 None 1146 C T 0.003 1 165845239 rsl0489359 None 83 A G 0.0029 1 165845921 rsl412336 None 496 A C 0.0046 1 165846218 rsl578704 None 568 A G 0.0049 1 186525471 186425471 186648423 222952 None rsl578705 None 569 A G 0.0049 1 186525536 rsl0494628 None 128 C T 0.0036 1 186548423 rsl0494627 None 127 C T 0.0021 1 186790071 186690071 186931835 241764 None rs9287136 None 1252 C T 0.0018 1 186831672 rsl0494626 None 126 C T 0.0047 1 186831835 rsl0494659 None 130 C T 0.0023 1 189007732 188907732 189165779 258047 None rs2785762 None 816 C G 0.0029 1 189010208 rsl0494660 None 131 C T 0.0033 1 189015552 rs7536312 None 1161 A G 0.0021 1 189015619 rslO494661 None 132 A T 0.0038 1 189016441 rsl0494662 None 133 C T 0.0027 1 189063888 rsl0494663 None 134 A G 0.002 1 189064337 rs6683269 None 1057 C T 0.0037 1 189064497 rsl0494664 None 135 A C 0.0036 1 189065779 rs2154329 None 715 C T 0.0046 1 196232097 196132097 196332097 200000 None rs301748 USH2A 855 A G 0.0041 1 213418522 213318522 213518522 200000 USH2A rsl0495082 None 137 C T 0.004 1 215101968 215001968 215201968 200000 LOC128153 rs2089918 None 694 A G 0.0035 1 231717337 231617337 231817337 200000 TARBPl rsl0508223 None 273 C T 0.0025 10 2154068 2054068 2254068 200000 None rsl0508416 LOC389938 279 A G 0.0031 10 10727688 10627688 11016891 389203 LOC389938 rs4749978 LOC389938 963 C G 0.0005 10 10744535 rs2224673 LOC389938 738 C G 0.0001 10 10758538 rsl0508417 LOC389938 280 A T O 10 10797859 rsl0508419 None 281 A G 0.0004 10 10910370 rsl473737 None 527 C T 0.0041 10 10916891

rsl537611 MCMlO 551 A G 0.0023 10 13213838 13113838 13314331 200493 OPTN rsl0508454 MCMlO 282 G T 0.0034 10 13214331 MCMlO C10orf49 rs950132 EPCl 1325 C T 0.0046 10 32628642 32528642 32728642 200000 EPCl rs7905537 None 1201 G T 0.0043 10 34235281 34135281 34416715 281434 PARD3 rsl61411 None 581 A G 0.005 10 34316715 rs9299552 PCDH15 1267 C T 0.0034 10 55585793 55485793 55685793 200000 PCDH15 rs7908118 None 1202 C T 0.0038 10 56557629 56457629 56709343 251714 None rs2050318 None 676 G T 0.0041 10 56609343 rsl0509301 RUFY2 299 C T 0.0042 10 69489280 69389280 69791343 402063 MAWBP rsl0509302 DNA2L 300 C G 0.0011 10 69575078 HNRPH3 rsl0509303 DNA2L 301 A C 0.0021 10 69575202 RUFY2 rs2298117 CXXC6 756 A G 0.0042 10 69691343 CXXC6 DNA2L rsl0509319 None 305 A G 0.0033 10 70747505 70647505 70876882 229377 NEUROG3 rsl0509318 None 304 A G 0.0028 10 70748147 C10orf35 rsl0509317 None 303 C G 0.0029 10 70776662 rsl0509316 None 302 A G 0.0024 10 70776882 rs7898235 None 1200 A C 0.0016 10 73382784 73282784 73490520 207736 ASCCl rsl0509767 None 309 G T 0.0016 10 73390520 C10orfl04 DDIT4 DNAJB12 CBARAl rs7917682 CBARAl 1204 G T 0.0024 10 73520486 73420486 73620821 200335 DNAJB12 rs7918099 CBARAl 1205 A G 0.0043 10 73520821 CBARAl rs7358173 None 1153 A G 0.005 10 89569434 89469434 89669434 200000 None rs2162361 C10orf59 718 C T 0.0028 10 89712286 89612286 89812726 200440 C10orf59 rs4934391 C10orf59 985 A G 0.0046 10 89712726

rs2032023 None 672 A C 0.005 10 112543668 112443668 112643668 200000 ADRA2A rslO498198 RRMl 162 C G 0.0039 11 4089040 3989040 4204538 215498 STIMl rs725518 RRMl 1144 C T 0.002 11 4093154 RRMl rs720106 RRMl 1132 A G 0.0024 11 4104287 rs54816 RRMl 1005 A G 0.0034 11 4104538 rsl549488 None 556 C G 0.0047 11 4396176 4296176 4504792 208616 SSAl rsl0500598 None 182 A G 0.0034 11 4396890 OR52K3P rsl0500600 OR51R1P 183 A G 0.0044 11 4404792 OR51R1P rs4128873 GALNTL4 918 C T 0.0035 11 11507330 11407330 11607330 200000 GALNTL4 rs4078145 None 912 A T 0.0035 11 11628202 11528202 11836288 308086 GALNTL4 rsl471013 None 526 A G 0.0024 11 11705272 USP47 rs897359 None 1238 C T 0.0014 11 11727598 rs2896587 None 843 A C 0.0024 11 11734173 rsl0500748 None 184 A T 0.0042 11 11736288 rs963497 None 1341 A G 0.0047 11 21603516 21503516 21721882 218366 NELLl rsl0500913 None 186 A G 0.0026 11 21621527 rs7112382 None 1105 A G 0.0034 11 21621882 rsl559759 None 559 G T 0.0036 11 35087360 34987360 35193481 206121 CD44 rs4756190 None 965 A G 0.0009 11 35088349 rs507230 None 990 C T 0.0039 11 35093481 rsl0501241 None 188 G T 0.0025 11 40660437 40560437 40760437 200000 None rsl0501242 None 189 A G 0.0017 11 40910759 40810759 41044758 233999 None rsl0501243 None 190 A G 0.0017 11 40910823 rsl0501244 None 191 A T 0.0017 11 40911075 rs7102885 None 1103 C T 0.0018 11 40930137 rsl0501245 None 192 C T 0.0022 11 40944758 rs2298457 NUMAl 757 C T 0.0046 11 71460519 71360519 71563971 203452 RNF121 rs6592456 NUMAl 1053 C T 0.0045 11 71463971 IL18BP NUMAl LOC220074 FLJ20625 DKFZP564M082

rsl0501438 LOC387795 193 A G 0.0007 11 78790787 78690787 78924409 233622 LOC387795 rs528048 LOC387795 998 C T 0.0003 11 78790934 rs530965 LOC387795 999 C T 0.0002 11 78791409 rs481975 LOC387795 977 A C 0.0001 11 78798027 rs546868 LOC387795 100 C T 0.0001 11 78799086 rsl0501439 LOC387795 194 C T 0.0001 11 78812154 rs514536 LOC387795 9 99933 C G 0.004 11 78824409 rsl0501471 None 195 A G 0.0045 11 80051682 79951682 80152306 200624 None rsl0501472 None 196 C T 0.0037 11 80052306 rsl391533 None 474 C T 0.0048 11 80396254 80296254 80605724 309470 None rsl566241 None 561 C T 0.0025 11 80444563 rsl608169 None 580 G T 0.0006 11 80477196 rsl829764 None 602 C T 0.0003 11 80477302 rsl589574 None 573 G T 0.0012 11 80477358 rs2373717 None 771 A T 0.0024 11 80505724 rsl542750 None 553 A G 0.0047 11 91310866 91210866 91426878 216012 None rsl0501763 None 200 C T 0.0035 11 91326878 rsl941437 LOC390241 638 C T 0.0022 11 91898278 91798278 91998278 200000 LOC390241 rs4129692 None 921 C T 0.0027 11 92979838 92879838 93181349 301511 FN5 rs4129691 None 920 G T 0.0001 11 92979850 MGC5306 rs2399681 None 777 A G O 11 92980052 PTD012 rs2399683 None 778 C T O 11 92980291 KIAA1731 rs7939460 KIAA1731 1207 C G 0.0012 11 93081349 rs503208 None 989 C G 0.002 11 103295656 103195656 103408638 212982 PDGFD rs7127296 None 1106 A C 0.0046 11 103308638 rs875430 None 1234 C T 0.0043 11 109153307 109053307 109318071 264764 None rs2002733 None 661 A G 0.0012 11 109154189 rs2570309 None 800 C T 0.002 11 109195092 rsl789819 None 596 C T 0.0033 11 109218071 rsl0505970 FLJ36004 243 C G 0.0022 12 25536337 25436337 25637084 200747 FLJ36004 rsl0505969 FLJ36004 242 A T 0.0037 12 25536631

rsl0505968 FLJ36004 241 A G 0.0049 12 25537084 rsl0506120 None 244 A G 0.0041 12 34126870 34026870 34226870 200000 ALGlO rsl0506121 None 245 C G 0.0044 12 34290302 34190302 34390302 200000 None rs274460 None 810 A G 0.0029 12 58238608 58138608 58497593 358985 SLC16A7 rs3847653 None 894 C G 0.004 12 58238640 rs3897770 None 901 A C 0.0036 12 58238933 rsl0506395 None 246 C T 0.0012 12 58258088 rsl391130 None 473 A G 0.0007 12 58270954 rsl0506396 None 247 G T 0.0006 12 58321404 rsl0506397 None 248 C T 0.0001 12 58321752 rsl0506398 SLCl6A7 249 C T 0.0015 12 58397593 rsl386486 TPH2 472 C T 0.0043 12 70698487 70598487 70798761 200274 TBC1D15 rsl386485 TPH2 471 A C 0.0045 12 70698634 TPH2 rsl386483 TPH2 470 A G 0.0044 12 70698761 rsl0506650 TRHDE 251 C T 0.0036 12 70964670 70864670 71083069 218399 TRHDE rs4550264 TRHDE 945 A G 0.0027 12 70964827 rsl0506651 TRHDE 252 A G 0.0035 12 70983069

Ul

O rs949593 None 1323 A C 0.0046 12 71725030 71625030 71825030 200000 None rsl402319 None 481 C T 0.0034 12 76658608 76558608 76758608 200000 NAV3 rsl0506761 None 254 A C 0.0034 12 76683540 76583540 76790978 207438 NAV3 rsl520726 None 543 C T 0.0021 12 76690978 rsl394380 None 475 A G 0.0044 12 97055132 96955132 97155132 200000 None rsl353761 None 455 A T 0.0014 12 101577909 101477909 101677909 200000 None rsl0507149 None 259 C T 0.0004 12 101602105 101502105 101748153 246048 PAH rs6539051 None 1046 G T 0.0005 12 101621075 rs7311768 None 1150 A G 0.0009 12 101621739 rsl0507150 None 260 C T 0.0014 12 101642141 rs6539055 None 1047 A G 0.0036 12 101648153 rsl896339 None 623 A T 0.0015 12 113829557 113729557 113949205 219648 None rsl0507255 None 263 C G 0.0015 12 113831271 rs7957333 None 1209 C T 0.0014 12 113831312 rsl863723 None 614 A G 0.0016 12 113840194

rs2021784 None 668 A C 0.0016 12 113849205 rs9315078 PSPCl 1289 A G 0.0018 13 18056452 17956452 18211924 255472 HSMPP8 rs2297584 PSPCl 755 A G 0.0005 13 18085758 PSPCl rs4769900 PSPCl 969 C T 0.0007 13 18111924 ZNF237 rsl413476 LOC400099 499 A G 0.0023 13 18238020 18138020 18338020 200000 PSPCl ZNF237 ZNF198 LOC400099 rs9315282 ZNF198 1291 A T 0.004 13 18391977 18291977 18491977 200000 ZNF198 rsl555619 None 558 C T 0.0025 13 20654983 20554983 20780871 225888 None rs4278603 None 933 C T 0.0009 13 20655026 rs9316871 None 1298 C T 0.0002 13 20659921 rs9316902 None 1299 A T 0.0006 13 20680457 rs6490720 None 1041 A G 0.0041 13 20680871 rs3002251 None 852 C T 0.0046 13 23417821 23317821 23591092 273271 PABPC3 rs2497614 None 794 A C 0.0028 13 23418426 FLJ25477 rs2994906 None 851 C T 0.0029 13 23491092 rs9315443 LOC390393 1292 A G 0.0044 13 35109331 35009331 35231087 221756 LOC400120 rs2224655 None 737 A G 0.0035 13 35117500 RFXAP rs9315445 None 1293 A C 0.0034 13 35130928 SMAD9 rsl0507441 None 264 A C 0.0038 13 35131087 LOC390393 rsl008913 None 2 C T 0.0011 13 41527828 41427828 41671499 243671 DNAJDl rs9315991 None 1294 G T O 13 41529541 FLJ10094 rs9316002 None 1295 A G 0.0011 13 41571499 rs2182377 None 726 G T 0.0047 13 46385371 46285371 46485371 200000 SUCLA2 NUDTl5 VDRIP rs9318293 None 1300 C T 0.0049 13 72969141 72869141 73112529 243388 None rs7983591 None 1213 A C 0.0008 13 72999299 rsl0507828 None 266 C T 0.0041 13 73012529

rsl0492637 GPC6 114 A G 0.0046 13 92224868 92124868 92324868 200000 GPC6 rs9582457 VGCNLl 1337 C T 0.0037 13 99518459 99418459 99659913 241454 VGCNLl rs9300654 VGCNLl 1268 C T 0.0028 13 99524895 rsl0508056 VGCNLl 267 G T 0.0026 13 99526897 rsl0508058 VGCNLl 268 A G 0.0033 13 99559913 rs9301021 None 127 C T 0.0044 13 103674248 103574248 103776948 202700 None rs9301022 None 127 C T 0.0032 13 103676948 rsll620131 None 422 A C 0.0005 13 107835145 107735145 108022110 286965 None rsl0492480 None 113 C T 0.0002 13 107847427 rsl410425 None 491 C T 0.0001 13 107896160 rsl0492479 None 112 A G 0.0003 13 107913803 rsl0492478 None 111 A C 0.0004 13 107922110 rs719737 None 1130 C T 0.0008 13 108048350 107948350 108148350 200000 IRS2 rslO483414 AKAP6 23 A G 0.0043 14 31055625 30955625 31173099 217474 AKAP6 rslO483416 AKAP6 24 C T 0.0015 14 31065873 rs7157533 AKAP6 111 C T 0.0017 14 31066698 Ul K> rs7157744 AKAP6 111 A T 0.0016 14 31066871 rsl956223 AKAP6 643 A G 0.0016 14 31072068 rs3784203 AKAP6 887 A T 0.0018 14 31073099 rsl0483523 LRFN5 26 A T 0.0049 14 40254131 40154131 40354131 200000 LRFN5 rsl0498373 None 163 A G 0.0028 14 41060504 40960504 41175621 215117 None rs9323071 None 1310 A T 0.0024 14 41067677 rsl0498374 None 164 A C 0.0024 14 41072782 rs8009697 None 1215 C T 0.0044 14 41075621 rsl0483694 None 27 A G 0.0022 14 56505552 56405552 56619154 213602 None rsl0483695 None 28 A G 0.0004 14 56505597 rsl78493 None 594 C T 0.0009 14 56517556 rsl78497 None 595 A C 0.001 14 56519154 rsl0483763 KCNH5 29 A G 0.0018 14 61556822 61456822 61658529 201707 KCNH5 rsl951805 KCNH5 642 A C 0.0021 14 61558195 rs9323431 KCNH5 1311 A C 0.0041 14 61558529 rs2056855 LOC145497 679 C T 0.0035 14 75287180 75187180 75395330 208150 KIAA1036

rsl0483879 LOC145497 30 C T 0.0027 14 75288211 KIAA0759 rs2885625 LOC145497 839 A G 0.001 14 75294790 C14orfl66B rs6574333 LOC145497 1051 A G 0.0021 14 75295330 LOC145497 rs9323707 LOC400234 1312 A G 0.0019 14 80076248 79976248 80176248 200000 SELlL

LOC400234 rs7177870 None 1124 C T 0.0049 15 24842209 24742209 24942209 200000 GABRA5 rslO519989 MGC14798 397 A C 0.0033 15 33246629 33146629 33346629 200000 MGC14798 rs3887013 RGMA 900 A G 0.0022 15 91343895 91243895 91456600 212705 CHD2 rs997941 RGMA 1363 A G 0.0028 15 91356600 RGMA rsl0492874 WWOX 116 C G 0.0042 16 77932158 77832158 78040235 208077 CLECSFl rs9319518 WWOX 1304 C G 0.005 16 77940235 WWOX rs2077576 WWOX 688 A G 0.0044 16 78118291 78018291 78218291 200000 WWOX

Ul rs4130513 WWOX 922 A G 0.0028 16 78238277 78138277 78372914 234637 WWOX rslO514437 WWOX 349 C T 0.0006 16 78272387 rs2738646 WWOX 809 C G 0.0033 16 78272914 rsl0492859 CDH13 115 A G 0.0015 16 82641499 82541499 82744597 203098 CDH13 rs759831 CDH13 1169 A C 0.0001 16 82643345 rsl982608 CDH13 651 C T 0.0003 16 82644465 rs7498941 CDH13 1157 A G 0.0027 16 82644597 rslO521151 KIAA0753 405 C T 0.0034 17 6728171 6628171 6858576 230405 PITPNM3 rsl0491082 LOC342531 96 C T 0.003 17 6758152 TXNL5 rs2040847 LOC342531 673 A G 0.0042 17 6758576 CGI-125 SLC13A5 KIAA0753 LOC342531 LOC342531 rs7219451 KRT25D 1137 C T 0.0025 17 39330167 39230167 39479119 248952 KRT24 rs2469828 None 792 C T 0.001 17 39377625 KRT25A rs2469816 None 790 A G 0.0043 17 39379119 KRT25B KRT25C

KRT25D KRTlO MGC21518 KRT12 KRT20 KRT23 rslO512495 None 332 C T 0.0033 17 60887422 60787422 61003496 216074 FLJ25818 rs954562 None 1334 C T 0.0026 17 60903496 FLJ12760 rslO512496 TLK2 333 C T 0.0041 17 61137732 61037732 61237732 200000 TLK2 MRC2 rs918077 None 1241 C T 0.0049 17 70762501 70662501 70862501 200000 SOX9 rs8089170 PTPRM 1222 A G 0.0047 18 7980780 7880780 8141285 260505 PTPRM rsl0502366 PTPRM 203 A T 0.0009 18 7981006 rs674823 PTPRM 1063 A G 0.0016 18 8025339 rsl0513902 PTPRM 348 A T 0.0017 18 8040297 rsl0513901 PTPRM 347 C T 0.0017 18 8041285 rs4799483 None 974 C T 0.0038 18 34401661 34301661 34587395 285734 None rsl346234 None 452 G T 0.0038 18 34405689 rsl0502700 None 211 A G 0.0038 18 34417134 rs4627439 None 951 G T 0.0015 18 34486191 rs3744905 None 881 G T 0.0035 18 34487395 rsl0502772 None 212 C T 0.0042 18 37436083 37336083 37653585 317502 None rsl0502774 None 213 G T 0.0027 18 37506007 rsl865290 None 615 A T 0.0012 18 37507545 rs8092873 None 1226 A G 0.0013 18 37508323 rs9304252 None 1277 A T 0.0009 18 37534860 rs7242858 None 1140 G T 0.0037 18 37553585 rsl944404 RIT2 639 C T 0.0031 18 38784739 38684739 38885296 200557 RIT2 rsl0502805 RIT2 214 C G 0.0041 18 38785296 rsl497965 None 534 A G 0.004 18 56738096 56638096 56862416 224320 None rsl0503048 None 215 C T 0.0021 18 56745407 rs720261 None 1133 A G 0.0028 18 56762416 rs931850 None 1303 A G 0.0032 18 59542803 59442803 59673654 230851 SERPINB4

rsl522722 None 547 C T 0.0019 18 59570510 SERPINB3 rs3928359 None 905 A C 0.0024 18 59573654 SERPINBIl

SERPINB7 rs309231 None 859 C T 0.004 18 64544485 64444485 64734518 290033 FLJ20793 rsl676853 None 588 C T 0.0015 18 64598339 C18orfl4 rsl0503122 None 217 C T 0.0002 18 64598510 rs8092610 None 1225 C T 0.0001 18 64610859 rs2086079 None 691 A C 0.0003 18 64621145 rsl0503123 None 218 A G 0.0007 18 64623492 rs6566386 None 1049 A C 0.0034 18 64634518 rs2110049 LOC388526 699 A T 0.0033 19 33056517 32956517 33203464 246947 LOC388526 rsl0500226 LOC388526 177 G T 0.0011 19 33079622 rsl0516700 LOC388526 375 A G 0.0005 19 33080969 rsl0500227 LOC388526 178 A C 0 19 33102850 rsl0500228 LOC388526 179 C T 0 19 33103335 rs9304853 LOC388526 1278 A T 0 19 33103370 rs9304854 LOC388526 1279 A C 0.0021 19 33103464

Ul Ul rs272411 LILRAl 807 C T 0.0039 19 59803539 59703539 59986493 282954 FLJ00060 rs400322 LILRB4 909 A G 0.0041 19 59864390 LILRA2 rsl654658 None 587 A G 0.0031 19 59886493 LILRAl LILRB4 ILTlO KIR3DL3 KIR2DL3 KIR2DS2 KIR2DL1 rs4669167 None 954 C T 0.0026 2 5415069 5315069 5545029 229960 None rsl453787 None 516 A G 0.0015 2 5445029 rs238634 LOC339789 775 A G 0.0035 2 8435287 8335287 8535287 200000 LOC339789 rslO518958 COMMDl 395 A G 0.0049 2 62251507 62151507 62351507 200000 COMMDl rsl0496105 PELIl 141 A G 0.0019 2 64295280 64195280 64443870 248590 VPS54 rs7563423 None 1164 A G 0.0003 2 64319936 PELIl rs714672 None 1109 A G 0.0009 2 64320856

rsl0496106 None 142 C T 0.0009 2 64321198 rs717382 None 1121 A G 0.0011 2 64321669 rs7558568 None 1162 A C 0.0008 2 64331179 rs7562080 None 1163 A G 0.0015 2 64331740 rsl0496107 None 143 G T 0.0016 2 64343870 rsl2072 REGlA 429 A G 0.005 2 79325042 79225042 79450682 225640 REG-III rslO496213 REGL 145 A C 0.0012 2 79336691 REGlB rs2117725 None 703 C G 0.0046 2 79350682 REGlA PAP REGL rs723839 None 1139 C G 0.0049 2 123161810 123061810 123294482 232672 None rsl0496580 None 146 A C 0.005 2 123194482 rs3769361 GPD2 883 A G 0.003 2 157599796 157499796 157750266 250470 GPD2 rs3769368 GPD2 884 C T 0.0024 2 157613543 rs7570567 GPD2 1166 C T 0.0031 2 157621171 rs2288760 GPD2 753 A T 0.0041 2 157629867 rsl432573 None 507 C G 0.0047 2 157650266

Ul rslO497163 None 149 G T 0.0043 2 157742506 157642506 157842506 200000 None rslO497189 ACVRl 150 A G 0.0048 2 158827349 158727349 159025728 298379 ACVRl rsl0497190 ACVRl 151 A G 0.0012 2 158841785 rslO497191 ACVRl 152 A G 0.0008 2 158869762 rslO497192 ACVRl 153 C T 0.0006 2 158874245 rs7605386 ACVRl 1171 C G 0.0005 2 158881484 rs9288697 ACVRl 1256 A C 0.0003 2 158897363 rslO497193 None 154 A G 0.001 2 158912223 rs6437117 None 1032 A T 0.0044 2 158925728 rs3903306 None 902 A T 0.004 2 160651226 160551226 160751264 200038 BAZ2B rs6432539 None 1031 C T 0.0048 2 160651264 rsl0490079 MYO3B 89 C T 0.005 2 171641213 171541213 171743501 202288 MYO3B rs741283 MYO3B 1154 G T 0.0024 2 171643501 rs2164857 PDEIlA 719 A C 0.0049 2 178811680 178711680 178915390 203710 PDEIlA rsl438048 PDEIlA 508 A C 0.0042 2 178815390 rs523437 None 997 A G 0 . 004 239685559 239585559 239785608 200049 TRAF3IP1

rs567962 None 1007 C T 0.0043 2 239685608 ASBl rsl0485822 SNPH 49 C G 0.0046 20 1241412 1141412 1514846 373434 PSMFl rsl884389 None 618 C T 0.002 20 1405582 C20orf46 rsl884390 None 619 C T 0.0016 20 1405818 SNPH rsl0485823 None 50 A G 0.0047 20 1414846 SDCBP2

FKBPlA

NSFLlC

PTPNS1L2 rs6076199 MGC10715 1016 A G 0.0011 20 2466755 2366755 2571778 205023 TGM6 rs6083460 MGC10715 1018 A G 0.0001 20 2471631 SNRPB rs6083461 MGC10715 1019 A T O 20 2471778 MGC10715 TMC2 rsl0485601 TMC2 44 A G 0.0002 20 2589190 2489190 2689502 200312 MGC10715 rs6115181 TMC2 1023 A G 0.0005 20 2589254 TMC2 rsl0485602 TMC2 45 C T 0.0015 20 2589502 NOL5A IDH3B

Ul rs6019794 KCNBl 1011 C T 0.0016 20 48694867 48594867 48817052 222185 KCNBl rs756529 KCNBl 1165 C T 0.0022 20 48696430 PTGIS rs237459 KCNBl 772 C T 0.0026 20 48717052 rs2831249 None 823 A C 0.003 21 28231943 28131943 28360918 228975 C21orf94 rsl974422 None 646 C T 0.0044 21 28234231 rs2831286 None 824 C T 0.0031 21 28260918 rs717205 LOC388819 1119 A G 0.0033 21 34231301 34131301 34383137 251836 ITSNl rs2017190 LOC388819 664 C T 0.0007 21 34231309 ATP5O rs2070513 None 686 G T 0.0005 21 34274270 MRPS6 rs2834327 None 825 A T 0.0011 21 34283137 LOC388819 rs3856852 None 897 A G 0.0026 3 3206647 3106647 3306647 200000 IL5RA TRNTl CRBN rs2347104 None 761 A G 0 .0041 3 11875101 11775101 12014530 239429 MGC16471 rsl0510408 None 310 C T 0 .0024 3 11888064 rs51579 None 995 C T 0 .0008 3 11888124

rs447394 None 941 G T 0.0042 3 11914530 rs9311694 None 1283 A C 0.0042 3 58997976 58897976 59235365 337389 FLJ42117 rsl913157 None 630 C G 0.0025 3 59131716 rsl512828 None 538 A C 0.0028 3 59135365 rsl521409 None 544 A G 0.0009 3 118178542 118078542 118307557 229015 None rsl462840 None 523 C T 0.0037 3 118183396 rslO511365 None 316 C T 0.0028 3 118206735 rslO511366 None 317 C T 0.0036 3 118207557 rs953641 PLSl 1333 A G 0.0019 3 143748645 143648645 143941670 293025 XRNl rs953239 TRPCl 1332 G T 0.0014 3 143767114 ATR rs2049328 TRPCl 675 C T 0.0009 3 143769488 PLSl rs7641514 TRPCl 1174 A G 0.0025 3 143841670 TRPCl rsl523076 None 549 C T 0.0047 3 146693647 146593647 146916161 322514 None rs2687860 None 804 A G 0.0012 3 146761400 rs6770324 None 1066 C T 0.0009 3 146792671 rs2140300 None 710 A G 0.0036 3 146816161

Ul

06 rs475553 None 964 C T 0.0032 3 166697033 166597033 166797033 200000 None rsl68987 STK32B 589 A C 0.0035 4 5499399 5399399 5601132 201733 STK32B rs2369705 STK32B 764 A G 0.0038 4 5501132 rsl449776 None 511 A G 0.0037 4 27434527 27334527 27595173 260646 None rs990965 None 1355 C T 0.0032 4 27489847 rsl503466 None 537 C T 0.0016 4 27495090 rsl503465 None 536 A G 0.0016 4 27495173 rs9291304 GABRBl 1259 A G 0.0029 4 47044998 46944998 47144998 200000 GABRBl rslO516731 None 377 A G 0.0048 4 86457178 86357178 86594911 237733 None rsl0516740 None 378 A G 0.0048 4 86494911 rslO516839 None 379 A C 0.005 4 90966734 90866734 91066734 200000 SNCA rsl0489025 LOC339979 77 A C 0.0032 4 109741503 109641503 109846552 205049 FLJ37673 rsl0489026 LOC339979 78 C G 0.0012 4 109741553 LOC339979 rs7667905 LOC339979 1176 A G 0.0004 4 109745465 rsl0489027 LOC339979 79 A G 0.0017 4 109746552

rsl468223 ANK2 525 C T 0.0039 4 114597479 114497479 114703481 206002 ANK2 rs362492 ANK2 879 A G 0.0034 4 114598248 rs3025748 ANK2 856 C T 0.0041 4 114603481 rsl376088 None 467 C T 0.0021 4 140072748 139972748 140173774 201026 None rsl376089 None 468 A G 0.0012 4 140073568 rsl376091 None 469 A G 0.0024 4 140073774 rs920208 None 1242 A G 0.0037 4 148548703 148448703 148648703 200000 None rsl841272 None 608 C G 0.0028 4 157383393 157283393 157509071 225678 TDO2 rslO517626 TDO2 385 A C 0.0027 4 157409071 rslO517654 PDGFC 386 G T 0.0023 4 158358389 158258389 158464399 206010 GLRB rslO517655 PDGFC 387 A G 0.0008 4 158358536 PDGFC rs6811964 PDGFC 1069 C T 0.001 4 158363081 rslO517657 PDGFC 388 A C 0.0017 4 158363655 rs7662187 PDGFC 1175 C G 0.0033 4 158364399

Ul rs9308066 None 1281 A G 0.0028 4 165245707 165145707 165345707 200000 None rs438418 None 936 A G 0.0032 5 2902174 2802174 3072326 270152 IRX2 rs9313016 None 1286 A C 0.0042 5 2972326 CEI rsl374008 None 464 A G 0.0012 5 61300470 61200470 61487098 286628 None rslO514931 None 353 A T 0.0006 5 61300983 rs9291745 None 1260 C T 0.0009 5 61307285 rs2161499 None 717 A C 0.0017 5 61387098 rs346435 None 874 A C 0.001 5 62620128 62520128 62720128 200000 None rs281455 None 817 C T 0.0044 5 67304156 67204156 67424355 220199 None rsl0515062 None 354 A T 0.0045 5 67324096 rs382190 None 889 A G 0.0028 5 67324355 rs2115127 CMYA5 702 A G 0.0045 5 79125572 79025572 79275146 249574 CMYA5 rsl643992 CMYA5 585 A T 0.0028 5 79133562 rs6453484 CMYA5 1033 C T 0.0026 5 79165786 rs9283795 CMYA5 1248 C T 0.0025 5 79166420

rs2404670 CMYA5 779 A G 0.004 5 79175146 rslO515282 None 355 C T 0.0032 5 98111861 98011861 98283284 271423 RGMB rsl605714 None 577 C T 0.0023 98112838 CHDl rs719246 None 1126 C T 0.0027 98134141 rslO515283 None 356 C T 0.0017 98169888 rsl979980 RGMB 650 G T 0.0041 98183284 rs286809 FBXL17 837 C T 0.0025 107534853 107434853 107737830 302977 FBXL17 rs286797 FBXL17 836 A G 0.0009 107559070 rslO515385 FBXL17 358 A C 0.0012 107604483 rs286763 FBXL17 835 C T 0.0024 107607518 rs2966821 FBXL17 848 A C 0.0038 107611102 rs2122158 FBXL17 706 C T 0.0048 107637830 rsl0515406 None 360 A G 0.0024 108987234 108887234 109087234 200000 LOC391

MAN2A1 rs383096 None 892 A G 0.004 125259035 125159035 125359035 200000 None rs7721549 None 1183 C T 0.0048 5 144839202 144739202 144939202 200000 None o rs716376 None 1118 A G 0.0023 5 157527972 157427972 157652114 224142 None rsl614336 None 582 A C 0.0019 5 157532763 rsll73476 None 424 G T 0.0014 5 157537804 rsl540944 None 552 A G 0.0013 5 157547994 rslO515758 None 365 A G 0.0028 5 157552114 rsll57122 GABRAl 417 C T 0.0015 5 161300209 161200209 161400209 200000 GABRAl rslO515855 None 369 C G 0.0046 5 162719997 162619997 162849780 229783 CCNGl rs300238 None 853 A G 0.0035 5 162731265 LOC134492 rs6873695 None 1073 C T 0.005 5 162749780 HMMR rs6601146 None 1054 G T 0.0044 5 180403167 180303167 180503167 200000 BTNL8

BTNL3 BTNL9 rsl60693 None 578 C T 0.0029 6 2738529 2638529 2865713 227184 WRNIPl rs2118940 None 704 A G 0.0019 6 2763874 SERPINBl rs9328130 None 1314 C T 0.0022 6 2765713 SERPINB9

rs2753245 C6orfl49 812 C G 0.0034 6 5203091 5103091 5326448 223357 C6orfl49 rs4141760 None 926 G T 0.0006 6 5220364 FARSl rs9328291 None 1315 A G 0.0008 6 5221747 rs9328292 None 1316 A G 0.0009 6 5226448 rsl0484878 C6orf33 42 C T 0.004 6 52283650 52183650 52389538 205888 IL17F rsl0484877 C6orf33 41 C T 0.0036 6 52289538 MCM3 C6orf33 rsl0484647 C6orfl42 38 A G 0.003 6 54112210 54012210 54284342 272132 C6orfl42 rs9296744 C6orfl42 1262 C T 0.0014 6 54176818 TINAG rsl0484646 None 37 A C 0.0015 6 54179189 rs9296745 None 1263 C T 0.0014 6 54179227 rsl0484644 None 36 A G 0.0016 6 54181892 rs6913087 None 1077 A G 0.0018 6 54183885 rs2894818 None 842 A G 0.0028 6 54184342 rsl0499021 None 168 A G 0.0021 6 99138965 99038965 99238965 200000 None rs9322661 None 1307 C T 0.0017 6 102940065 102840065 103144877 304812 None

rsl578026 None 567 A G 0.0013 6 102972398 c\ rs479856 None 973 C G 0.0011 6 102986050 rs9322662 None 1308 C T 0.0028 6 102991994 rs9322664 None 1309 A G 0.0041 6 103044877 rs7765824 None 1188 A C 0.0042 6 119130214 119030214 119234543 204329 C6orf204 rsl0485389 None 43 C T 0.0035 6 119133914 rs6932535 None 1080 C T 0.0028 6 119134543 rs2328539 PLAGLl 760 A T 0.0005 6 144304399 144204399 144404399 200000 C6orf93

PLAGLl rslO484614 STXIl 35 C T 0.0003 6 144461092 144361092 144681092 320000 PLAGLl rsl983773 STXIl 652 A C 0.0008 6 144462337 SF3B5 rs6935462 None 1082 A T 0.0007 6 144493571 STXIl rs667765 None 1056 C T 0.0037 6 144581092 UTRN rs7741672 None 1185 C T 0.0035 6 145333306 145233306 145433689 200383 None rs6924480 None 1079 C T 0.0039 6 145333689 rs7763189 None 1186 A G 0.002 6 148125635 148025635 148232647 207012 None

rsl0484683 None 39 A G 0.0034 6 148132647 rsll58619 None 418 A C 0.0015 6 160202439 160102439 160407001 304562 WTAP rs6901166 None 1076 C T 0.0021 6 160277497 ACAT2 rs645851 IGF2R 1034 A G 0.0011 6 160307001 TCPl

MRPLl8 PNLDCl MASl IGF2R rs713055 PARK2 1107 A G 0.0024 6 162480611 162380611 162595042 214431 PARK2 rs2849597 PARK2 828 A G 0.0005 6 162489378 rsl893556 PARK2 621 C T 0.0011 6 162494041 rs2849589 PARK2 827 C T 0.0035 6 162495042 rs654384 SDKl 1048 C T 0.0037 7 3910997 3810997 4010997 200000 SDKl rs9969156 PHF14 1359 C T 0.0025 7 10935851 10835851 11036097 200246 PHF14 rslO499381 PHF14 169 C T 0.0013 7 10936071 rsl0499382 PHF14 170 A T 0.004 7 10936097

K* rs702479 None 1099 C T 0.0046 7 12548772 12448772 12648772 200000 SCIN

ARL4A rslO486616 None 56 A G 0.004 7 33527810 33427810 33689026 261216 None rslO486618 None 57 C G 0.0014 7 33569645 rslO486619 None 58 C T 0.0009 7 33569830 rs7788027 None 1192 A G 0.0023 7 33589026 rs2348460 FLJ21075 762 A G 0.0025 7 47587550 47487550 47778146 290596 PKDlLl rs7806630 FLJ21075 1194 C T 0.0028 7 47587621 FLJ21075 rsl0499668 PKDlLl 172 A G 0.0015 7 47678146 HUSl rslO224913 None 5 A C 0.0033 7 79600797 79500797 79705307 204510 None rs6467126 None 1037 A C 0.0013 7 79603430 rsl0486935 None 59 A G 0.0008 7 79603851 rs7777441 None 1191 A G 0.0008 7 79604422 rslO74388 None 410 C T 0.0016 7 79605305 rslO74389 None 411 G T 0.0012 7 79605307 rslO238431 None 7 A G 0.0046 7 82562263 82462263 82675171 212908 SEMA3E rsl0270433 None 11 A T 0.002 7 82575171

rsl0487867 None 61 C T 0.0049 7 83130182 83030182 83302282 272100 SEMA3A rs701276 None 1096 A G 0.0016 7 83142116 rs701294 None 1097 G T 0.0015 7 83156363 rsl0239654 SEMA3A 8 C T 0.0029 7 83202282 rsl362985 None 459 A G 0.002 7 133447945 13334794 rs3800756 None 888 C T 0.0021 7 133519414 SLC35B4 rsl791001 None 598 C G 0.0033 7 133541172 AKRlBl rslO487921 None 62 A G 0.0044 7 145822182 145722182 145922182 200000 CNTNAP2 rs2215798 CNTNAP2 731 A G 0.0045 7 146978322 146878322 147111287 232965 CNTNA rsl0488348 CNTNAP2 65 C T 0.0025 7 146999108 rs2708264 CNTNAP2 806 G T 0.004 7 147011287 rs7011065 CSMDl 1095 G T 0.0044 8 4124065 4024065 4225908 201843 CSMDl rs813585 CSMDl 1227 C G 0.0023 8 4125908 rsl0503725 MSCP 222 C T 0.0016 23418475 23318475 23519248 200773 ENTPD4 rs4593549 MSCP 949 A G 0.0012 23418670 MSCP rs7819907 MSCP 1196 C T 0.0009 23418915 rs9314268 MSCP 1288 C T 0.001 23418973 rsl0503726 MSCP 223 C T 0.002 23419204 rs4872143 MSCP 982 C T 0.0044 23419248 rs4242477 None 931 A T 0.0044 52768802 52668802 52870650 201848 None rsl0504127 None 226 A G 0.0039 52770650 rsl0504596 None 228 C T 0.0039 8 76738283 76638283 76838283 200000 HNF4G rsl914927 None 631 A C 0.004 78745117 78645117 78849973 204856 None rs2139321 None 708 A G 0.0026 78749516 rsl607534 None 579 A C 0.0016 78749973 rs7001645 RIMS2 1092 C G 0.0031 105079933 104979933 105180574 200641 RIMS2 rsl0505054 RIMS2 233 C T 0.0042 105080007 rs9297344 RIMS2 1264 A C 0.004 105080574 rs723107 None 1138 A G 0.0038 8 105731815 105631815 105831815 200000 LRP12

rsl521775 None 546 A G 0.0017 8 106000463 105900463 106164864 264401 None rs285866 None 831 A G 0 8 106020040 rs285790 None 829 C T 0.0002 8 106033280 rs285839 None 830 A G 0.0018 8 106048055 rsl460582 None 522 C T 0.0048 8 106064864 rs9283944 None 1249 A G 0.0046 8 107290692 107190692 107412262 221570 None rs9297381 None 1265 C T 0.0024 8 107290914 rs6469061 None 1038 C T 0.0014 8 107312223 rs905556 None 1239 C T 0.0011 8 107312262 rsl0505428 ZHX2 239 A G 0.0032 8 123812929 123712929 123912929 200000 ZHX2 rs945658 None 1320 G T 0.005 9 1606639 1506639 1726435 219796 None rsl323256 None 440 C T 0.0029 9 1608419 rsl323224 None 439 A G 0.0011 9 1626435 rs438405 RCLl 935 A C 0.0019 9 4814607 4714607 4941661 227054 AK3L1 rsl0511460 RCLl 318 C G 0.0016 9 4817222 RCLl rs456044 RCLl 946 C T 0.0006 9 4841661 c

\ rs719673 None 1129 A G 0.0006 9 4947650 4847650 5083082 235432 RCLl rs2381194 None 773 C T 0.0003 9 4949331 JAK2 rsl327493 JAK2 444 C G 0.0015 9 4983082 rslO511581 LOC401492 319 A G 0.0038 9 13405530 13305530 13560671 255141 LOC401492 rslO491751 None 98 C T 0.0015 9 13434932 rs9298688 None 1266 C T 0.0003 9 13459833 rs987290 None 1353 A G 0.0039 9 13460671 rs2060850 FLJ31810 683 A G 0.0032 9 28091541 27991541 28191541 200000 FLJ31810 rslO491884 FLJ31810 106 C T 0.0044 9 28552149 28452149 28652149 200000 FLJ31810 rs2589628 TMCl 801 C T 0.003 9 70811449 70711449 70911449 200000 TRPM3

TMCl rs2769613 None 815 C T 0.0035 9 83364910 83264910 83464995 200085 FRMD3 rs2841475 None 826 C T 0.004 9 83364995 rsl034097 C9orf97 14 C G 0.004 95766284 95666284 95962814 296530 C9orfl02

rs3176757 XPA 866 C T 0.0029 9 95816896 C9orf97 rs953199 LOC392371 1331 G T 0.0014 9 95862814 XPA

LOC392371 rs4742820 GRIN3A 962 A G 0.0036 9 99774423 99674423 99930334 255911 NR4A3 rsl323435 GRIN3A 442 A G 0.0029 9 99812015 STX17 rsl323434 GRIN3A 441 A G 0.0026 9 99812131 TXNDC4 rslO512285 GRIN3A 330 C T 0.0023 9 99812872 GRIN3A rsl337710 GRIN3A 448 A G 0.005 9 99830334 rs2416864 NT_008470 783 C T 0.001 9 120630058 120530058 120791463 261405 FBXW2 rsl0513404 NT_008470 343 C T 0.0008 9 120643278 PSMD5 rsl318392 ORlJ4 438 A G 0.0007 9 120658438 PHFl9 rsl411270 0R1N2 492 C G 0.0027 9 120691463 TRAFl

NT_008470 ORlJ4 OR1N2 Ul rslO521366 RPS6KA6 408 C T 0.0039 X 82124827 82024827 82224827 200000 RPS6KA6 rs724981 None 1143 C T 0.0044 X 82335552 82235552 82435552 200000 None dbSNP_rs_ID: SNP identification number in NCBI dbSNP database build 124 Gene locus: Gene positioned in the physical position pointed by the SNP according to NCBI Human Genome Build 35

Sequence ID: Sequence identification number Allele A: Alternate SNP allele or its complementary nucleotide in the position indicated by dbSNP rs ID and basepair position

Allele B : Alternate SNP allele or its complementary nucleotide in the position indicated by dbSNP rs ID and basepair position

P-value : P-value from haplotype sharing analysis Position : Basepair Position, SNP physical position according to NCBI Human Genome Build 35

Gene_content: Haplotype gene content, genes positioned within lOOKbp up/downstream from the physical position of the SNPs bordering the haplotype genomic region found using NCBI MapViewer, based on NCBI Human Genome Build 35

Table 4. Haplotype genomic regions with the strongest association with HT in the haplotype sharing analysis (HaploRec + HPM) with 5 SNPs. d G P S E E G b e O t n x e S n S a d t n N e i r e e

P t t n

1 i s c r o o i o s c n o n

U n t

I S e D n

t rs515279 None 994 A G 0 .0049 1 4554061 4454061 4684310 230249 SHREWl rslO489134 None 81 C G 0 .0015 1 4562378 rslO489133 None 80 C T 0 .0049 1 4584310 rs4660918 RAD54L 952 C T 0.0041 1 46443714 46343714 46618723 275009 TSPAN-I rsl0489769 MGC22960 86 A G 0.0039 1 46518723 FLJ20277 RAD54L MUFl UQCRH MGC22960 FAAH rs9326028 SSBP3 1313 C T 0.0034 1 54462646 54362646 54630375 267729 LOC200008 rsl0489809 SSBP3 87 C T 0.0002 1 54469422 MRPL37 rs7524749 SSBP3 1160 C T 0 1 54491264 SSBP3 rs2076571 SSBP3 687 C T 0.001 1 54530120 rsl0489566 SSBP3 85 C G 0.0014 1 54530375 rs542873 DABl 1002 A G 0.0046 1 57426550 57326550 57526550 200000 DABl rs531496 None 1000 C T 0.0018 1 61002405 60902405 61148550 246145 None rsl0493297 None 117 G T 0.0009 1 61003143 rs602295 None 1012 A T 0.0004 1 61004714 rs310159 None 861 C T 0.001 1 61032913 rsl0493298 None 118 C T 0.0049 1 61048550

rsl281611 None 435 C T 0.0019 1 82610585 82510585 82769142 258557 None rsl986902 None 653 A G 0.0006 1 82611768 rsl281590 None 434 A G 0.0007 1 82616264 rslO489861 None 88 C T 0.003 1 82669142 rs721599 None 1136 C G 0.0022 1 83240652 83140652 83342288 201636 None rslO487981 None 63 C T 0.0047 1 83242288 rs477862 COL24A1 972 C T 0.0049 1 86193890 86093890 86337825 243935 COL24A1 rs474106 COL24A1 961 A G 0.0005 1 86194307 rs473232 COL24A1 959 C T 0.0004 1 86194386 rsl0493787 COL24A1 122 C G 0.0004 1 86195125 rslO518362 COL24A1 393 A G 0.0005 1 86195653 rsl0518360 COL24A1 392 C T 0.0023 1 86237825 rsl0494009 None 123 C G 0.0033 1 104422787 104322787 104587618 264831 LOC388656 rsl928326 None 635 C T 0.0024 1 104482567 LOC440598 rs6586445 None 1052 A C 0.0024 1 104485930 rsl928322 None 634 A G 0.0043 1 104487618 rs2861427 None 834 G T 0.0028 1 185715978 185615978 186091821 475843 None rs2861426 None 833 C T 0.0012 1 185716050 rsl912914 None 628 A G 0.0006 1 185776923 rs2175550 None 724 A G 0.0004 1 185811059 rsl912941 None 629 C T 0.0003 1 185837726 rs4845303 None 980 A T 0.0002 1 185884000 rs6428195 None 1030 C G 0.0002 1 185892552 rsl935654 None 636 C T 0.0003 1 185952796 rsl935659 None 637 A G 0.0003 1 185956354 rsl578704 None 568 A G 0.0002 1 185968869 rsl578705 None 569 A G 0.0002 1 185968934 rsl0494628 None 128 C T 0.0003 1 185991821 rsl0494627 None 127 C T 0.0005 1 186233469 186133469 186375070 241601 None rs9287136 None 1252 C T 0.0021 1 186275070 rsl572474 None 562 A G 0.0047 1 188318629 188218629 188658913 440284 None rsl338034 None 449 C T 0.0037 1 188358939 rsl0494658 None 129 A C 0.0036 1 188421032 rs833961 None 1231 C G 0.0008 1 188449185

rsl0494659 None 130 C T 0.0001 1 188451130 rs2785762 None 816 C G 0.0016 1 188453606 rsl0494660 None 131 C T 0.0009 1 188458950 rs7536312 None 1161 A G 0.0004 1 188459017 rslO494661 None 132 A T 0.0008 1 188459839 rsl0494662 None 133 C T 0.0008 1 188507286 rsl0494663 None 134 A G 0.0001 1 188507735 rs6683269 None 1057 C T 0.0001 1 188507895 rsl0494664 None 135 A C 0 1 188509177 rs9287120 None 1251 C G 0.0003 1 188558913 rsl0494673 None 136 C T 0.0016 1 188804177 188704177 188904177 200000 RGS18 rs647908 USH2A 1040 G T 0.0046 1 212493121 212393121 212656039 262918 USH2A rs9308440 XM_372814 1282 G T 0.0023 1 212548330 rsl992099 USH2A 654 A G 0.0034 1 212556039 rslll2903 None 412 A G 0.0048 1 235664628 235564628 235810329 245701 None rs7521497 None 1159 C T 0.0012 1 235703668 rs2105233 None 696 A G 0.0014 1 235710329 rs6734151 None 1060 A G 0.0021 2 5420431 5320431 5520431 200000 None rslO12566 None 4 G T 0.0016 2 11933881 11833881 12033881 200000 LPINl rs6708911 None 1059 C G 0.002 2 12005429 11905429 12106921 201492 LPINl rs966391 None 1346 A G 0.0039 2 12006921 rs7582749 QPCT 1167 C G 0.0025 2 37510988 37410988 37702284 291296 PRKCN rs2287094 QPCT 752 C T 0.0012 2 37511339 QPCT rsl0490445 None 91 G T 0.001 2 37529135 rs2192947 None 728 A G 0.0013 2 37602284 rs6745501 COMMDl 1061 C T 0.0031 2 62188424 62088424 62319430 231006 COMMDl rslO518958 COMMDl 395 A G 0.0022 2 62188624 LOC388954 rsl0496096 COMMDl 140 C G 0.0012 2 62219430 rsl0496095 None 139 A C 0.0046 2 62325264 62225264 62425264 200000 COMMDl

LOC388954 B3GNT1 rsl997454 None 656 A G 0.0014 2 76683211 76583211 76798833 215622 None

rs7592517 None 1168 C T 0.0035 2 76688934 rs2139502 None 709 A G 0.0039 2 76698500 rsl519991 None 542 A C 0.0045 2 76698833 rsl921734 None 632 C T 0.0045 2 77222252 77122252 77565585 443333 None rsl837426 None 607 A G 0.0005 2 77306805 rsl866565 None 616 C T 0 2 77325905 rsl0496205 None 144 A G 0 2 77405362 rs290039 None 845 C T 0.0019 2 77465585 rsl487042 None 530 A G 0.0002 2 77842706 77742706 77957830 215124 None rs994214 None 1357 C T 0.0003 2 77856897 rsl0520195 None 399 A G 0.0001 2 77857830 rs2861215 None 832 C T 0.0009 2 77958447 77858447 78058447 200000 None rsl2072 REGlA 429 A G 0.0041 2 79262160 79162160 79373809 211649 UNQ429 rslO496213 REGL 145 A C 0.0022 2 79273809 REGlB

REGlA

REGL

PAP rs2109312 None 697 C T 0.0031 2 128292061 128192061 128392154 200093 WDR33 rs2109313 None 698 A G 0.0024 2 128292154 POLR2D

MGC4268 rs6756311 None 1065 A G 0.005 2 138714811 138614811 138814811 200000 None rs9287536 LRPlB 1253 C T 0.0032 2 141139308 141039308 141239308 200000 LRPlB rs967295 None 1347 A C 0.0036 2 145854184 145754184 145985484 231300 None rsl0496976 None 148 C T 0.0043 2 145885484 rs6746500 None 1062 C T 0.0032 2 146491334 146391334 146591334 200000 LOC4420 rsl0490387 LOC130576 90 C T 0.005 2 149883856 149783856 149983856 200000 LOC1305 rs9288697 ACVRl 1256 A C 0.0034 2 158520326 158420326 158620326 200000 ACVRl rsl370656 PDEIlA 463 A C 0.0022 2 178433505 178333505 178558300 224795 PDEIlA

rs2164857 PDEIlA 719 A C 0.0011 2 178434643 rsl438048 PDEIlA 508 A C 0.001 2 178438353 rsl0497488 PDEIlA 155 A C 0.0007 2 178446084 rsl370655 PDEIlA 462 C T 0.0048 2 178458300 rsl0497895 LOC344471 157 C T 0.004 2 208752799 208652799 208933065 280266 LOC389072 rsl0497893 CRYGEPl 156 A C 0.0006 2 208803303 LOC344471 rs796287 CRYGB 1210 G T 0.0027 2 208833065 CRYGEPl

CRYGD

CRYGC

LOC442066

CRYGB

CRYGA

LOC389073

LOC130429

IDHl rsl0497952 ERBB4 159 C T 0.0022 2 212548864 212448864 212648864 200000 ERBB4 rs2222182 None 734 G T 0.005 2 215314636 215214636 215426661 212025 LOC402117 rs9288498 None 1254 A C 0.0044 2 215314796 LOC391481 O rs9288499 None 1255 C T 0.0036 2 215315184 BARDl rsl040217 LOC391481 16 A G 0.0037 2 215326661 rsl649882 SPlOO 586 G T 0.0017 2 231160817 231060817 231260817 200000 LOC93349 SPlOO HMG1L3 rsl61912 None 583 A G 0.004 3 7796996 7696996 7913242 216246 GRM7 rs45840 None 948 C T 0.0015 3 7797471 rsl61927 None 584 A G 0.0022 3 7813242 rslO514689 None 352 A G 0.0025 3 35284798 35184798 35463148 278350 LOC442078 rs7625092 LOC389105 1173 A G 0.0022 3 35361572 LOC389105 rsll60577 LOC389105 420 A C 0.0019 3 35363086 rsll60578 LOC389105 421 C T 0.0035 3 35363148 rs3849526 FLJ42117 895 A T 0.002 3 58829160 58729160 58929160 200000 FLJ42117 rs9311694 None 1283 A C 0.0003 3 59015681 58915681 59115681 200000 FLJ42117 rsl913157 None 630 C G 0 3 59149421 59049421 59370772 321351 None

rsl512828 None 538 A C 0 3 59153070 rs2165999 None 720 C T 0.0005 3 59239357 rsl0510805 None 312 C T 0.0013 3 59244082 rs7613873 None 1172 A G 0.0044 3 59270772 rsl473857 None 528 A G 0.002 3 103118335 103018335 103337290 318955 MGC15606 rs771829 LOC152225 1181 C T 0.0003 3 103174504 MAIL rsl514471 LOC152225 540 A G 0 3 103179898 LOC152225 rsl513120 LOC152225 539 C T O 3 103180369 rslO511192 LOC152225 314 C T O 3 103196322 rs771765 None 1180 A G 0.0004 3 103221763 rs978697 None 1352 C T 0.0031 3 103237290 rsl521409 None 544 A G 0.002 3 118340331 118240331 118468524 228193 None rsl462840 None 523 C T 0.0035 3 118345185 rslO511365 None 316 C T 0.0034 3 118368524 rs3846211 None 893 A G 0.0045 3 187789243 187689243 187920935 231692 CRYGS rs9290835 None 1258 A T 0.0014 3 187801488 FLJ10560 rslO29353 AHSG 13 C T 0.0035 3 187820935 DNAJBIl

AHSG

FETUB

HRG

LOC442099

KNGl rs2370156 None 766 C G 0.004 4 34858973 34758973 35098967 339994 None rs7679959 None 1178 C G 0.0015 4 34922573 rslO517338 None 381 C G 0.0005 4 34939974 rs959297 None 1338 A T 0.0009 4 34979810 rsl480972 None 529 A G 0.0033 4 34998967 rs9291304 GABRBl 1259 A G 0.0026 4 46970384 46870384 47070384 200000 GABRBl rsl0488850 None 74 C T 0 . 0013 4 55298473 55198473 55452010 253537 KIT rsl0488849 None 73 C T 0 . 0009 4 55351790 rsl0488848 None 72 A C 0 . 002 4 55352010 rslO517413 None 382 C G 0.0041 4 58498976 58398976 58606986 208010 None rs3905283 None 903 A C 0.0042 4 58506986

rs6821362 None 1070 A G 0.0049 4 61614979 61514979 61760388 245409 None rslO517518 None 383 C T 0.0032 4 61624182 rs767645 None 1177 A T 0.0006 4 61660160 rslO517519 None 384 A T 0.0035 4 61660388 rs293443 None 847 C T 0.0039 4 69411859 69311859 69511859 200000 LOC345378 LOC441018 rsl0516708 None 376 C T 0.0038 4 85194717 85094717 85340203 245486 None rsl827814 None 601 C T 0.0017 4 85212132 rs725997 None 1145 C G 0.0011 4 85212727 rs2017802 None 666 C T 0.0021 4 85240203 rsl0489026 LOC339979 78 C G 0.0019 4 109640337 109540337 109745336 204999 LOC339979 rs7667905 LOC339979 1176 A G 0.0003 4 109644249 LOC391681 rsl0489027 LOC339979 79 A G 0.0013 4 109645336 rslO516557 SEC24B 373 A G 0.0048 4 110753010 110653010 110944263 291253 SEC24B rslO516558 SEC24B 374 C T 0.0029 4 110807600 LOC389217 rs2089273 None 693 A T 0.0011 4 110821552 FLJ20647 K* rsl0488910 FLJ20647 75 A G 0.0026 4 110844263 rs4833470 None 979 C T 0.005 4 112145059 112045059 112269892 224833 LOC391686 rslO488914 None 76 A G 0.0021 4 112169892 rsl376089 None 468 A G 0.0035 4 139853546 139753546 139953546 200000 LOC152594 rslO517654 PDGFC 386 G T 0.0042 4 158138367 158038367 158243059 204692 PDGFC rslO517655 PDGFC 387 A G 0.0021 4 158138514 rs6811964 PDGFC 1069 C T 0.0044 4 158143059 rs9308065 None 1280 A G 0.0036 4 165020972 164920972 165125685 204713 None rs9308066 None 1281 A G 0.0019 4 165025685 rslO517877 None 389 C T 0.0044 4 167437519 167337519 167541111 203592 TLLl rslO517878 None 390 C T 0.0025 4 167437549 rs4691246 None 956 C T 0.002 4 167437606 rslO517879 None 391 G T 0.0035 4 167441111 rslO512675 None 336 C G 0.0019 5 2739258 2639258 2839258 200000 IRX2

CEI

rslO512672 None 335 G T 0.0005 5 2855065 2755065 3117980 362915 IRX2 rs438418 None 936 A G 0.0004 2902436 CEI rs9313016 None 1286 A C 0.0005 2972588 LOC391734 rs9313018 None 1287 A G 0.0034 3017980 LOC442129 rs995553 None 1358 C G 0.0048 8881383 8781383 9008403 227020 None rslO512984 None 341 C G 0.0045 8908403 rs7724797 None 1184 A C 0.004 31131278 31031278 31239623 208345 LOC391774 rsl2658568 None 433 A G 0.0031 31139623 CDH6 rs2115127 CMYA5 702 A G 0.0039 79077255 78977255 79226829 249574 PAPD4 rsl643992 CMYA5 585 A T 0.0042 79085245 CMYA5 rs6453484 CMYA5 1033 C T 0.0014 5 79117469 rs9283795 CMYA5 1248 C T 0.0007 79118103 rs2404670 CMYA5 779 A G 0.005 79126829 rsl605714 None 577 C T 0.0032 98064521 97964521 98235041 270520 LOC402222 rs719246 None 1126 C T 0.0017 98085824 RGMB rslO515283 None 356 C T 0.0002 98121571 CHDl rsl979980 RGMB 650 G T 0.0024 98134967 rs2302981 RGMB 758 A G 0.0039 98135041 rs724719 LOC391819 1142 C T 0.0033 5 108775429 108675429 109038917 363488 LOC285638 rsl0515401 LOC391819 359 A G 0.0024 5 108856709 PJA2 rsl0515406 None 360 A G 0.0022 5 108938917 LOC391819 rs383096 None 892 A G 0.0036 5 125210718 125110718 125310718 200000 None rsl007400 KIAA1985 1 C T 0.0023 5 148362828 148262828 148570256 307428 KIAA1985 rs384979 LOC255187 896 C T 0.0008 5 148439460 LOC255187 rslO515622 LOC255187 364 G T 0.0006 5 148468253 ABLIM3 rsl363522 LOC255187 460 C T 0.0005 5 148469763 rsl422586 None 502 C T 0.0014 5 148470256 rs4704935 None 957 A T 0.0022 5 155387010 155287010 155487010 200000 None rs249882 None 795 C T 0.0022 5 155572134 155472134 155705573 233439 SGCD rs30280 None 857 C G 0.0045 5 155605573

rslO484199 None 32 A G 0.0007 5 157430213 157330213 157603797 273584 LOC345471 rs716376 None 1118 A G 0 5 157479655 rsl614336 None 582 A C 0 .0003 157484446 rsll73476 None 424 G T 0 .0007 157489487 rsl540944 None 552 A A GG 00 ..00004499 55 157499677 rslO515758 None 365 AA GG 00 ..00003399 55 157503797 rslO515768 None 366 A G 0.0044 5 158017072 157917072 158129553 212481 EBF rs824848 None 1230 A G 0.0013 5 158019033 rs6881040 None 1075 A G 0.0019 5 158028752 rs403334 None 910 A C 0.0023 5 158029229 rslO515769 None 367 C T 0.0043 5 158029553 rs4128400 None 916 C G 0.0036 5 161087892 160987892 161187892 200000 GABRA6

LOC441113 rsll57122 GABRAl 417 C T 0.0003 5 161251892 161151892 161419863 267971 GABRAl rs2279020 GABRAl 750 C T 0.002 5 161255467 rs4144483 GABRAl 927 A G 0.0035 5 161256450 rslO515836 None 368 C T 0.0045 5 161319863 rs4128628 None 917 C T 0.0041 5 178971483 178871483 179071483 200000 LOC441120

RUFYl HNRPHl LOC285679 LOC389352 CANX rslO516146 MAMLl 372 A G 0.0042 5 179099580 178999580 179199580 200000 LOC285679

LOC389352 CANX MAMLl LTC4S MGAT4B SQSTMl LOC51149 rs511574 PHACTRl 992 G T 0.0018 6 12824508 12724508 12973311 248803 PHACTRl rs6922482 PHACTRl 1078 C T 0.0022 6 12873311 rs8541 None 1232 C T 0.0021 6 13398217 13298217 13509896 211679 PHACTRl

rs202020 None 667 C G 0.0032 6 13409896 TBC1D7 GFODl rsl0484858 BPAGl 40 C T 0.0038 6 56571971 56471971 56769232 297261 DST rs6941626 DST 1084 C T 0.0033 6 56607148 rslO498811 DST 166 A G 0.0047 6 56669232 rs9320728 None 1305 C T 0.004 6 120323232 120223232 120423232 200000 None rs9321214 None 1306 C T 0.0029 6 130524915 130424915 130677705 252790 L3MBTL3 rs6569665 SAMD3 1050 C T 0.0036 6 130575427 SAMD3 rs6934450 SAMD3 1081 A G 0.0043 6 130577705 rslO484614 STXIl 35 C T 0.0006 6 144522215 144422215 144742215 320000 SF3B5 rsl983773 STXIl 652 A C 0.0004 6 144523460 MRPL42P3 rs6935462 None 1082 A T 0.0005 6 144554694 STXIl rs667765 None 1056 C T 0.0041 6 144642215 LOC285741

UTRN rs6938409 UTRN 1083 A G 0.0047 6 144958637 144858637 145087523 228886 UTRN rsl830271 UTRN 603 C T 0.0027 6 144963781 Ul rs951573 UTRN 1328 A G 0.0019 6 144987523 rs2758778 None 813 A G 0.0045 6 153099916 152999916 153266436 266520 SYNEl rs633596 None 1028 C T 0.0023 6 153157601 MYCTl rs3823082 VIP 890 C T 0.0047 6 153166436 VIP rs2146162 ACAT2 711 C T 0.0049 6 160151513 160051513 160251513 200000 SOD2

WTAP ACAT2 TCPl MRPLl8 PNLDCl rsl998167 None 657 A G 0 .0035 6 166688847 166588847 166789073 200226 MGC35308 rsl998168 None 658 A G 0 .0025 6 166689073 C6orf83

LOC401284 BRP44L rs2235280 RPS6KA2 740 A G 0.0042 6 166856907 166756907 166956907 200000 BRP44L

RPS6KA2

rs6462545 SDKl 1036 A G 0.0044 7 3852653 3752653 4039900 287247 SDKl rsl0485860 SDKl 52 C T 0.0026 7 3863524 rs654384 SDKl 1048 C T 0.0023 7 3939900 rsll78363 None 426 A G 0.0034 7 17951650 17851650 18113337 261687 LOC402463 rsll78328 LOC402463 425 G T 0.0024 7 18006698 rs6461373 None 1035 G T 0.0018 7 18006935 rslO486419 LOC402463 54 C T 0.0037 7 18013337 rs4719652 None 958 C T 0.005 7 21031040 20931040 21131040 200000 LOC340274 rs9638787 DNAHIl 1342 C G 0.0038 7 21423805 21323805 21619605 295800 SP4 rsl0226107 DNAHIl 6 A G 0.0016 7 21452680 DNAHIl rs2177520 DNAHIl 725 C G 0.0027 7 21471062 rsl0499538 DNAHIl 171 A G 0.0012 7 21471340 rs7793951 DNAHIl 1193 C G 0.0018 7 21473279 rs970604 DNAHIl 1348 A G 0.0018 7 21478560 rslO485971 DNAHIl 53 A C 0.0019 7 21519605 rslO486618 None 57 C G 0.0019 7 33600653 33500653 33789384 288731 BMPER rslO486619 None 58 C T 0.0005 7 33600838 rs7788027 None 1192 A G 0.001 7 33620034 rs315853 None 863 A G 0.0023 7 33689384 rs2348460 FLJ21075 762 A G 0.0047 7 47620010 47520010 47891917 371907 MGC16075 rs7806630 FLJ21075 1194 C T 0.003 7 47620081 FLJ21075 rsl0499668 PKDlLl 172 A G 0.0011 7 47710606 PKDlLl rs3176499 HUSl 865 A G 0.0036 7 47791917 HUSl

MGC33329

LOC136288 rs717707 ABCA13 1123 C T 0.005 7 48206690 48106690 48306690 200000 ABCA13 rs921909 None 1244 A T 0.0044 7 50018956 49918956 50118956 200000 LOC340228 rsl581590 None 572 C G 0.0041 7 53880000 53780000 54011504 231504 None rsl0499727 None 173 C T 0.0027 7 53897460 rsl0499728 None 174 A G 0.0028 7 53904808 rs953160 None 1330 A G 0.003 7 53911397 rs956316 None 1336 C T 0.0033 7 53911504

rslO487817 None 60 A G 0.0049 7 105552534 105452534 105701508 248974 PBEFl rslO499961 None 175 C T 0.0025 7 105563140 rs2014402 None 663 A G 0.0049 7 105578138 rs2519681 None 798 C T 0.0042 7 105578447 rsl79861 None 599 C T 0.0037 7 105600903 rs719917 None 1131 C T 0.0043 7 105601508 rsl365358 None 461 A G 0.002 7 135363114 135263114 135569609 306495 None rsl0270360 LOC401406 10 A G 0.0005 7 135407033 rs730694 LOC401406 1149 C T 0 7 135407458 rsl0488406 None 66 C T 0 7 135408567 rs2114337 None 701 A G 0.0004 7 135412215 rsl0488407 None 67 C T 0.004 7 135469609 rsl0500165 CNTNAP2 176 A G 0.0049 7 145980635 145880635 146107522 226887 CNTNA rs4537227 CNTNAP2 944 A G 0.0037 7 146007522 rsl599405 None 576 A T 0.0048 7 155187279 155087279 155287279 200000 SHH

LOC389602 rs7814546 None 1195 C T 0.0046 8 12730375 12630375 12856234 225859 FLJ23749 rs2068280 None 685 G T 0.0035 8 12736493 LOC340357 rs4831837 None 978 A G 0.0025 8 12756234 FLJ36980 rsl346277 SGCZ 453 A G 0.0022 8 14204068 14104068 14347492 243424 SGCZ rsl0503493 SGCZ 219 G T 0.0019 8 14247492 rs823603 None 1229 A C 0.0036 8 16861200 16761200 16967896 206696 FGF20 rs823600 None 1228 G T 0.0038 8 16861804 LOC286097 rs963080 None 1340 A G 0.0038 8 16867896 rsl464252 None 524 C T 0.0045 8 60472233 60372233 60572233 200000 None rsl0504292 None 227 A G 0.0037 8 60586442 60486442 60686442 200000 None rsl0504596 None 228 C T 0.0026 8 76850876 76750876 76950876 200000 None rsl0504677 PKIA 229 G T 0.0047 8 79623737 79523737 79755531 231794 PKIA rs2062233 PKIA 684 A G 0.0046 8 79655531 CGI-62

rs416011 None 928 C T 0.0018 88602922 88502922 88769709 266787 None rsl0504835 None 231 A G 0.0025 88616896 rsl0504836 None 232 A C 0.0043 88669709 rsll60054 None 419 A G 0.0048 8 106006662 105906662 106106662 200000 None rsl0505087 ZFPM2 234 C T 0.004 8 106877254 106777254 106988057 210803 ZFPM2 rs6990997 ZFPM2 1091 C T 0.0027 8 106881703 rs7007352 None 1093 C T 0.0032 8 106888057 rs9297381 None 1265 C T 0.0024 8 107403507 107303507 107524855 221348 LOC346887 rs6469061 None 1038 C T 0.001 8 107424816 rs905556 None 1239 C T 0.0009 8 107424855 rsl789967 None 597 G T 0.0027 8 107526431 107426431 107626431 200000 None rsl0505137 LOC392262 235 C T 0.0034 8 111210785 111110785 111342982 232197 LOC392262 rsl0505138 LOC392262 236 A T 0.003 8 111211034 rs2060688 LOC392262 682 C T 0.001 8 111220823 rsl0505139 LOC392262 237 C T 0.0018 8 111220849 rsl0505140 LOC392262 238 A G 0.0009 8 111223708 rs921382 LOC392262 1243 C G 0.0011 8 111236214 rs4735150 LOC392262 960 C T 0.0025 8 111236704 rs2198044 LOC392262 729 A G 0.0023 8 111242982 rsl412254 None 495 G T 0.0028 9 1500230 1400230 1602232 202002 None rslO491859 None 104 C T 0.0034 9 1500299 rslO491858 None 103 A G 0.0041 9 1500495 rslO491857 None 102 C T 0.005 9 1502232 rs456044 RCLl 946 C T 0.0032 9 4841661 4741661 4941661 200000 LOC392282

RCLl

LOC441384 rs719673 None 1129 A G 0.0015 9 4947650 4847650 5088639 240989 RCLl rs2381194 None 773 C T 0.0008 9 4949331 LOC441384 rsl327493 JAK2 444 C G 0.0009 9 4983082 JAK2

4988639 rsl374172 None 466 A C 0.0049 9 12018131 11918131 12121256 203125 None rs2077861 None 690 A G 0.0036 9 12018387 rsl446253 None 509 C G 0.0032 9 12021256

rs947144 ADAMTSLl 1321 A G 0.0046 9 18643380 18543380 18771452 228072 ADAMTSLl rslO511661 ADAMTSLl 320 A G 0.0026 9 18644351 rsl412672 ADAMTSLl 497 C G 0.0039 9 18670679 rs776760 ADAMTSLl 1189 A G 0.0037 9 18671452 rslO491828 FLJ31810 101 G T 0.003 9 28030600 27930600 28191541 260941 FLJ31810 rsl452353 FLJ31810 512 A G 0.0009 9 28030937 rsl343456 FLJ31810 450 C T 0.0012 9 28039518 rsl0511820 FLJ31810 321 G T 0.0005 9 28045603 rs2383761 FLJ31810 774 A G 0.0006 9 28054538 rsl452356 FLJ31810 513 C T 0.0003 9 28057491 rs7853840 FLJ31810 1197 A G 0.0015 9 28058081 rs7858580 FLJ31810 1198 A G 0.0009 9 28059562 rslO511821 FLJ31810 322 A G 0.002 9 28064589 rsl452357 FLJ31810 514 C T 0.003 9 28090846 rs993038 FLJ31810 1356 C G 0.0021 9 28091281 rs2060850 FLJ31810 683 A G 0.0012 9 28091541 rslO511824 FLJ31810 323 A G 0.005 9 28195162 28095162 28295162 200000 FLJ31810 rslO491883 FLJ31810 105 C T 0.0044 9 28552256 28452256 28718807 266551 FLJ31810 rslO511829 FLJ31810 324 C G 0.0048 9 28618807 rslO512162 None 327 A G 0.0042 9 85091455 84991455 85237345 245890 None rs2769613 None 815 C T 0.0046 9 85137345 rs2814726 None 818 C T 0.0048 9 85244200 85144200 85353684 209484 None rslO512167 None 328 C T 0.0046 9 85253684 rs2417359 None 784 A G 0.0024 9 102187111 102087111 102287111 200000 None rsl0513402 None 342 C T 0.0043 9 122244490 122144490 122497997 353507 MRRF rs950104 None 1324 A G 0.0006 9 122244779 PTGSl rs2416863 NT 008470 782 C T 0.0002 9 122332531 ORlJl rs2416864 NT 008470 783 C T 0 9 122333567 ORlJ2 rsl318392 ORlJ4 438 A G 0.0001 9 122361947 ORlJ4 rsl411270 LOC138882 492 C G 0.0001 9 122394972 ORlNl rsl831369 OR1N2 604 A G 0.0002 9 122395096 OR1N2 rsl411271 OR1N2 493 C G 0.0003 9 122395332 ORlL8

rsl411272 0R1N2 494 C T 0.0005 9 122395904 ORlHlP rslO41355 None 17 A G 0.0011 9 122397215 ORlQl rslO24288 None 9 C G 0.0025 9 122397449 ORlBl rs2149931 None 713 C T 0.0039 9 122397997 rs7912369 None 1203 A G 0.0018 10 1995604 1895604 2238650 343046 LOC439946 rsl010784 None 3 C G 0.0011 10 2013899 LOC399707 rsl335311 None 447 C G 0.0001 10 2014269 rsl0508220 None 272 A G 0.0001 10 2014591 rsl335310 None 446 C T 0.0001 10 2074135 rs2026493 None 670 A G 0.0006 10 2114063 rs4880556 None 983 A G 0.0031 10 2138650 rsl0508229 None 274 A G 0.0021 10 2381642 2281642 2483152 201510 LOC399708 rsl0508230 None 275 A G 0.002 10 2383152 LOC387630 rs649537 FBXOl8 1043 A C 0.0047 10 5985678 5885678 6098078 212400 GDI2 rs668498 FBXOl8 1058 C T 0.003 10 5998078 ANKRDl6 FBXOl8 IL15RA LOC399713 00 O IL2RA rsl0508410 None 276 C G 0.0029 10 10710236 10610236 10814839 204603 None rsl0508411 None 277 A G 0.0029 10 10711607 rsl0508412 None 278 C T 0.0028 10 10713082 rs960791 None 1339 A T 0.0032 10 10714839 rsl0508562 CACNB2 283 C T 0.0044 10 18845512 18745512 18953283 207771 CACNB2 rsl0508563 CACNB2 284 A C 0.003 10 18852597 NOPDl rs7081811 CACNB2 1101 A G 0.0018 10 18853283 rsl0508771 None 286 A T 0.0042 10 32532098 32432098 32764642 332544 LOC441550 rs3006608 None 854 C T 0.0026 10 32532124 LOC441551 rsl0508773 EPCl 287 C T 0.004 10 32615450 LOC439953 rs950132 EPCl 1325 C T 0.0022 10 32664642 EPCl rs4445583 None 939 C T 0.0002 10 52173015 52073015 52472683 399668 FLJ31958 rsl0508933 ACF 289 C G O 10 52240121 LOC439978 rsl0509071 None 295 A G 0.0001 10 52257286 LOC441561 rs4567398 ACF 947 C T 0.0011 10 52286928 LOC399773 rsl0490967 None 94 A G 0.003 10 52372683 ACF

rsl0509012 PCDH15 290 G T 0.0013 10 55796840 55696840 56066306 369466 PCDH15 rsl832879 PCDH15 605 C T 0.0009 10 55878340 rs2026414 PCDH15 669 A G 0.0008 10 55878742 rs9299552 PCDH15 1267 C T 0.0004 10 55911196 rsl0509013 PCDH15 291 A G 0.0022 10 55957107 rsl781451 PCDH15 593 C T 0.0045 10 55966306 rsl900493 None 624 A G 0.0036 10 56783626 56683626 57184485 500859 LOC3 rs7908118 None 1202 C T 0.001 10 56883032 rs2050318 None 676 G T 0.0006 10 56934746 rsl0509034 None 292 C T 0.001 10 56962466 rs997418 None 1361 A G 0.0015 10 56976835 rsl413668 None 500 A G 0.0028 10 56985141 rsl0509035 None 293 G T 0.0019 10 57015785 rs4336940 None 934 A G 0.0021 10 57039123 rsl0509036 None 294 A G 0.0031 10 57040245 rs2244956 None 743 C G 0.0049 10 57084485

00 rs4474385 ANK3 942 A T 0.0032 10 61563083 61463083 61696196 233113 ANK3 rsl0509123 ANK3 296 A C 0.0006 10 61563151 rsl0509124 ANK3 297 C T 0.0005 10 61563739 rs3213829 ANK3 869 G T 0.0004 10 61563904 rs4948254 ANK3 987 A T 0.0013 10 61569339 rs4245585 ANK3 932 C T 0.004 10 61596196 rsl904620 CTNNA3 625 A G 0.005 10 68721550 68621550 68821550 200000 CTNNA3 rs987312 None 1354 A G 0.0033 10 85304655 85204655 85469801 265146 None rsl0509478 None 307 A T 0.004 10 85369801 rsl0509408 MINPPl 306 C T 0.0042 10 89300261 89200261 89408314 208053 MINPPl rsl408377 MINPPl 487 C T 0.0017 10 89300642 rs2147287 None 712 A G 0.0016 10 89308314 rs2209672 None 730 A G 0.0022 10 92020205 91920205 92120599 200394 None rsl0509597 None 308 A C 0.0031 10 92020599 rs7069564 None 1100 C T 0.0028 10 112887060 112787060 112987060 200000 ADRA2A

rs2468826 None 789 C T 0.0042 11 18127264 18027264 18227264 200000 LOC113174 SAA3P MRGX3 MRGX4 SAA4 SAA2 rsl0500911 None 185 A C 0.0033 11 21568879 21468879 21742888 274009 NELLl rs963497 None 1341 A G 0.0006 11 21595783 rsl0500913 None 186 A G 0.0002 11 21613794 rs7112382 None 1105 A G 0.0003 11 21614149 rs7107412 None 1104 C T 0.0011 11 21642613 rsl459865 None 521 A G 0.0036 11 21642888 rs4086865 None 913 C T 0.005 11 25968769 25868769 26068769 200000 None rsl346099 None 451 C G 0.0047 11 35066313 34966313 35187935 221622 PDHX rsl425800 None 504 C T 0.0029 11 35066493 CD44 rs353589 None 876 A G 0.0023 11 35077802 rs353587 None 875 A G 0.0013 11 35079237 rsl559759 None 559 G T 0.0004 11 35079627 K* rs4756190 None 965 A G 0.0001 11 35080616 rs507230 None 990 C T 0.0002 11 35085748 rs634096 None 102 C T 0.0017 11 35087935 rsl0501486 None 197 C T 0.0046 11 80347478 80247478 80558705 311227 None rsl391533 None 474 C T 0.0006 11 80347594 rsl608169 None 580 G T 0.0006 11 80428536 rsl829764 None 602 C T 0.0012 11 80428642 rs2373717 None 771 A T 0.0009 11 80457064 rsl0501487 None 198 A T 0.0042 11 80458705 rsl941437 LOC390241 638 C T 0.0036 11 91849773 91749773 91951009 201236 LOC440062 rsl0501790 LOC440062 201 C T 0.0042 11 91851009 rs721346 None 1135 A C 0.0021 11 103242667 103142667 103376131 233464 PDGFD rsl400549 None 479 C T 0.001 11 103245119 rs503208 None 989 C G 0.0002 11 103263149 rs7127296 None 1106 A C 0.0034 11 103276131 rsl789819 None 596 C T 0.0048 11 109185632 109085632 109368427 282795 LOC260340 rs715312 None 1112 C T 0.0026 11 109222549

rs666899 None 1055 A G 0.002 11 109239458 rsl0488748 None 70 A G 0.0046 11 109268427 rsl0502283 LOC338661 202 C T 0.0031 11 123258475 123158475 123358896 200421 OR6M2P rsl054041 LOC338661 409 C T 0.0049 11 123258896 OR6M3P

LOC338661

OR8D4

OR4D5

OR6T1

ORlOSl rsl0492107 PRKWNKl 107 A G 0.0026 12 842330 742330 972280 229950 PRKWNKl rs2051852 PRKWNKl 678 C T 0.0023 12 872280 HSN2 RAD52 ELKS rs7954090 ELKS 1208 C T 0.0022 12 1034157 934157 1134157 200000 ELKS rslO492194 None 108 C T 0.0035 12 16806772 16706772 16907436 200664 None rs7296019 None 1148 A C 0.0039 12 16807436 rs7135355 None 1108 G T 0.0023 12 58108434 58008434 58238327 229893 None rs276002 None 814 A G 0.0001 12 58138327 rs274460 None 810 A G 0 12 58238608 58138608 58421404 282796 SLC16A7 rs3847653 None 894 C G 0 12 58238640 rs3897770 None 901 A C 0 12 58238933 rsl0506395 None 246 C T 0 12 58258088 rsl391130 None 473 A G 0 .0004 12 58270954 rsl0506396 None 247 G T 0 .0019 12 58321404 rslll75617 None 415 A C 0.0039 12 63677987 63577987 63777987 200000 LOC400046

WIFl rsl0506645 TPH2 250 A G 0.0046 12 70671767 70571767 70884135 312368 TBC1D15 rs4760754 TPH2 966 A C 0.001 12 70675106 TPH2 rsl487275 TPH2 531 A C 0.0002 12 70696559 rsl386486 TPH2 472 C T 0 12 70698487 rsl386485 TPH2 471 A C 0 12 70698634 rsl386483 TPH2 470 A G 0.0001 12 70698761

rs7977245 None 1212 C T O 12 70784135 rs2687491 None 803 A G 0.0017 12 70901536 70801536 71001536 200000 LOC283392

TRHDE rsl394380 None 475 A G 0.0022 12 97055132 96955132 97178944 223812 None rsl842328 None 609 C T 0.0025 12 97078944 rsl0507103 EB-I 255 C T 0.002 12 97866110 97766110 97968064 201954 EB-I rsl0507104 EB-I 256 A G 0.0014 12 97868064 rs2888378 EB-I 840 A G 0.0007 12 97978643 97878643 98106090 227447 EB-I rs2372643 EB-I 768 A G 0.0005 12 97988506 rs2372644 EB-I 769 A C 0.0017 12 97993228 rs4762559 EB-I 967 C T 0.0013 12 98001108 rsl0507107 EB-I 257 C G 0.0025 12 98006090 rs2270861 DRIM 747 C T 0.0026 12 100238849 100138849 100345515 206666 DRIM rs2373444 DRIM 770 C T 0.0039 12 100245515

ARLl rs6539051 None 1046 G T 0.0048 12 101621075 101521075 101721075 200000 LOC283432 oo rs9316335 None 1296 G T 0.0048 13 20856918 20756918 20960207 203289 LOC440127 rs9316337 None 1297 C T 0.0043 13 20860207 LOC387904

GRK6PS

LOC387905

FLJ25952 rsl555619 None 558 C T 0.0033 13 21754983 21654983 21880939 225956 None rs9316871 None 1298 C T 0.0013 13 21759921 rs9316902 None 1299 A T 0.0011 13 21780457 rs6490720 None 1041 A G 0.0026 13 21780871 rs6490721 None 1042 G T 0.0047 13 21780939 rs9315991 None 1294 G T 0.0013 13 42629541 42529541 42729541 200000 DNAJDl

FLJ10094 rs9318485 None 1301 A G 0.004 13 76935786 76835786 77075376 239590 SCEL rs9318486 None 1302 A C 0.0009 13 76965059 rs4884068 None 984 C G 0.0004 13 76965482 rsl323618 None 443 A G 0.0024 13 76975376

rs2086428 FARPl 692 C T 0.0025 13 97797872 97697872 97915213 217341 FARPl rs7330217 FARPl 1152 A G 0.0027 13 97799173 STK24 rs2892734 FARPl 841 A G 0.003 13 97815213 rsl0508138 None 269 C T 0.0025 13 103749582 103649582 103871158 221576 None rs728555 None 1147 A G 0.0011 13 103755724 rs9300909 None 1269 A G 0.0008 13 103756340 rs9284215 None 1250 C T 0.0027 13 103757709 rsl0508139 None 270 C T 0.004 13 103771158 rsll620131 None 422 A C 0.0012 13 108935145 108835145 109122110 286965 None rsl0492480 None 113 C T 0.0007 13 108947427 rsl410425 None 491 C T O 13 108996160 rsl0492479 None 112 A G O 13 109013803 rsl0492478 None 111 A C 0.0002 13 109022110 rs719737 None 1130 C T 0.0044 13 109148350 109048350 109248350 200000 IRS2 rsl0483355 STRN3 22 A G 0.0033 14 30472655 30372655 30611516 238861 COCH rsl0483354 STRN3 21 A C 0.0012 14 30500092 STRN3 Ul rsl977130 STRN3 647 C T 0.0032 14 30511516 AP4S1 rs243294 NPAS3 786 A G 0.0004 14 32793167 32693167 32942075 248908 NPAS3 rs2173802 NPAS3 723 A G 0 14 32817425 rsl886781 NPAS3 620 A G 0 14 32818656 rs716193 NPAS3 1117 G T 0 14 32824348 rs8007568 NPAS3 1214 C G 0 14 32834319 rsl0483435 NPAS3 25 G T 0 14 32842075 rsl0483694 None 27 A G 0.0022 14 57585264 57485264 57685309 200045 UBA52P3 rsl0483695 None 28 A G 0.0018 14 57585309 rs7152153 None 111 C T 0.005 14 76265708 76165708 76513050 347342 CYCSPl rs4435183 KIAA0759 938 C T 0.0038 14 76323852 LAMRlP3 rs2056855 LOC145497 679 C T 0.0028 14 76366892 KIAA1036 rsl0483879 LOC145497 30 C T 0.0028 14 76367923 KIAA0759 rs2885625 LOC145497 839 A G 0.0005 14 76374502 C14orfl66B rs6574333 LOC145497 105 A G 0.0009 14 76375042 RPL22P2 rs741854 None 115 A G 0.0015 14 76413050 RPLPlPl

rs8010717 LOC388001 1217 C T 0.0044 14 79480194 79380194 79581032 200838 NRXN3 rs8010105 LOC388001 1216 A G 0.0015 14 79480345 LOC388001 rs8014855 LOC388001 1218 C T 0.0019 14 79481032 rs9323707 LOC400234 1312 A G 0.0022 14 81155960 81055960 81255960 200000 SELlL

EEF1A1P2 rsl257920 None 431 A T 0.0039 14 97760147 97660147 97860147 200000 None rs976451 EMLl 1351 G T 0.0034 14 99415166 99315166 99515166 200000 EMLl

LOC341965 RPS2P3 rs2224585 MGC4645 736 A G 0.0023 14 99938712 99838712 100058306 219594 SLC25A29 rsl951522 MGC4645 641 C T 0.0029 14 99958306 C14orf68 WARS

NDUFB3P4 LOC440198 MGC4645 rs4778334 None 971 A G 0.0041 15 20592297 20492297 20692297 200000 CYFIPl NIPA2 NIPAl LOC400320 LOC339003 rsl458885 None 520 A C 0.0017 15 33249052 33149052 33496024 346972 NANOGP8 rslO519989 MGC14798 397 A C 0.0003 15 33317865 LOC441722 rs318360 None 867 A G 0.003 15 33396024 LOC390572 LOC440272 LOC441723 MGC14798 rs3825847 BGl 891 C T 0.002 15 76250541 76150541 76350541 200000 KIAA1055 CIB2 IDH3A BGl DNAJA4 rsl0520640 None 401 C G 0.0049 15 85153480 85053480 85285010 231530 None rsl452459 None 515 A G 0.005 15 85185010

rs7601 PRCl 1170 C T 0.0025 15 89310596 89210596 89426322 215726 FURIN rs6496742 PRCl 1044 C T 0.0006 15 89324040 FES rsll857612 PRCl 428 C T 0.0018 15 89326322 MAN2A2 MGC45386 SMAP-I MGC14386 PRCl VPS33B LOC390638 rsl400786 SLC03A1 480 A C 0.0032 15 90387143 90287143 90487143 200000 SLCO3A1 rs7178880 None 1125 A G 0.0035 15 90512987 90412987 90621604 208617 SLCO3A1 rsl0520704 None 403 A G 0.0026 15 90521604 rs9302552 None 1274 A C 0.0046 16 62071933 61971933 62173509 201576 None rsl0500474 None 181 A G 0.0036 16 62073509 rs2077576 WWOX 688 A G 0.003 16 76896265 76796265 76996265 200000 WWOX

00 rs4130513 WWOX 922 A G 0.0013 16 77016251 76916251 77195856 279605 WWOX rslO514437 WWOX 349 C T 0.0006 16 77050361 rs2738646 WWOX 809 C G 0.0016 16 77050888 rsl397927 WWOX 477 A G 0.0035 16 77095856 rsl0514506 CDYL2 350 A G 0.004 16 79278578 79178578 79404911 226333 CDYL2 rs8047401 CDYL2 1221 C T 0.0017 16 79304514 rsl0514507 CDYL2 351 C G 0.0031 16 79304695 rs3100179 CDYL2 860 A T 0.0045 16 79304911 rs2469825 None 791 A C 0.0042 17 36095188 35995188 36359516 364328 SMARCEl rs2462957 None 788 C T 0.004 17 36095487 MGC45562 rs2429555 None 785 C G 0.0027 17 36137973 KRT24 rs4132126 KRT25D 925 A G 0.0044 17 36205780 KRT25A rs7219451 KRT25D 1137 C T 0.0024 17 36210528 KRT25B rs2469828 None 792 C T 0.0008 17 36257986 KRT25C rs2469816 None 790 A G 0.002 17 36259480 KRT25D rs9303297 None 1275 C T 0.0041 17 36259516 KRTlO

MGC21518

KRT12

KRT20

KRT23 rs551920 LOC388458 1006 C G 0.0022 18 4261385 4161385 4390528 229143 LOC388458 rs523436 LOC388458 996 A G 0.0014 18 4285384 rs627777 LOC388458 1026 C T 0.0009 18 4290528 rsl0502579 None 205 C T 0.0035 18 27824861 27724861 28111131 386270 KIAA1012 rs627346 LOC390848 1025 A G 0.0023 18 27910954 LOC342705 rsl0502582 None 206 A T 0.0007 18 27991040 RNFl25 rsl0502583 None 207 G T 0.0019 18 28011131 LOC390848 LOC440491 RNFl38 MEPlB Clδorfll rs4627439 None 951 G T 0.0031 18 34488202 34388202 34588202 200000 None rsl0502772 None 212 C T 0.0036 18 37438094 37338094 37634376 296282 NPMlPl rsl0502774 None 213 G T 0.002 18 37508018 rsl865290 None 615 A T 0.0017 18 37509556 rs8092873 None 1226 A G 0.0018 18 37510334 90 rs9304251 None 1276 G T 0.0031 18 37534376 rs8091714 None 1224 A C 0.0042 18 51803567 51703567 51915280 211713 None rsl978502 None 648 C G 0.002 18 51815225 rsl978503 None 649 A G 0.0013 18 51815280 rsl403302 None 483 C G 0.0043 18 59525016 59425016 59745607 320591 SERPINB4 rs952857 None 132 G T 0.0043 18 59525552 SERPINB3 rsl522723 SERPINBIl 548 C T 0.003 18 59535960 SERPINBIl rsl395266 SERPINBIl 476 C T 0.0002 18 59541312 SERPINB7 rs931850 None 130 A G O 18 59544814 SERPINB2 rsl522722 None 547 C T O 18 59572521 SERPINBlO rsl0503087 None 216 A C 0.0014 18 59627434 rsl701586 None 590 A G 0.0036 18 59645607 rsl573400 None 564 A G 0.003 18 65077486 64977486 65180058 202572 None rs572166 None 1008 A G 0.0016 18 65078530 rs998156 None 1365 A C 0.0033 18 65078841 rs481598 None 976 A T 0.0049 18 65080058 rsl457856 None 518 C T 0.0034 19 57649297 57549297 57749935 200638 ZNF610

rs2168792 None 721 C G 0.0017 19 57649935 LOC400713

LOC284373

ZNF528

ZNF534

LOC441862

ZNF578

LOC388558 rs2058318 LOC440544 680 C G 0.0039 19 61554788 61454788 61655118 200330 LOC440544 rs2058319 LOC440544 681 C T 0.0032 19 61555118 ZNF542 ZNF582 ZNF583 FLJ14011 rs3971706 MGC9913 908 A G 0.0039 19 61697881 61597881 61797881 200000 ZNF583

FLJ14011

MGC9913

ZNF471

ZFP28

FLJ26175 rsl294690 FKBPlA 436 A G 0.0046 20 1319697 1219697 1520408 300711 SNPH rs6042018 None 1013 C T 0.0006 20 1332298 SDCBP2 rs6042209 None 1014 A G 0.0001 20 1354212 FKBPlA rsl884389 None 618 C T O 20 1358582 NSFLlC rsl884390 None 619 C T 0.0002 20 1358818 PTPNS1L3 rsl0485823 None 50 A G 0.0007 20 1367846 LOC441937 rs715217 PTPNS1L3 1111 A G 0.0015 20 1420408 PTPNS1L2

SIRPBl rs6108011 None 1021 A G 0.0043 20 7500504 7400504 7670826 270322 None rs6108015 None 1022 C G 0.0016 20 7515858 rs6086141 None 1020 C T 0.0031 20 7570826 rsl408872 None 488 A G 0.0044 20 37804766 37704766 37904766 200000 None rsl0485825 None 51 C T 0.0038 20 61608092 61508092 61729912 221820 KCNQ2 rsl86332 PTK6 613 C T 0.0048 20 61629912 EEF1A2 C20orfl49 PTK6

SRMS

MGC5356

PRIC285

LOC200213

GMEB2

LOC388807 rs2825583 None 820 C T 0.0039 21 19734374 19634374 19893599 259225 None rs2825601 None 821 A G 0.0011 21 19766620 rs2825610 None 822 G T 0.0009 21 19793455 rsl489734 None 532 A G 0.0038 21 19793599 dbSNP_rs_ID: SNP identification number in NCBI dbSNP database build 124 Gene locus: Gene positioned in the physical position pointed by the SNP according to NCBI Human Genome Build 35

P-value : P-value from haplotype sharing analysis O Position : Basepair Position, SNP physical position according to NCBI Human Genome Build 35

Table 5. Haplotype blocks (n = 14) with the strongest association with HT based on HaploRec + HPM analysis. dbSNP_rs_ID Gene locus Sequence_ID Chr Risk allele Variants Chi-square P-value rs4845303 None 980 1 A A/T 23.70 <1.0E-5 rs6428195 None 1030 1 C C/G rsl935659 None 637 1 G A/G rsl997454 None 656 2 A A/G 19.73 1.00E-05 rs2139502 None 709 2 G A/G rsl519991 None 542 2 C A/C rsl521409 None 544 3 A A/G 23.54 <1.0E-5 rslO511365 None 316 3 C C/T rslO511366 None 317 3 T C/T rs7679959 None 1178 4 C C/G 21.37 <1.0E-5 rslO517338 None 381 4 G C/G

*O rs959297 None 1338 4 A A/T rs2278677 T 749 6 G A/G 21.29 <1.0E-5 rs3886091 None 899 6 C C/G rsl998167 None 657 6 A A/G rsl998168 None 658 6 G A/G rs2235280 RPS6KA2 740 6 G A/G rsl0521062 None 404 9 A A/C 18.40 0.00002 rslO512296 None 331 9 A A/G rsl924001 None 633 9 C C/G rs2417359 None 784 9 G A/G rsl0508933 ACF 289 10 G C/G 19.56 1.00E-05 rsl0509071 None 295 10 G A/G rsl0490967 None 94 10 A A/G rsl0508771 None 286 10 T A/T 18.76 0.00001 rs3006608 None 854 10 C C/T rsl0508773 EPCl 287 10 C C/T rs950132 EPCl 1325 10 C C/T

rsl386486 TPH2 472 12 C C/T 19.54 1.00E-05 rsl386485 TPH2 471 12 A A/C rsl386483 TPH2 470 12 G A/G rs7977245 None 1212 12 T C/T rs276002 None 814 12 A A/G 18.81 0.00001 rs274460 None 810 12 A A/G rsl245383 None 430 14 G A/G 18.77 0.00001 rs2133829 None 707 14 C C/T rs2173738 None 722 14 T C/T rs2050528 None 677 14 T C/T rs202970 None 671 14 C C/T rsl395266 SERPINBIl 476 18 T C/T 23.73 <1.0E-5 rs931850 None 1303 18 A A/G rsl522722 None 547 18 C C/T rs2221511 SERPINBIl 733 18 A A/G 22.42 <1.0E-5 rs4940595 SERPINBIl 986 18 T G/T K* rsl522723 SERPINBIl 548 18 C C/T rsl395266 SERPINBIl 476 18 C C/T rs2825555 None 819 21 A A/G 23.11 <1.0E-5 rs2825583 None 820 21 T C/T rs2825601 None 821 21 G A/G rs2825610 None 822 21 G G/T rsl489734 None 532 21 A A/G dbSNP_rs_ID: SNP identification number in NCBI dbSNP database build 124 Gene_locus: Gene positioned in the physical position pointed by the SNP according to

NCBI Human Genome Build 35

Sequence_ID: Sequence identification number Chr: Chromosome

Risk_allele: Allele in at-risk haplotype Variants: Variant alleles present in the SNP Chi-square: Chi-square value based on 2x2 table (haplotype present (not-present) in cases and controls)

P-value: P-value corresponding the chi-square value with 1 df

Table 6. Genes associated with HT according to point wise or haplotype analyses (n = 722) .

Chromosome I Gene

1 DABl

1 APG4C

1 CAPON

1 COL24A1

1 DPT

1 EAT2

1 FAAH

1 FAFl

1 FLJ20277

1 FLJ32825

1 GADD45A

1 GNGl2

1 LOC116123

1 LOC128153

1 LOC200008

1 LOC284680

1 LOC388656

1 LOC391046

1 LOC399701

1 LOC400758

1 LOC440598

1 MAST2

1 MGC22960

1 MGC29875

1 MGC8902

1 MRPL37

1 MUFl

1 POGK

1 PRKCL2

1 RAD54L

1 RGS18

1 RGS7

1 SEC22L1

1 SHREWl

1 SIAT7C

1 SIPA1L2

1 SSBP3

1 TARBPl

1 TSPAN-I

1 UQCRH

1 USH2A

1 XM_372814

2 COMMDl

2 CRYGEPl

2 ERBB4

2 LOC130576

2 MY03B

2 REGL

2 SPlOO

2 ACVRl

2 ACVRl AOX2

ASBl

B3GNT1

BARDl

BAZ2B

CRYGA

CRYGB

CRYGC

CRYGD

CTNNA2

FLJ13110

FSHR

GORASP2

GPD2

HMG1L3

IDHl

LANCLl

LHCGR

LOC130429

LOC339789

LOC344471

LOC388954

LOC389072

LOC389073

LOC391481

LOC402117

LOC442053

LOC442066

LOC93349

LPINl

LRPlB

LTBPl

MGC4268

PAP

PDEIlA

PELIl

POLR2D

PRKCE

PRKCN

QPCT

REG-III

REGlA

REGlB

TLKl

TRAF3IP1

UNQ429

VPS54

WDR33

LOC152225

AHSG

ATR

CRBN

CRYGS

DGKG

DNAJBIl

FETUB

FLJ10560

FLJ12604

FLJ42117

GRM7 HRG

IL5RA

KCNABl

KNGl

LOC152225

LOC389105

LOC442078

LOC442099

MAIL

MGC15606

MGC16471

MRPL47

PLSl

SCHIPl

TRAD

TRNTl

TRPCl

XRNl

LOC339979

PDGFC

ANK2

FLJ20647

FLJ37673

GABRBl

GLRB

KIAA0882

KIT

LOC152594

LOC255130

LOC339979

LOC345378

LOC389217

LOC391681

LOC391686

LOC441018

PDGFC

SEC24B

SNCA

STK32B

TDO2

TLLl

ABLIM3

ADAMTS12

BTNL3

BTNL8

BTNL9

CANX

CCNGl

CDH6

CEI

CHDl

CMYA5

CTNND2

EBF

FBXL17

FLJ10904

GABRAl GABRAl

GABRA6

HMMR

HNRPHl

IL12B

IRX2

KIAA1061

KIAA1985

LOC134492

LOC255187

LOC285638

LOC285679

LOC345471

LOC389285

LOC389352

LOC391734

LOC391774

LOC391819

LOC391858

LOC402222

LOC441113

LOC441120

LOC442129

LOC51149

LTC4S

MAMLl

MAN2A1

MGAT4B

NDFIPl

PAPD4

PJA2

RGMB

RUFYl

SGCD

SQSTMl

STXIl

ACAT2

BAI3

BPAGl

BRP44L

C6orfl42

C6orfl49

C6orfl57

C6orf204

C6orf33

C6orf65

C6orf83

C6orf93

CRISP2

DST

FARSl

GFODl

IGF2R

IL17F

L3MBTL3

LOC285741

LOC389370

LOC401255

LOC401284 MASl

MCM3

MGC35308

MRPLl8

MRPL42P3

MYCTl

PARK2

PHACTRl

PLAGLl

PNLDCl

RPS6KA2

SAMD3

SEC5L1

SERPINBl

SERPINB9

SF3B5

SLC35F1

SOD2

SYNEl

T

TBC1D7

TCBAl

TCPl

TINAG

UTRN

VIP

WRNIPl

WTAP

UTRN

DNAHIl

ABCAl3

AKRlBl

ARL4

ARL4A

BMPER

CNTNAP2

DGKI

DNAHIl

FLJ21075

FLJ32786

HDAC9

HIC

HUSl

LOC136288

LOC340228

LOC340274

LOC389602

LOC401406

LOC402463

LOC402640

MGC16075

MGC33329

OSBPL3

PBEFl

PHF14

PKDlLl

PKDlLl SCIN

SDKl

SEMA3A

SEMA3E

SHH

SLC35B4

SP4

UNQ739

SGCZ

ZFPM2

ASAHl

CGI-62

CSMDl

EFA6R

ENTPD4

FGF20

FLJ23749

FLJ36980

HNF4G

LOC286097

LOC340357

LOC346887

LOC392262

LRP12

MATN2

MSCP

PKIA

PSD3

RBPMS

RIMS2

RRM2B

ZHX2

NT 008470

ORlJ4

ADAMTSLl

AK3L1

C9orfl02

C9orf97

ECM2

FBXW2

FLJ31810

FRMD3

GRIN3A

JAK2

LOC138882

LOC392282

LOC392371

LOC401492

LOC441384

MRRF

NR4A3

NTRK2

ORlBl

ORlHlP

ORlJl

ORlJ2

ORlJ4

ORlL8

ORlNl

OR1N2 ORlQl

PHFl9

PSMD5

PTGSl

RCLl

STX17

TMCl

TRAFl

TRPM3

TXNDC4

XPA

CTNNA3

LOC389938

PCDH15

ACF

ADRA2A

ANK3

ANKRDl6

ASCCl

C10orfl04

C10orf35

C10orf49

C10orf59

C10orf64

CACNB2

CBARAl

CTNNA3

CXXC6

DDIT4

DNA2L

DNAJB12

EPCl

FBXOl8

FLJ31958

GDI2

HNRPH3

IL15RA

IL2RA

LOC387630

LOC389970

LOC399707

LOC399708

LOC399713

LOC399773

LOC439946

LOC439953

LOC439978

LOC441550

LOC441551

LOC441561

MAWBP

MCMlO

MINPPl

MPP7

MYO3A

NEUROG3 NOPDl

NY-BR-I

OPTN

PARD3

RUFY2

NUMAl

CD44

DKFZP564M082

FAT3

FLJ20625

FN5

GALNTL4

GAS2

IL18BP

KIAA1731

LOC113174

LOC220074

LOC260340

LOC338661

LOC387795

LOC390241

LOC390263

LOC440062

MGC5306

MRGX3

MRGX4

NELLl

NUMAl

ORlOSl

OR4D5

OR51R1P

OR52K3P

OR6M2P

OR6M3P

OR6T1

OR8D4

PDGFD

PDHX

PTD012

RNFl21

RRMl

SAA2

SAA3P

SAA4

SSAl

STIMl

USP47

EB-I

TPH2

ALGlO

ARLl

DRIM

EB-I

ELKS

FLJ36004

HSN2

LOC283392 LOC283432

LOC390359

LOC400019

LOC400046

NAV3

PAH

PRKWNKl

RAD52

SLCl6A7

TBC1D15

TPH2

TRHDE

VPS29

WIFl

DNAJDl

FARPl

FLJ10094

FLJ25477

FLJ25952

GPC6

GRK6PS

HSMPP8

IRS2

LOC387904

LOC387905

LOC390393

LOC400099

LOC400120

LOC440127

NUDTl5

PABPC3

PSPCl

RFXAP

SCEL

SMAD9

STK24

SUCLA2

VDRIP

VGCNLl

ZNF198

ZNF237

LOC145497

LOC388001

LOC400234

NPAS3

AKAP6

AP4S1

C14orfl66B

C14orf68

COCH

CYCSPl

EEF1A1P2

EMLl

KCNH5

KIAA0759

KIAA1036

LAMRlP3

LOC341965

LOC388001 LOC440198

LRFN5

MGC4645

NDUFB3P4

NPAS3

NRXN3

RPL22P2

RPLPlPl

RPS2P3

SELlL

SLC25A29

STRN3

UBA52P3

WARS

MGC14798

ADAMlO

ARNT2

ARRDC4

BGl

CHD2

CIB2

CYFIPl

DNAJA4

FES

FURIN

GABRA5

IDH3A

KIAA1055

LOC339003

LOC390561

LOC390572

LOC390638

LOC400320

LOC440272

LOC441722

LOC441723

MAN2A2

MEIS2

MGC14386

MGC14798

MGC45386

MTHFS

NANOGP8

NIPAl

NIPA2

NTRK3 pp9099

PRCl

RASGRFl

RGMA

SIAT8B

SLCO3A1

SMAP-I

VPS33B

CDYL2

WWOX

CDH13

CLECSFl

RRN3

WWOX CGI-125

FLJ12760

FLJ25818

KIAA0753

KRTlO

KRT12

KRT20

KRT23

KRT24

KRT25A

KRT25B

KRT25C

KRT25D

LOC342531

MGC21518

MGC45562

MRC2

PITPNM3

SLC13A5

SMARCEl

SOX9

TLK2

TXNL5

LOC388458

SERPINBIl

C18orflO

Clδorfll

C18orfl4

FLJ20793

KIAA1012

KIAA1328

LOC342705

LOC390848

LOC440491

MEPlB

NETOl

NPMlPl

PTPRM

RIT2

RNFl25

RNFl38

SERPINBlO

SERPINB2

SERPINB3

SERPINB4

SERPINB7

FLJ00060

FLJ14011

FLJ26175

GRLFl

ILTlO

KIR2DL1

KIR2DL3

KIR2DS2

KIR3DL3

LILRAl

LILRA2 19 LILRB4

19 LOC284373

19 LOC388526

19 LOC388558

19 LOC400713

19 LOC440544

19 LOC441862

19 MGC9913

19 ZFP28

19 ZNF471

19 ZNF528

19 ZNF534

19 ZNF542

19 ZNF578

19 ZNF582

19 ZNF583

19 ZNF610

20 SNPH

20 C20orfl49

20 C20orf46

20 EEF1A2

20 FKBPlA

20 GMEB2

20 IDH3B

20 KCNBl

20 KCNQ2

20 LOC200213

20 LOC388807

20 LOC441937

20 MGC10715

20 MGC5356

20 NOL5A

20 NSFLlC

20 PRIC285

20 PROCR

20 PSMFl

20 PTGIS

20 PTK6

20 PTPNS1L2

20 PTPNS1L3

20 SDCBP2

20 SIRPBl

20 SNPH

20 SNRPB

20 SRMS

20 TGM6

20 TMC2

21 ATP5O

21 C21orf94

21 ITSNl

21 LOC388819

21 MRPS6

22 DGCR2

22 FBLNl

X RPS6KA6

Gene name according to HUGO Gene Nomenclature Committee (HGNC) Table 7. A multivariate logistic model predicting the risk of hypertension, including haplotypes and individual SNP markers.

A t r

P i r S e k d i H A

C T 1 t G 1

O e O e C r G n r 1 O e e e F e

V n g S r f O a e C e e f r S O n i q i 9 i 1 E n O n U C 5 V a O Q t t e i % a b C C e Y S n e 1

1 U h I n P N C n 0 C u e S r D t e P Y t R I e

rsl521409 None 3 544 None A A/G 6,27 ,130 -6. 904 0.00 rslO511365 None 3 316 C C/T rslO511366 None 3 317 T C/T

Haplotype rsl0508771 None 10 286 LOC441550 T A/T 139, 23,1 9. 045 8477 [87.2,823831] <0.001 rs3006608 None 10 854 LOC441551 C C/T rsl0508773 EPCl 10 287 LOC439953 C C/T rs950132 EPCl 10 1325 EPCl C C/T

Haplotype

rs2221511 SERPINBIl 18 733 SERPINB4 A A/G 118,37,8 -3.421 0.033 [0.004,0.242] 0.001 rs4940595 SERPINBIl 18 986 SERPINB3 T G/T rsl522723 SERPINBIl 18 548 SERPINBIl C C/T rsl395266 SERPINBIl 18 476 SERPINB7 C C/T

SNP-marker** rsl992906 None 5 655 G A/G 138,22,3 4.154 63.7 [6.61,614] <0.001 rsl0270360 LOC401406 7 10 G A/G 47,90,26 2.593 13.4 [3.12,57.3] <0.001 rsl318392 OR1J4 9 438 G A/G 47,86,30 -3.299 0.037 [0.007,0.195] <0.001 rs2209672 None 10 730 A A/G 33,94,36 -3.032 0.048 [0.011,0.216] <0.001 rs503208 None 11 989 G C/G 78,68,17 2.619 13.7 [3.15,59.8] <0.001

Constant 7.473 1760.389 0.003

SNP identification number according to NCBI dbSNP database build 124.

Gene locus, gene locus as reported by NCBI dbSNP database build 124

The 8-variable model predicts 91.4 % of HT cases correctly.

The statistics are based on 163 subjects of which 81 were HT cases and 82 controls.

* Haplotypes coded as 0, if no haplotype, 1 if one haplotype and 2 if two haplotypes o

** Genotypes coded as 0, if major allele homozygote, 1 if heterozygote and 2 if minor allele homozygote

Haplotype gene content, genes positioned within lOOKbp up/downstream from the physical position of the SNPs bordering the haplotype genomic region found using NCBI MapViewer

HT = haplotype

OR = Odds ration in multivariate logistic model

95% CI = 95% confidence interval for odds ratio

Table 8. A multivariate logistic model predicting the risk of hypertension including haplotypes,individual SNP markers and phenotypic measurements.

A t r

P i r S e k d i H A

C T 1 t G 1

O e O e C r G n r 1 O e e e F e

V n g S r f a e C e e f O r S O n i q i 9 i 1 E n O n U C 5 V a O Q t t e i % a b C C e Y S n e 1

1 U h I n P N C n 0 C u e S r D t e P Y t R I e

Haplotype* rsl521409 None 3 544 None A A/G 6,27,130 -3.629 0.026 [0.004, 0.177] <0.001 rslO511365 None 3 316 C C/T rslO511366 None 3 317 T C/T

Haplotype rs2221511 SERPINBIl 18 733 SERPINB4 A A/G 118,37,8 -1.828 0.161 [0.054, 0.478] 0.001 rs4940595 SERPINBIl 18 986 SERPINB3 T G/T rsl522723 SERPINBIl 18 548 SERPINBIl C C/T rsl395266 SERPINBIl 18 476 SERPINB7 C C/T

SNP-marker** rsl997454 None 2 656 G A/G 103,53,7 -1.194 0.303 [0.112, 0.821] 0.019

rsl0270360 LOC401406 7 10 G A/G 47,90,26 1.379 3.97 [1.65, 9.56] 0.002 rsl318392 OR1J4 9 438 G A/G 47,86,30 -2.035 0.131 [0.049, 0.348] <0.001 rs2209672 None 10 730 A A/G 33,94,36 -1.608 0.200 [0.075, 0.533] 0.001 rs503208 None 11 989 G C/G 78,68,17 1.392 4.03 [1.73, 9.38] 0.001

BMI (kg/m2) n.a. 0.248 1.281 [1.067, 1.537] 0.008

Obesity in the family n.a. 1.508 4.52 [1.49, 13.7] 0.008

Constant -2 . 542 0 . 079 0 . 376

SNP identification number according to NCBI dbSNP database build 124.

Gene locus, gene locus as reported by NCBI dbSNP database build 124

The 9-variable model predicts 87.1 % of HT cases correctly.

* Haplotypes coded as 0, if no haplotype, 1 if one haplotype and 2 if two haplotypes

** Genotypes coded as 0, if major allele homozygote, 1 if heterozygote and 2 if minor allele homozygote n.a. denotes not applicable o 00

HT = Haplotype

OR = Odds ratio in multivariate logistic model

95% CI = 95% confidence interval for odds ratio

Table 9. Linear regression model for systolic and diastolic blood pressure using individual SNP markers

SBP DBP

Variable Closest gene* Sequence ID Coefficient P-value Coefficient P-value

Drug treatment 8.403 0.001 4.695 0.02 rsl860933 LOC391839, SPINK5 1366 -4.673 <0.001 rs4236780 STARS, ANGPTl 1367 -5.659 <0.001 rs2000112 0R1N2, 0R1L8 660 -4.481 0.001 rs931850 SERPINBIl, SERPINB7 1303 -5.084 0.001 rs2192947 QPCT, CDC42EP3 728 3.656 0.001 rs9328292 C6orfl49, FARSl 1316 -3.486 <0.001 rsl409367 S100A7, S100A6 490 -6.839 <0.001 rsl893814 ODZ4, PRCP 622 3.747 <0.001 rs2263356 PHF2, BARXl 746 3.209 <0.001 rs6826647 TLLl, SP0CK3 1368 -2.786 <0.001 rsl913157 FLJ42117, LOC339902 630 -2.721 <0.001

O

Constant 139.698 <0.001 101.901 <0.001

Adjusted R2 0.247 0.301

SBP, systolic blood pressure

DBP, diastolic blood pressure

*, Closest gene up and downstream according to NCBI MapViewer

Sequence ID, sequence identification number

Table 10. Associations of selected SNP markers with the mean systolic blood pressure in mmHg.

Homozygote for Homozygote for minor allele Heterozygote major allele SNP marker Closest gene* Seq_ID Mean SD N Mean SD N Mean SD N P-value rs6826647 TLLl 1368 134.6 17.7 55 131.7 15.1 129 129.3 14.2 64 0.067

SPOCK3 rsl409367 S100A7 490 149.5 18.6 5 146.8 6.4 5 131.3 15.1 213 0.008

S100A6 rs9328292 C6orfl49 1316 124.7 16.7 36 132.0 13.9 108 134.8 16.1 73 0.001

FARSl rsl395266 SERPINB3 476 124.6 10.2 16 127.2 14.3 65 135.2 16.1 150 0.009

SERPINBIl**

SERPINB7 rsl893814 ODZ4 622 132.1 16.1 21 135.0 17.3 90 129.7 14.2 115 0.522

PRCP rs931850 SERPINBIl 1303 125.1 10.3 15 127.2 14.0 75 135.2 16.0 151 0.014

SERPINB7 rsl860933 LOC391839 1366 137.1 17.7 60 130.8 14.5 97 128.0 14.7 69 0.001

SPINK5 rsl386483 TBC1D15 470 135.7 16.2 63 130.5 14.6 119 130.3 16.3 66 0.049

TPH2**

LOC283392 rs4236780 STARS 1367 124.6 13.1 21 129.4 15.7 105 135.0 15.2 123 0.004

ANGPTl rsl913157 FLJ42117 630 133.9 9.3 20 127.9 13.4 107 134.8 17.3 122 0.788

LOC339902 rs2263356 PHF2 746 133.8 18.4 19 135.5 14.7 67 129.7 14.8 129 0.281

BARXl rs2000112 0R1N2 660 126.5 12.3 19 127.2 15.9 76 133.8 14.8 132 0.047

OR1L8

* Closest gene up and downstream according to NCBI MapViewer.

** the marker is intragenic for this gene.

P-value: statistical significance of the linear component of variation across the three genotypes from ANOVA model.

Seq. ID: sequence identification number.

Table 11. Associations of selected SNP markers with the mean diastolic blood pressure in mmHg.

Homozygote for Homozygote for minor allele Heterozygote major allele

SNP marker Closest gene* Seq_ID Mean SD N Mean SD N Mean SD N P-value rs6826647 TLLl 1368 89.0 11.8 55 85.9 9.2 129 82.6 8.6 64 <0.001

SPOCK3 rsl409367 S100A7 490 101.4 12.1 5 90.1 6.0 5 85.6 9.5 213 <0.001

S100A6 rs9328292 C6orfl49 1316 80.4 9.4 36 85.7 9.3 108 1.3 10.0 73 <0.001

FARSl rsl395266 SERPINB3

SERPINBIl** 476 80.0 7.4 16 83.5 9.1 65 87.7 10.2 150 0.003

SERPINB7 rsl893814 ODZ4 622 90.5 11.0 21 87.4 10.2 90 83.6 9.3 115 0.004

PRCP rs931850 SERPINBIl 1303 80.5 7.4 15 83.3 9.0 75 87.7 10.2 151 0.006

SERPINB7 rsl860933 LOC391839 1366 88.3 10.6 60 85.2 9.2 97 84.1 9.2 69 0.013

SPINK5 rsl386483 TBC1D15 470 89.1 11.2 63 84.4 9.5 119 85.0 8.9 66 0.019

TPH2**

LOC283392 rs4236780 STARS 1367 82.5 8.0 21 84.6 10.3 105 87.3 9.7 123 0.040

ANGPTl rsl913157 FLJ42117 630 83.3 5.3 20 84.0 10.1 107 87.8 10.0 122 0.060

LOC339902 rs2263356 PHF2 746 88.2 10.2 19 89.1 10.0 67 83.9 9.6 129 0.072

BARXl rs2000112 0R1N2 660 83.2 7.4 19 84.2 9.1 76 86.4 9.9 132 0.169

OR1L8

* Closest gene up and downstream according to NCBI MapViewer

** the marker is intragenic for this gene

P-value: statistical significance of the linear component of variation across the three genotypes from ANOVA model

Seq_ID: sequence identification number

w

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Claims

1. A method for identification of an individual who has an altered risk of or susceptibility for developing HT, the method comprising the steps of: a) providing a biological sample taken from said individual; b) collecting personal and clinical information of said individual; c) determining the nucleotides present in one or several of the polymorphic sites as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid; and d) combining the SNP marker data with personal and clinical information to assess the risk of an individual to develop HT.

2. The method according to claim 1, wherein the altered risk is an increased risk of HT.

3. The method according to claim 1 , wherein the altered risk is a decreased risk of HT.

4. The method according to claim 1, wherein the polymorphic sites are those present in the haplotypes presented in tables 3, 4, 5, 7 and 8.

5. The method according to claim 1, wherein the polymorphic sites are associated with the SNP markers set forth in tables 2 to 5 and 7 to 11.

6. The method according to claim 5, wherein the polymorphic sites are in complete linkage disequilibrium with the SNP markers set forth in tables 2 to 5 and 7 to 11.

7. The method according to claim 6, wherein the polymorphic sites are in complete linkage disequilibrium in the population in which the said method is used.

8. A method for identification of an individual who has an altered risk of or susceptibility for developing HT, the method comprising the steps of a) providing a biological sample taken from a subject b) determining the nucleotides present in one or several of the polymorphic sites as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid c) combining the SNP marker data to assess the risk of an individual to develop HT

9. The method according to claim 8, wherein the altered risk is an increased risk of HT.

10. The method according to claim 8, wherein the altered risk is a decreased risk of HT.

11. The method according to claim 8, wherein the polymorphic sites are those present in the haplotypes presented in tables 3, 4, 5, 7 and 8.

12. The method according to claim 8, wherein the polymorphic sites are associated with the SNP markers set forth in tables 2 to 5 and 7 to 11.

13. The method according to claim 12, wherein the polymorphic sites are in complete linkage disequilibrium with the SNP markers set forth in tables 2 to 5 and 7 to 11.

14. The method according to claim 13, wherein the polymorphic sites are in complete linkage disequilibrium in the population in which the said method is used.

15. The method according to claim 1, wherein said one or several polymorphic sites reside within a HT risk gene or genes as set forth in table 6.

16. The method according to claim 1, wherein the HT risk genes reside in the genome regions which are defined by the haplotype pattern mining analysis, the genes set forth in tables 3, 4, 5, 7 and 8.

17. The method according to claim 1, wherein the polymorphic sites are associated with the haplotype regions, haplotypes or SNP markers defining the haplotypes set forth in tables 3, 4,

5, 7 and 8.

18. The method according to claim 17, wherein the polymorphic sites are in complete linkage disequilibrium with the haplotype regions, haplotypes or SNP markers defining the haplotypes set forth in tables 3, 4, 5, 7 and 8.

19. The method according to claim 18, wherein the polymorphic sites are in complete linkage disequilibrium in the population in which the said method is used.

20. The method according to claim 1, wherein one or several of the SNP markers are selected from the group consisting of the following haplotypes or individual SNPs: a) rsl521409 (A/G) (SEQ ID NO: 544), rslO511365 (C/T) (SEQ ID NO: 316) and rslO511366 (C/T) (SEQ ID NO: 317) defining the haplotype ACT (or nucleotides from the complementary strand); b) rsl0508771 (A/T) (SEQ ID NO: 286), rs3006608 (C/T) (SEQ ID NO: 854), rslO5O8773 (C/T) (SEQ ID NO: 287) and rs950132 (C/T) (SEQ ID NO: 1325) defining the haplotype TCCC (or nucleotides from the complementary strand); c) rs2221511 (A/G) (SEQ ID NO: 733), rs4940595 (G/T) (SEQ ID NO: 986), rsl522723 (C/T) (SEQ ID NO: 548) and rs 1395266 (C/T) (SEQ ID NO: 476) defining the haplotype ATCC (or nucleotides from the complementary strand); d) rsl992906 (A/G) (SEQ ID NO: 655) defining the risk allele G; e) rsl0270360 (A/G) (SEQ ID NO: 10) defining the risk allele G; f) rsl318392 (A/G) (SEQ ID NO: 438) defining the risk allele G; g) rs2209672 (A/G) (SEQ ID NO: 730) defining the risk allele A; h) rs503208 (C/G) (SEQ ID NO: 989) defining the risk allele G

21. The method according to claim 1, wherein one or several of the SNP markers are selected from the group consisting of the following haplotypes or individual SNPs: a) rsl521409 (A/G) (SEQ ID NO: 544), rslO511365 (C/T) (SEQ ID NO: 316) and rslO511366 (C/T) (SEQ ID NO: 317) defining the haplotype ACT (or nucleotides from the complementary strand); b) rs2221511 (A/G) (SEQ ID NO: 733), rs4940595 (G/T) (SEQ ID NO: 986), rsl522723 (C/T) (SEQ ID NO: 548) and rsl 395266 (C/T) (SEQ ID NO: 476) defining the haplotype ATCC (or nucleotides from the complementary strand); c) rsl997454 (A/G) (SEQ ID NO: 656) defining the risk allele G; d) rsl0270360 (A/G) (SEQ ID NO: 10) defining the risk allele G; e) rsl318392 (A/G) (SEQ ID NO: 438) defining the risk allele G; f) rs2209672 (A/G) (SEQ ID NO: 730) defining the risk allele A; g) rs503208 (C/G) (SEQ ID NO: 989) defining the risk allele G

22. The method according to claim 1, wherein one or several of the SNP markers are selected from the group consisting of the following haplotypes: a) rs4845303 (A/T) (SEQ ID NO: 980), rs6428195 (C/G) (SEQ ID NO: 1030) and rsl935659 (AJG) (SEQ ID NO: 637) defining the haplotype ACG (or nucleotides from the complementary strand); b) rsl997454 (A/G) (SEQ ID NO: 656), rs2139502 (A/G) (SEQ ID NO: 709) and rsl519991 (AJC) (SEQ ID NO: 542) defining the haplotype AGC (or nucleotides from the complementary strand); c) rsl521409 (A/G) (SEQ ID NO: 544), rslO511365 (C/T) (SEQ ID NO: 316) and rslO511366 (C/T) (SEQ ID NO: 317) defining the haplotype ACT (or nucleotides from the complementary strand); d) rs7679959 (C/G) (SEQ ID NO: 1178), rslO517338 (C/G) (SEQ ID NO: 381) and rs959297 (A/T) (SEQ ID NO: 1338) defining the haplotype CGA (or nucleotides from the complementary strand); e) rs2278677 (A/G) (SEQ ID NO: 749), rs3886091 (C/G) (SEQ ID NO: 899), rsl998167 (A/G) (SEQ ID NO: 657), rsl998168 (A/G) (SEQ ID NO: 658) and rs2235280 (A/G) (SEQ ID NO: 740) defining the haplotype GCAGG (or nucleotides from the complementary strand); f) rsl0521062 (AJC) (SEQ ID NO: 404), rslO512296 (A/G) (SEQ ID NO: 331), rsl924001 (C/G) (SEQ ID NO: 633) and rs2417359 (A/G) (SEQ ID NO: 784) defining the haplotype

AACG (or nucleotides from the complementary strand); g) rslO5O8933 (C/G) (SEQ ID NO: 289), rsl0509071 (A/G) (SEQ ID NO: 295) and rsl0490967 (AJG) (SEQ ID NO: 94) defining the haplotype GGA (or nucleotides from the complementary strand); h) rsl0508771 (A/T) (SEQ ID NO: 286), rs3006608 (C/T) (SEQ ID NO: 854), rslO5O8773 (C/T) (SEQ ID NO: 287) and rs950132 (C/T) (SEQ ID NO: 1325) defining the haplotype TCCC (or nucleotides from the complementary strand); i) rsl386486 (C/T) (SEQ ID NO: 472), rsl386485 (AJC) (SEQ ID NO: 471), rsl386483 (AJG) (SEQ ID NO: 470) and rs7977245 (C/T) (SEQ ID NO: 1212) defining the haplotype CAGT (or nucleotides from the complementary strand); j) rs276002 (AJG) (SEQ ID NO: 814) and rs274460 (AJG) (SEQ ID NO: 810) defining the haplotype AA (or nucleotides from the complementary strand); k) rsl245383 (A/G) (SEQ ID NO: 430), rs2133829 (C/T) (SEQ ID NO: 707), rs2173738 (C/T) (SEQ ID NO: 722), rs2050528 (C/T) (SEQ ID NO: 677) and rs202970 (C/T) (SEQ ID NO: 671) defining the haplotype GCTTC (or nucleotides from the complementary strand); 1) rsl395266 (C/T) (SEQ ID NO: 476), rs931850 (AJG) (SEQ ID NO: 1303) and rsl522722 (C/T) (SEQ ID NO: 547) defining the haplotype TAC (or nucleotides from the complementary strand); m) rs2221511 (AJG) (SEQ ID NO: 733), rs4940595 (G/T) (SEQ ID NO: 986), rsl522723 (C/T) (SEQ ID NO: 548) and rs 1395266 (C/T) (SEQ ID NO: 476) defining the haplotype ATCC (or nucleotides from the complementary strand); n) rs2825555 (AJG) (SEQ ID NO: 819), rs2825583 (C/T) (SEQ ID NO: 820), rs2825601 (AJG) (SEQ ID NO: 821), rs2825610 (G/T) (SEQ ID NO: 822) and rsl489734 (AJG) (SEQ ID NO: 532) defining the haplotype ATGGA (or nucleotides from the complementary strand)

23. A method for assessing susceptibility or predisposition to HT in an individual, the method comprising determining alteration of expression levels of one or several of the genes of table 6 in the individual, wherein a difference in expression is indicative of susceptibility to HT.

24. The method according to claim 23, wherein alteration of expression levels is determined by assessing transcription levels of one or several of the genes of table 6 in the individual.

25. The method according to claim 23, wherein alteration of expression levels is determined by assessing translation of mRNAs encoded by one or several of the genes of table 6 in the individual.

26. A method for assessing susceptibility or predisposition to HT in an individual, the method comprising determining alteration of biological activity of one or several ot the polypeptides encoded by one or several of the genes of table 6 in the individual, wherein a difference in biological activity of one or several of the polypeptides is indicative of susceptibility to HT.

27. The method according to claim 26, wherein alteration of biological activity is determined by assessing structure of one or several ot the polypeptides encoded by one or several of the genes of table 6 in the individual.

28. The method according to claim 26, wherein alteration of biological activity is determined by assessing amount of one or several of the metabolites of a polypeptide or polypeptides encoded by one or several of the genes of table 6 in the individual.

29. The method according to claim 1, wherein the personal and clinical information, i.e. non- genetic information concerns age, gender, behaviour patterns and habits, biochemical measurements, clinical measurements, obesity, the family history of HT, cerebrovascular disease, other cardiovascular disease, hypercholesterolemia, obesity and diabetes, waist-to-hip circumference ratio (cm/cm), socioeconomic status, psychological traits and states, and the medical history of the subject.

30. The method according to claim 29, wherein the behaviour patterns and habits include tobacco smoking, physical activity, dietary intakes of nutrients, alcohol intake and consumption patterns and coffee consumption and quality.

31. The method according to claim 29, wherein the biochemical measurements include determining blood, serum or plasma VLDL, LDL, HDL, total cholesterol, triglycerides, apolipoprotein (a), fibrinogen, ferritin, transferrin receptor, C-reactive protein, glucose or insulin concentration.

32. The method according to claim 29, wherein the non-genetic measurements are those presented in table 8.

33. The method according to claim 29, wherein the non-genetic information contains BMI and history of obesity in the family of the subject.

34. The method according to claim 29 further comprising a step of calculating the risk of HT using a logistic regression equation as follows:

Risk of HT = [1 + e -^{(a + ∑(bl*Xl)}] -¹ _? where e is Napier's constant, Xi are variables associated with the risk of HT, bi are coefficients of these variables in the logistic function, and a is the constant term in the logistic iunction.

35. The method according to claim 34, wherein a and bi are determined in the population in which the method is to be used.

36. The method according to claim 34, wherein Xi are selected among the variables that have been measured in the population in which the method is to be used.

37. The method according to claim 34, wherein Xi are selected among the SNP markers of tables 2 to 5 and 7 to 11, among haplotype regions and haplotypes of tables 3, 4, 5, 7 and 8 and among non-genetic variables of the invention.

38. The method according to claim 34, wherein bi are between the values of -20 and 20 and/or wherein Xi can have values between -99999 and 99999 or are coded as 0 (zero) or 1 (one).

39. The method according to claim 34, wherein i are between the values 0 (none) and 100,000.

40. The method according to claim 1, wherein subject's short term, median term, and/or long term risk of HT is predicted.

41. A method for identifying compounds useful in prevention or treatment of HT comprising determining the effect of a compound on biological networks and/or metabolic pathways related to one or several polypeptides encoded by HT risk genes of table 6 in living cells; wherein a compound altering activity of one or several said biological networks and/or metabolic pathways is considered useful in prevention or treatment of HT.

42. The method according to claim 41 comprising determining the effect of a compound on a biological activity of one or several polypeptides encoded by HT risk genes of table 6 in living cells; wherein a compound altering biological activity of a polypeptide is considered useful in prevention and/or treatment of HT.

43. A method for prevention or treatment of HT comprising administering to a mammalian subject in need of such treatment an effective amount of a compound in a pharmaceutically acceptable carrier enhancing or reducing biological activity of one or several polypeptides encoded by HT risk genes of table 6; and/or enhancing or reducing activity of one or several biological networks and/or metabolic pathways related to said polypeptides.

44. The method according to claim 43 comprising administering to a mammalian subject in need of such treatment an effective amount of a compound in a pharmaceutically acceptable carrier enhancing or reducing expression of one or several HT risk genes of table 6; and/or enhancing or reducing the expression of one or several genes in biological networks and/or metabolic pathways related to polypeptides encoded by said HT risk genes.

45. The method according to claim 43 comprising administering to a mammalian subject in need of such treatment an effective amount of a compound in a pharmaceutically acceptable carrier enhancing or reducing activity of one or several pathophysiological pathways involved in cardiovascular diseases and related to polypeptides encoded by HT risk genes of table 6.

46. The method according to claim 43, said method comprising the steps of: a) providing a biological sample taken from a subject; b) determining the nucleotides present in one or several of the polymorphic sites associated with altered expression and/or biological activity and present in HT risk genes of table 6 in said individual's nucleic acid; and c) combining polymorphic site genotype data to select effective therapy for treating HT in said subject.

47. The method according to claim 43, said method comprising the steps of: a) providing a biological sample taken from a subject; b) determining expression of one or several HT risk genes of table 6 and/or determining biological activity of one or several polypeptides encoded by the HT risk genes of table 6 in said individual's sample; and c) combining the expression and/or biological activity data to select effective therapy for treating HT in said subject.

48. The method according to claim 43, wherein said treatment is gene therapy or gene transfer.

49. The method according to claim 48, wherein said treatment comprises the transfer of one or several HT risk genes of table 6 or variants, fragments or derivatives thereof.

50. The method according to claim 48, wherein said HT risk genes of table 6 or variants, fragments or derivatives thereof are associated with reduced risk of HT.

51. The method according to claim 48, wherein said treatment comprises treating regulatory regions and/or gene containing region of one or more HT risk genes of table 6 or variants, fragments or derivatives thereof in somatic cells of said subject.

52. The method according to claim 48, wherein said treatment comprises treating regulatory regions and/or gene containing region of one or more HT risk genes of table 6 or variants, fragments or derivatives thereof in stem cells.

53. The method according to claim 52, wherein said treatment comprises treating regulatory regions and/or gene containing region of one or more HT risk genes of table 6 or variants, fragments or derivatives thereof in stem cells in tissues affected by cardiovascular diseases.

54. The method according to claim 43, wherein said compound is a recombinant polypeptide encoded by an HT risk gene of table 6 or variant, fragment or derivative thereof.

55. The method according to claim 43, wherein said treatment is based on siRNA hybridising to mRNA and/or to hnRNA of a HT risk gene of table 6.

56. The method according to claim 43, wherein said treatment is based on siRNA hybridising to mRNA and/or to hnRNA of one or several genes in biological networks and/or metabolic pathways related to polypeptides encoded by said HT risk genes of table 6.

57. The method according to claim 43, wherein said method of treating is a dietary treatment or a vaccination.

58. The method according to claim 43 comprising a therapy restoring, at least partially, the observed alterations in biological activity of one or several polypeptides encoded by HT risk genes of table 6 in said subject, when compared with HT free healthy subjects.

59. The method according to claim 43 comprising a therapy restoring, at least partially, the observed alterations in expression of one or several HT risk genes of table 6 in said subject, when compared with HT free healthy subjects.

60. A method for monitoring the effectiveness of treatment of HT in a human subject the method comprising measuring mRNA levels of HT risk genes of table 6, and/or levels of polypeptides encoded by said HT risk genes, and/or biological activity of polypeptides encoded by said HT risk genes in a biological sample taken from said subject; alteration of mRNA levels or polypeptide levels or biological activity of a polypeptide following treatment being indicative of the efficacy of the treatment.

61. A method for predicting the effectiveness of a given therapeutic for HT in a given individual comprising screening for the presence or absence of the HT associated SNP markers, haplotypes or haplotype regions in one or several of the HT risk genes of claim 15.

62. A method for predicting the effectiveness of a given therapeutic for HT in a given individual, the method comprising the steps of: a) providing a biological sample taken from a subject b) determining the nucleotides present in one or several of the polymorphic sites as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid; and c) combining the SNP marker data to predict the effectiveness of a given therapeutic in an individual for HT.

63. A method for diagnosing of a subtype of HT in an individual having HT, the method comprising the steps of: a) providing a biological sample taken from a subject; b) determining the nucleotides present in one or several of the SNP markers as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid; and d) combining the SNP marker data to assess the subtype of HT of an individual..

64. The method according to claim 63, wherein said one or several SNP markers reside within a HT risk gene or genes as set forth in table 6.

65. The method according to claim 63, wherein the HT risk genes reside in the genome region which is defined by the haplotype pattern mining analysis, the genes and regions set forth in tables 3, 4, 5, 7 and 8.

66. The method according to claim 63, wherein the polymorphic sites are associated with the haplotype regions, haplotypes or SNP markers defining the haplotypes set forth in tables 3, 4, 5, 7 and 8.

67. The method according to claim 63, wherein the polymorphic sites are in complete linkage disequilibrium with the haplotype regions, haplotypes or SNP markers defining the haplotypes set forth in 3, 4, 5, 7 and 8.

68. The method according to claim 63, wherein the polymorphic sites are in complete linkage disequilibrium in the population in which the said method is used.

69. The method according to any one of claims 43 or 60 to 63 further comprising a step of combining non-genetic information with the results obtained according to any one of claims

44 to 68.

70. The method according to claim 69, wherein the non-genetic information concerns age, gender, behaviour patterns and habits, biochemical measurements, clinical measurements, obesity, the family history of HT, cerebrovascular disease, other cardiovascular disease, hypercholesterolemia, obesity and diabetes, waist-to-hip circumference ratio (cm/cm), socioeconomic status, psychological traits and states, and the medical history of the subject.

71. The method according to claim 69, wherein the behaviour patterns and habits include tobacco smoking, physical activity, dietary intakes of nutrients, alcohol intake and consumption patterns and coffee consumption and quality.

72. The method according to claim 69, wherein the biochemical measurements include determining blood, serum or plasma VLDL, LDL, HDL or total cholesterol or triglycerides, apolipoprotein (a), fibrinogen, ferritin, transferrin receptor, C-reactive protein, glucose, serum or plasma insulin concentration.

73. The method according to claim 69, wherein the non-genetic measurements are those presented in table 8.

74. The method according to claim 69, wherein the non-genetic information contains the BMI and history of obesity in the family of the subject.

75. A method for measuring HT risk gene product protein expression, production or concentration in a biological sample taken from a subject, wherein said HT risk gene is as defined in table 6, the method comprising the steps of: a) providing a biological sample taken from a subject to be tested; and b) detecting the expression, production or concentration of said protein in said sample, wherein altered expression, production or concentration indicates an altered risk of cardiovascular disease in said subject

76. A test kit based on a method according to claim 1 for assessment of an altered risk of or susceptibility for HT in a subject.

77. A test kit for determining the nucleotides present in one or several of the SNP markers as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid for assessment of an altered risk of HT in a subject.

78. A test kit for determining the nucleotides present in one or several of the SNP markers as set forth in tables 2 to 5 and 7 to 11 in said individual's nucleic acid for assessment of an altered risk of HT in a subject, containing: a) reagents and materials for assessing nucleotides present in one or several SNP markers as set forth in tables 2 to 5 and 7 to 11 ; and b) software to interpret the results of the determination.

79. The test kit according to claim 76 further comprising PCR primer set for amplifying nucleic acid fragments containing one or several SNP markers as set forth in tables 2 to 5 and 7 to 11 from the nucleic acids of the subject.

80. The test kit according to claim 76 comprising a capturing nucleic acid probe set specifically binding to one or several SNP markers present in HT associated markers and haplotype regions as set forth in tables 2 to 5 and 7 to 11.

81. The test kit according to claim 76 comprising a microarray or multiwell plate to assess the genotypes.

82. The test kit according to claim 76 comprising a questionnaire for obtaining patient information concerning age, gender, height, weight, waist and hip circumference, skinfold and adipose tissue thicknesses, the proportion of adipose tissue in the body, the family history of diabetes and obesity, the medical history concerning HT.

83. A test kit for detecting the presence of SNP markers in one or several of HT risk genes as set forth in table 6 in a biological sample, wherein said SNP markers are more frequently present in a biological sample of a subject susceptible to HT compared to a sample from a subject not susceptible to HT, the kit comprising: a) reagents and materials for assessing nucleotides present in SNP markers in one or several of HT risk genes as set forth in table 6; and b) software to interpret the results of the determination.

84. The test kit of claim 83 further comprising PCR primer set for amplifying nucleic acid fragments containing said SNP markers from HT risk genes as set forth in table 6 from the nucleid acids of the subject.

85. The test kit of claim 83 comprising a capturing nucleic acid probe set specifically binding to one or several SNP markers present in HT risk genes as set forth in table 6.

86. The test kit of claim 83 comprising a microarray or multiwell plate to assess the genotypes.

87. The test kit of claim 83 comprising a questionnaire for obtaining patient information concerning age, gender, height, weight, waist and hip circumference, skinfold and adipose tissue thicknesses, the proportion of adipose tissue in the body, the family history of diabetes and obesity, the medical history concerning HT.

88. A test kit based on a method according to any one of claims 46, 47, 60 to 63 or 75.

89. The test kit of claim 88 further comprising PCR primer set for amplifying nucleic acid fragments containing said SNP markers from HT risk genes as set forth in tables 2 to 5 and 7 to 11 from the nucleid acids of the subject.

90. The test kit of claim 88 comprising a capturing nucleic acid probe set specifically binding to one or several SNP markers present in HT risk genes as set forth in tables 2 to 5 and 7 to 11.

91. The test kit of claim 88 comprising a microarray or multiwell plate to assess the genotypes.

92. The test kit of claim 88 comprising a questionnaire for obtaining patient information concerning age, gender, height, weight, waist and hip circumference, skinfold and adipose tissue thicknesses, the proportion of adipose tissue in the body, the family history of diabetes and obesity, the medical history concerning HT.

93. The test kit of claim 76, 83 or 88, further comprising a marker set to assess the ancestry of an individual.

94. The test kit of claim 93 comprising a SNP marker set to assess the ancestry of an individual.

95. The test kit of claim 93 comprising a microsatellite marker set to assess the ancestry of an individual.

96. The method of claim 1 further comprising a marker set to assess the ancestry of an individual.

97. The method of claim 1 comprising a SNP marker set to assess the ancestry of an individual.

98. The method of claim 1 comprising a microsatellite marker set to assess the ancestry of an individual.

99. The method according to claim 1, wherein one or several of the SNP markers are selected from the group consisting of the following individual SNPs: a) rsl860933 (AT ) (SEQ ID NO:1366) defining the risk allele A b) rs4236780 (CG) (SEQ ID NO: 1367) defining the risk allele C c) rs2000112 (CT) (SEQ ID NO:660) defining the risk allele C d) rs931850 (AG) (SEQ ID NO: 1303) defining the risk allele A e) rs2192947 (AG) (SEQ ID NO:728) defining the risk allele G f) rs9328292 (AG) (SEQ ID NO: 1316) defining the risk allele A g) rsl409367 (CT) (SEQ ID NO:490) defining the risk allele C h) rsl 893814 (CT) (SEQ ID NO:622) defining the risk allele T i) rs2263356 (CT) (SEQ ID NO:746) defining the risk allele T j) rs6826647 (CT) (SEQ ID NO: 1368) defining the risk allele C k) rsl913157 (CG) (SEQ ID NO:630) defining the risk allele C

100. The method according to claim 99 further comprising a step of combining information from hypertension drug treatment of the subject to the genetic information of the subject.

101. The method according to claim 1, wherein one or several of the SNP markers are selected from the group consisting of the following individual SNPs: a) rs6826647 (CT) (SEQ ID NO: 1368) defining the risk allele C b) rsl409367 (CT) (SEQ ID NO:490) defining the risk allele C c) rs9328292 (AG) (SEQ ID NO: 1316) defining the risk allele A d) rsl 395266 (CT) (SEQ ID NO:476) defining the risk allele T e) rsl 893814 (CT) (SEQ ID NO:622) defining the risk allele T f) rs931850 (AG) (SEQ ID NO: 1303) defining the risk allele A g) rsl 860933 (AT ) (SEQ ID NO: 1366) defining the risk allele A h) rsl386483 (AG) (SEQ ID NO:470) defining the risk allele A i) rs4236780 (CG) (SEQ ID NO: 1367) defining the risk allele C j) rsl913157 (CG) (SEQ ID NO:630) defining the risk allele C k) rs2263356 (CT) (SEQ ID NO:746) defining the risk allele T

1) rs2000112 (CT) (SEQ ID NO:660) defining the risk allele C