Genome-wide association yields new sequence variants at ... · correction, but in the other...

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Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity

Supplementary Material

Gudmar Thorleifsson1*#, G Bragi Walters1*, Daniel F Gudbjartsson1, Valgerdur

Steinthorsdottir1, Patrick Sulem1, Anna Helgadottir1, Unnur Styrkarsdottir1, Solveig

Gretarsdottir1, Steinunn Thorlacius1, Ingileif Jonsdottir1,2, Thorbjorg Jonsdottir1,

Elinborg J Olafsdottir3, Gudridur H Olafsdottir3, Thorvaldur Jonsson2,4, Frosti

Jonsson1, Knut Borch-Johnsen5,6, Torben Hansen5, Gitte Andersen5, Torben

Jorgensen7,8, Torsten Lauritzen9, Katja K Aben10, André LM Verbeek11, Nel

Roeleveld11, Ellen Kampman11, Lisa R Yanek12, Lewis C Becker12, Laufey

Tryggvadottir3, Thorunn Rafnar1, Diane M Becker12, Jeffrey Gulcher1, Lambertus A

Kiemeney10,11,13, Oluf Pedersen5,6,8, Augustine Kong1, Unnur Thorsteinsdottir1,2 &

Kari Stefansson1,2#

*These authors contributed equally to this work 1 deCODE Genetics, 101 Reykjavik, Iceland.

2 Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland.

3I celandic Cancer Registry, 105 Reykjavik, Iceland.

4 Department of Surgery, University Hospital, 101 Reykjavik, Iceland.

5 Steno Diabetes Center, DK-2820 Copenhagen, Denmark.

6 Faculty of Health Science, University of Aarhus, DK-8000 Aarhus, Denmark.

7 Research Centre for Prevention and Health, Glostrup University Hospital, DK-2600 Glostrup,

Denmark. 8 Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark.

9 The Department of General Medical Practice, University of Aarhus, DK-8000 Aarhus, Denmark.

10 Comprehensive Cancer Centre East, 6500 HB Nijmegen, The Netherlands.

11 Radboud University Nijmegen Medical Center Department of Epidemiology & Biostatistics, 6500 HB

Nijmegen, The Netherlands. 12

The Johns Hopkins Sibling and Family Heart Study, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA. 13

Radboud University Nijmegen Department of Urology, 6500 HB Nijmegen, The Netherlands.

# Correspondence and request for materials should be addressed to: Gudmar Thorleifsson ([email protected]) or Kari Stefansson ([email protected])

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Supplementary Methods

Study Subjects.

Icelandic samples: Weight and BMI information, collected in our studies on obesity and cancer, were

available from 74,921 and 74,735 Icelanders, respectively, of which about 23% was self-reported.

25,344 of these individuals have been genotyped on an Illumina 317K or 370K SNP chip in one of

several genome-wide association studies recently conducted by deCODE Genetics. Combining them

with another 9,106 genotyped Icelandic individuals, who do not have BMI and weight information,

allowed us to impute the genotypes for a further 39,342 individuals with BMI and weight information

(as described below). The recruitment of the 1,405 T2D cases used in this study has been described

previously1. The 23,190 controls used for the T2D analysis were selected among the genotyped

Icelandic individuals, excluding known T2D cases and individuals taking diabetes related drugs. Only

T2D cases and controls with BMI information were included in the analysis. These studies were all

approved by the Data Protection Commission of Iceland and the National Bioethics Committee of

Iceland. Written informed consent was obtained from all participants. Personal identifiers associated

with phenotypic information and blood samples were encrypted using a third-party encryption system

as previously described2. Only individuals with a genotype yield over 96% were included in the study.

Dutch samples: Self-reported information on weight and BMI was available from participants in two

studies by the Radboud University Nijmegen Medical Centre (RUNMC). Participants in the first study,

the Nijmegen Bladder Cancer Study study, were bladder cancer cases (N = 1,164) identified through

the population-based cancer registry held by the Comprehensive Cancer Centre East in Nijmegen3.

The patients were invited by their treating physicians, and gave informed consent for a study on gene-

environment interactions in the development of cancer. The local IRB approved the use of the

available genotype information for an analysis of obesity related phenotypes. The other Dutch

samples came from the Nijmegen Biomedical Study4. This is an age-stratified survey of the general

population of Nijmegen performed in 2002-2003 by the RUNMC. Informed consent was obtained for a

study on genetic susceptibility and environmental risk factors for disease and disease-related

characteristics in general. Lifestyle information, family history of cancer, reproductive and medical

history as well as blood samples were available from a group of 6,700 individuals. From this group,

1,942 individuals were randomly selected as a control group for a genetic study on bladder cancer3.

The study protocol was approved by the Institutional Review Board of the RUNMC.

US samples: Subjects consisted of families identified from 1983-2006 from probands with a

premature coronary disease event prior to 60 years of age. This ongoing prospective family study (the

Johns Hopkins Sibling and Family Heart Study) was designed to determine the environmental and

genetic causes of premature chronic and cardiovascular diseases. Probands with documented

coronary artery disease (CAD) before the age of 60 were identified at the time of hospitalization in any

of 10 Baltimore area hospitals. Their apparently healthy 30-59 year old siblings without known CAD

were recruited. In 2002, adult offspring over 21 years of age of all participating siblings and probands

were recruited and underwent risk factor measurement and phenotypic characterization (including

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measurements of height and weight). In addition, the spouse was recruited for all participants for

which at least one offspring was recruited.

Danish Samples: Participants come from two population cohorts: (1) the population based Inter99

sample5 of middle-aged Danes recruited at the Research Centre for Prevention and Health in the

years 1999-2000; (2) the ADDITION study group6, a population-based sample recruited for a high-risk

screening and intervention study for type 2 diabetes in general practice and sampled through the

Department of General Practice at the University of Aarhus. All participants underwent a thorough

phenotype characterisation including questionnaire and interview. Physical examination included

measurements of height, weight, waist and hip circumferences. The case control study of type 2

diabetes included as patients all type 2 diabetes patients from the Inter99 cohort as well as patients

recruited from the outpatient clinic at the Steno Diabetes Center. The controls consisted of glucose-

tolerant subjects from the Inter99 cohort. Type 2 diabetes was diagnosed according to WHO criteria.

Informed written consent was obtained from all subjects before participation. The study was approved

by the Ethical Committee of Copenhagen County and was in accordance with the principles of the

Helsinki Declaration.

GIANT Samples: The GIANT consortium samples are the combined datasets from 13 genome-wide

association (GWA) studies, amounting to a total of 32,615 individuals. Included are six population-

based studies (CoLaus, SardiNIA, EPIC-Obesity, KORA, WTCCC/UK Blood services and the British

1958 Birth Cohort), cases and controls of two type 2 diabetes (T2D) case-control studies (DGI and

FUSION), and fives case series (NHS, PLCO, WTCCC/HT, WTCCC/CAD and WTCCC/T2D). All

studies report either measured or self-reported height and weight. The stage 1 of their study

comprises a meta-analysis of the genome-wide results for association between SNP variants and

BMI7 and we examined BMI association results for 43 SNPs from the GIANT meta-analysis.

Specifically for this paper, we also requested a meta-analysis of weight data for 43 SNPs from the

consortium GWAS (results provided by C.M. Lindgren, J.C. Randall and S. Li on behalf of the GIANT

Consortium).

SNP Genotyping.

Illumina genome-wide genotyping. The Icelandic study participants were genotyped using

genotyping systems and specialized software from Illumina; the Human Hap300 or Human Hap300-

duo+ (referred to as the 317K) or Human CNV370-Duo (referred to as the 370K) Bead Arrays

(Illumina, San Diego, CA, USA). In total, 311,388 single-nucleotide polymorphism (SNP) markers,

distributed across the human genome, were common to both platforms. The Dutch study participants

were genotyped with the Illumina Human Hap300-duo+ Bead Arrays and the American study

participants were genotyped with the Human Hap1000 (referred to as the 1M) Bead Array. For the

association analysis, we used 305,846 SNP markers, common to all three chip types, because 5,542

were deemed unusable due to low yield (less than 95% in at least one sample set), deviations from

Hardy-Weinberg expectations (P < 10-5

in at least one sample), or discrepancies in genotype

frequencies between the arrays.

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Single SNP Genotyping. Single SNP genotyping for the Danish samples was carried out at deCODE

genetics with the Centaurus (Nanogen, Bothell, WA, USA) platform8. The quality of each Centaurus

SNP assay was evaluated by genotyping each assay on the CEU samples and comparing the results

with the HapMap data. Assays with >1.5% mismatch rate were excluded and a linkage disequilibrium

(LD) test was used for markers known to be in LD. Key markers from the genome-wide analysis were

re-genotyped on more than 10% of samples and a mismatch was observed in less than 0.5% of

samples.

Quality control of samples. Genotypes of markers on the X chromosome were compared to the

reported gender of the individual and those where genotypes and gender did not match were removed

from the study. Seventy individuals were removed from the Icelandic sample, 10 from the Dutch

sample and 20 from the US sample.

We applied the STRUCTURE software package9 to all our genome-wide samples individually

and used the HapMap data to train the classification of individuals into Europeans, Asians and

Africans. Individuals with less than 95% European ancestry were removed from the Icelandic (N=37),

Dutch (N=67) and Americans of European descent (N=107) samples and individuals with less than

30% African ancestry were removed from the African American sample (N=6).

Association testing. All information on weight and BMI was corrected for year of birth and

standardized to have a standard normal distribution, within both sexes, for each study population

separately. In Iceland, year of birth was rounded to five years and used as a factor variable in the

correction, but in the other populations a linear term in year of birth was used to correct the

measurements. Measured and self reported weight and BMI were corrected separately in Iceland. For

each SNP, a classical linear regression, using the genotype as an additive covariate and weight or

BMI as a response, was fit to test for association.

All test statistics were scaled by the method of genomic controls10

using as an estimate of the

inflation factor the standard deviation of the z-statistic. The estimated inflation factors for weight and

BMI respectively were 1.223 and 1.184 in the Icelanders, 1.016 and 1.018 in the Dutch, 1.181 and

1.155 in the Americans of European descent, 1.147 and 1.150 in the African Americans and 1.048 and

1.034 in the DGI data. Adjusted P values were calculated by dividing the corresponding z-score by the

inflation factor.

Data from all the samples were combined by using an estimate of the effective sample size of

each population. For the non-Icelandic samples, the actual sample size divided by the inflation factor

squared was used as an estimate of the effective sample size used in combining weight and BMI

respectively: 2831.4 and 2822.07 for the Dutch, 1275.4 and 1225.0 for the Americans of European

descent, 881.64 and 884.91 for the African Americans, and 2500.84 and 2570.66 for the DGI sample.

For the Icelandic sample, a rough estimate of 20,000 was used as an estimate of the effective sample

size, both for weight and BMI, due to the complexities introduced by the family based association

described below. Inappropriate effective sample size estimates will reduce power, but will not affect

the validity of the analysis. An overall z-score was calculated by summing the z-scores weighted by

the square root of the effective sample size, over all populations, and dividing by the square root of the

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sum of the sample sizes. An overall estimate of the effect per allele was calculated by weighting

together the effects in each population by the population’s effective sample size.

The fraction of variance explained was calculated using the formula 2f (1 – f) a2, where f is the

frequency of the variant and a is its additive effect. As an estimate of the population frequency we

used a simple average of the frequency in the Icelandic, the Dutch, the Americans of European

descent and the Danish sample sets. For the calculation of the fraction of variance explained by the

SNPs in Tables 1 and 2 only one SNP was picked per locus.

For a description of the GIANT BMI meta-analysis see reference7. In the GIANT weight meta-

analysis, each of the thirteen studies involved performed quality control on genotyped SNPs and

samples, and subsequently imputed genotypes using the HapMap CEU reference panel. The weight

phenotype was inverse-normal transformed separately in each gender, and the gender-stratified

cohorts were tested for association using an additive model with age, sex and age2 as covariates. All

alleles were listed on the forward strand and meta-analysis was performed using METAL with genomic

control correction enabled and using the standard error weighting scheme.

Using family information to test for association in Iceland. The Icelandic genealogy database

currently contains 739,291 Icelanders with 650,692 of the Icelanders in the database having a father in

the database and 651,821 having a mother in the database. 363,960 of the individuals are born in the

20th century and of these 94.7% have both parents in the database, 0.2% have a father, but no

mother in the database, 1.8% have a mother but no father in the database, and 3.2% have no parent

in the database. The relatedness of closely related genotyped individuals in the Icelandic genealogy

has been verified, and links between individuals or between individuals and genotypes have been

removed as appropriate.

Weight and BMI information exists for many more Icelandic individuals than those who had

been genotyped. We used the available genotype information on the relatives of individuals who had

not been genotyped in order to extract more information on association from our data. A distribution

over the possible genotype configurations of each individual was obtained through peeling11

For

example, if the genotypes of an individual’s parent are available we can either infer one of his alleles

with full certainty (if the parent is homozygous) or can know that the individual has one of two alleles

with equal probabilities (if the parent is heterozygous). Given the probability distribution of possible

genotypes, the standard linear regression model can be implemented by calculating a weighted sum

over the possible genotypes. We only used relatives within two meiotic events of the individual, which

includes parents, offspring, siblings (full and half), grand-parents and grand-children as well as

spouses of the probands and the probands children. Weight and BMI information from a total of

39,342 ungenotyped individuals, with at least one close genotyped relative, were used. Estimates of

effects in the Icelandic sample were only based on unadjusted values, i.e. ignoring the imputed data

and the familial adjustment, for the individuals with both genotypes and weight or BMI information.

Correlation between SNPs and expression. The correlation between SNPs and expression of

genes at the eleven loci that showed association with BMI or weight, was tested in a dataset that

includes measurements of the expression of 23,720 transcripts in adipose tissue and in whole blood

from 674 and 1,002 Icelandic individuals, respectively. The collection of the tissue samples and the

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measurement of the expression was described previously12

. Of those individuals, 603 with adipose

tissue sample and 745 with blood sample had been genotyped with the Illumina 317K or 370K chip

and were used for the analysis. For each variant and each expression trait at the corresponding loci,

the correlation was tested by regressing the mean logarithm (log10) expression ratio (MLR) on the

number of copies of the variant a person carries. The effect of age and sex was taken into account by

including an Age×Sex term as an explanatory variable in the regression analysis. When analyzing

expression in blood, adjustment for differential cell count was also included. The analysis was

repeated adjusting for the weight of the individuals by including BMI or weight as explanatory variable.

All P-values were adjusted for relatedness of the individuals by simulating genotypes through the

Icelandic genealogy as previously described13

. The corresponding adjustment factors for the Chi2

statistic were 1.063 and 1.078 for adipose tissue and blood, respectively. The gene expression data is

available from the GEO database under the accession numbers GSE7965 and GPL3991.

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Supplementary Notes

Description of Genes at the Eleven Loci.

Upstream refers to the distance from the SNP to the start of the first exon and downstream refers to

the distance from the SNP to the end of the last exon of the largest refseq transcript.The “kb” refers to

kilobases or 1,000 bases.

1p31: rs2568958 and rs3101336 are located about 16.7 kb and 2.8 kb, respectively, upstream of

neuronal growth regulator 1 (NEGR1) which is a member of the immunoglobulin superfamily (iglon

family) and through its function as a cell adhesion molecule14,15

participates in the regulation of neurite

outgrowth in the developing brain16,17

.

1q25: rs10913469 is located in intron 15 of SEC16 homolog B (SEC16B , S. cerevisiae; also known

as leucine zipper transcription regulator 2, LZTR2). In order to transport proteins and lipids from the

endoplasmic reticulum (ER) to the Golgi complex the coat protein complex II (COPII) assembles onto

the ER membrane at discrete sites known as ER exit sites (ERES)18

which in mammalian cells are

defined by Sec16. In Drosophila Schneider 2 cell studies using RNAi, a subset of the Arf1–COPI

vesicular transport proteins were found to regulate droplet morphology and lipid utilization but did not

involve COPII19

.

Also, located at this locus, about 150 kb away is RAS protein activator like 2 (RASAL2) which

encodes a Ras GTPase-activating protein (RasGAP)-like protein that negatively regulates Ras activity

which itself plays a crucial role in the control of cell growth and differentiation20

.

2p25: rs2867125, rs4854344 and rs7561317 are located about 45.1 kb, 23.8 kb and 23 kb,

respectively, downstream of transmembrane protein 18 (TMEM18). TMEM18 is widely expressed in

fetal and adult human tissues (See TMEM18 URL a and b) and is well conserved among divergent

species especially mammals (See TMEM18 URL c). It has three to four potential membrane spanning

domains with a potential nuclear localization signal (NLS) sequence at its C-terminus. Little else was

known about this gene until in a recent publication, at least one of its roles, was identified as a

modulator of glioma directed stem cell migration, in a bid to find improved treatment of scattered

glioma clusters21

. Jurvansuu et al pointed out that neural stem cells (NSCs) and neural precursor cells

(NPCs) have an intrinsic tropism for sites of brain injury, including gliomas. In order to determine the

genes responsible for this tropism they screened a cDNA expression library and came up with

TMEM18. To further elucidate its role they performed overexpression and knock-down studies and

showed that TMEM18 is essential for the migration of NSCs and NPCs. The NSC/NPC cells

overexpressing TMEM18 showed typical morpphology of astrocytes. The knock-down and expression

studies indicated that TMEM18 is crucial for regulating general cell motility at its basal, physiologic

level expression, which is consistent with the highly conserved and its ubiquitously expressed pattern.

The predicted signal sequence localizes TMEM18 to the nucleus. This is supported by antibody

staining placing it in the nucleus and not near cytoskeletal structures which seems unusual for a

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protein involved in cell motility. However, it could be involved in steps downstream of chemoattractant

receptor signaling and thereby exert its influence on motility.

TMEM18 URLs:

(a) National Center for Biotechnology Information - EST Profile Viewer

http://www.ncbi.nlm.nih.gov/UniGene/ESTProfileViewer.cgi?uglist=Hs.43899

(b) Genomics Institute of the Novartis Research Foundation (GNF) – Symatlas,

http://symatlas.gnf.org/SymAtlas/

(c) NCBIs HomoloGene,

http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uid

s=17675

3q27: rs7647305 is located about 7.4 kb upstream of Ets variant gene 5 (ETV5). ETV5 is a

transcription factor that plays a role in development and cancer. It is widely expressed, predominantly

in brain and placenta, and to a lesser degree in lung, pancreas, and heart22

. The ETS family has a

select spatial and temporal expression pattern in pancreatic development with Etv5 being expressed

in cells proximal to pancreatic mesenchyme23

. As demonstrated by mouse knock-out studies, males

have reduced body weight, postnatally, and are infertile as ETV5 appears to be essential for self-

renewal of spermatogonial stem cells24

.

rs7647305 is located about 30.7 kb downstream of Diacylglycerol kinase gamma (DGKG).

DGKG, itself highly regulated, phosphorylates diacylglycerol (DAG) to form phosphatidic acid (PA).

DAG and PA are regulators of numerous target proteins, among them protein kinase C (PKC) and Ras

guanyl nucleotide-releasing proteins (RasGAP), involved in cell proliferation and differentiation and

numerous biological processes in eukaryotic cells25,26

. DGKG a member of DGK subclass I is highly

expressed in brain, in particular cerebellum, and the retina27,28

.

rs7647305 is located about 178.5 kb upstream of splicing factor, arginine/serine-rich 10

(SFRS10) which is involved in nuclear mRNA splicing, via the spliceosome29

. SFRS10 has at least 5

isoforms, each with a slightly different tissue specific expression pattern. Highest expression is in the

heart, skeletal muscle and pancreas, less abundant in kidney, placenta, brain and liver30

. During

human fetal development, SFRS10 transcript levels are tightly regulated in a tissue- and temporal-

specific pattern31

.

6p21: There are several genes located at this locus and therefore only the closest genes and those of

relevance to prior obesity association are mentioned here.

rs2844479 is located about 10.1 kb upstream of allograft inflammatory factor 1 (AIF1). AIF1 is

an evolutionarily conserved, Ca2+-binding EF-hand protein involved in immune dysfunction and

smooth muscle cell activation which is cytokine inducible, tissue-specific, and shows increased

expression in response to vascular injury incurred during balloon angioplasty in rat studies32

. It is

produced by activated macrophages during chronic transplant rejection, in inflammatory brain lesions

and inflammatory skin disorders33

. Sequence variants in AIF1 are associated with systemic

sclerosis34,35

.

rs2844479 is located about 12.2 kb upstream of natural cytotoxicity triggering receptor 3

precursor (NCR3). NCR3 is a natural killer (NK) cell activating receptor involved in the destruction of

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tumor cells and immature dendritic cells36

. An NCR3 sequence variant (rs2736191) has been

significantly associated with increased risk of mild malaria37

. NCR3 and LST1 showed significantly

increased expression and could be upregulated in rheumatoid arthritis affected blood and synovium38

.

rs2844479 is located about 15.6 kb upstream of HLA-B associated transcript-2 (BAT2). BAT2

is a proline rich protein with similarities to proteins with large proline-rich domains, such as some

nuclear proteins, collagens, elastin, and synapsin, yet its function is unknown39

. A microsatellite

marker close to BAT2 has been shown to associate with age-at-onset of insulin-dependent diabetes

mellitus40

and susceptibility to rheumatoid arthritis41

.

rs2844479 is located about 16.3 kb downstream of leukocyte specific transcript 1 (LST1).

LST1 is expressed in leukocytes and dendritic cells, and it is characterized by extensive alternative

splicing42

resulting in isoforms that code for transmembrane as well as soluble LST1.

rs2844479 is located about 26.8 kb downstream of tumor necrosis factor (TNF) (TNF

superfamily, member 2), also known as TNFalpha is a pleiotropic proinflammatory cytokine secreted

by, for example macrophages and adipocytes and is involved in a diverse range of biological

processes including cell proliferation, differentiation, apoptosis, lipid metabolism, coagulation,

inflammation, tumorigenesis, endothelial functions, viral replication and the adipocytokine signaling

pathway. It has also been implicated in numerous diseases including autoimmune diseases (eg.

psoriasis and rheumatoid arthritis), Alzheimer’s disease43

, asthma44

, cancer, insulin resistance and

diabetes45,46

, and obesity47-55

.

rs2844479 is located about 30.9 kb downstream of lymphotoxin alpha (LTA) (TNF superfamily,

member 1), also known as TNFbeta is a cytokine produced and secreted by activated lymphocytes. It

forms heterotrimers with lymphotoxin-beta which anchors lymphotoxin-alpha to the cell surface. LTA

mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, plays a role in

apoptosis and is also involved in the formation of the secondary lymphoid organs during development.

In a recent publication lymphotoxin was identified, along with tumor necrosis factor (ligand)

superfamily, member 14 (TNFSF14, also known as LIGHT), as critical regulators of key enzymes that

control lipid metabolism56

. Using low density lipoprotein receptor (LDLR) deficient mice, unable to

control lipid levels in the blood, the authors were able to attenuate the dyslipidemia by inhibiting the

lymphotoxin and LIGHT signaling and therefore concluded that the immune system directly influences

lipid metabolism. LTA has also been implicated in myocardial infarction57

, diabetes58,59

, and obesity60

among numerous other diseases.

rs2844479 is located about 60.7 kb upstream of Casein kinase 2, beta polypeptide (CSNK2B)

encodes a regulatory subunit of the tetrameric casein kinase II, a ubiquitous serine/threonine kinase

which is one of the most pleiotropic protein kinases with numerous substrates and involved in wide

ranging processes, such as signal transduction, neoplasia, cell survival, viral infection, gene

expression, protein synthesis, and affects cytoskeletal and structural proteins and metabolic

pathways61

.

rs2844479 is located about 222.6 kb upstream of heat shock 70kDa protein 1B (HSPA1B)

which is a member of the heat shock protein 70 family and is involved in the stabilization of proteins

against aggregation and damage caused by various stressful stimuli by binding to denatured or

inappropriately folded proteins and helps newly translated proteins to fold in the cytosol and

organelles. It is an intronless gene that clusters with two other HSP70 genes which encode identical

10

(HSPA1A) or highly similar (HSPA1L) proteins. Among the proteins HSPA1B binds to are the

peroxisome proliferator-activated receptors (PPARs) where it is involved in their folding, subcellular

localization and activation. PPARG has been shown to play a major role in adipose tissue formation

and insulin sensitivity62

. Variants in HSPA1B have been associated with a number of diseases

including obesity (rs1061581)63

, Alzheimer’s disease64

, coronary artery disease65

and nasopharyngeal

carcinoma66

.

11p14: As there appear to be two association signals at this locus only 1 SNP, representing the

correlated SNPs from each signal, will be shown relative to the position of the genes discussed.

rs4923461 and rs925946 are located about 19.5 kb and 9.2 kb, respectively, downstream of

brain derived neurotrophic factor (BDNF). BDNF is a neurotrophic factor that promotes differentiation

and survival of developing neurons and their maintainance in the adult nervous system67,68

. BDNF has

a complex pattern of expression in the brain69

and its high expression in the ventromedial

hypothalamus (VMH) is regulated by nutritional state and MC4R signalling70

. Xu showed that mice

with lower expression of the BDNF receptor were hyperphagic and gained excessive weight on high

fat diets and that mice with deficient MC4R signalling, could have their hyperphagia and excessive

weight gain suppressed by infusing BDNF into their brain70

. Sequence variants in BDNF have been

extensively studied in several populations with conflicting evidence regarding association with

numerous neurological and behavioural disorders, including Alzheimer’s and Huntington’s disease,

Schizophrenia, cognitive and attention deficits, and eating disorders. A non-synonymous sequence

variant, resulting in the valine-66-to-methionine polymorphism (rs6265), within the 5’ pro-BDNF

sequence was shown, to have a dominant risk effect of the Met allele (the A allele of rs6265) to eating

disorders71

and that the Met-Met homozygotes had a lower BMI compared to individuals with the Val-

Met/Val-Val genotype72

. We also observed an association between the A allele (Met66) of rs6265 and

decreased BMI and weight.

A noncoding RNA was transcribed from a gene that overlaps with BDNF on the opposite

strand (BDNFOS)69

. Using a PCR-based assay, BDNF and BDNFOS transcripts were shown to form a

double-stranded RNA duplex in human cerebellum in vivo73

.

rs4923461 and rs925946 are located about 128.6 kb and 138.9 kb, respectively, upstream of

lin-7 homolog C (LIN7C also known as MALS-3 or VELI3) that is involved in cell polarity in renal

development74

, in exocytosis on the pre-synaptic side75

and receptor localization on the post-synaptic

side76

of neurons in the developing and mature brain. It is interesting to note that when LIN7A and

LIN7B (also known as MALS-1 and -2 respectively) are both knocked out in the mouse, LIN7C (ie.

MALS-3) is up-regulated to compensate77

. LIN7C is expressed both in brain and peripheral tissues.

rs4923461 and rs925946 are located about 162.6 kb and 172.9 kb, respectively, upstream of

leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4), an orphan receptor with an

unknown physiological role in the family of G protein-coupled, seven-transmembrane, N-terminal

extracellular domain containing leucine-rich repeat proteins, as follicle-stimulating hormone (FSHR),

thyroid-stimulating hormone (TSHR) and leutenizing hormone/human chorionic gonadothrophin

(LH/cCGR) receptors. It is highly expressed in adult human pancreas but otherwise widely

expressed78-80

. Only 40% of LGR4 null mice were viable at birth and most of them died within 2 days.

The live mice showed decreased body weight and a decrease in kidney and liver weights,

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demonstrating the importance of LGR4 during embryonic growth, as well as kidney and liver

development80,81

.

12q13: rs7138803 is located about 14 kb donwstream of Fas apoptotic inhibitory molecule 2 (FAIM2).

FAIM2 protects against Fas mediated apoptosis and is widely expressed with relatively higher

expression observed in the hippocampus of the rat82,83

.

rs7138803 is located about 10 kb upstream of BCDIN3 domain containing (BCDIN3D) which

is a relatively unknown gene with suggested methyltransferase activity, as it contains one bicoid-

interacting protein 3 (Bin3) domain. Bin3, which shows similarity to a number of protein

methyltransferases that modify RNA-binding proteins, interacts with Bicoid, which itself directs pattern

formation in the early Drosophila embryo84

.

rs7138803 is located about 89 kb dowstreamstream of testis enhanced gene transcript (BAX

inhibitor 1) (TMBIM6; also known as TEGT). TMBIM6 is potentially a multi pass ER membrane protein

involved in the suppression of apoptosis and is found upregulated in some cancer cells.

There are a number of other genes at this locus which will not be discussed.

16p11: rs7498665 is located in exon 5 and rs4788102 and rs8049439 are located about 1.9 kb to 37

kb upstream of the refseq for Src-homology-2 (SH2) domain containing putative adapter protein 1

(SH2B1). SH2B1 is a Janus kinase 2 (JAK2) interacting protein, which is a tyrosine kinase essential in

cellular signalling by multiple hormones, including leptin85

, and cytokines86

. SH2B-/- knock-out mice

were severely hyperphagic and obese and developed a metabolic syndrome characterized by

hyperleptinemia, hyperinsulinemia, hyperlipidemia, hepatic steatosis, and hyperglycemia87,88

. SH2B1

transgenic knock-out mice that expressed rat SH2B1 in their neural tissue only did not develop the

metabolic disorder89

. Jamshidi performed an association test between rs7498665 A>G, (threonine-

484-to-alanine) and obesity related traits in a cohort of 2455 Caucasian female twins (from the UK

Adult Twin Registry) and found a significant association between the G allele (Ala484) and increased

serum leptin, total fat, waist circumference and body weight90

. The Thr484Ala polymorphism is a non-

synonymous coding SNP found to have a neutral effect on SH2B1 structure and function using two

prediction programs90

. We also observed an association between the G allele (Ala484) of rs7498665

and increased BMI and weight, thereby replicating this association.

rs7498665, rs4788102 and rs8049439 are located about 6 kb to 52 kb upstream of the

ATPase, Ca2+ transporting, fast twitch 1 gene (ATP2A1 also known as SERCA1). ATP2A1 is an

ATPase which pumps Ca ions from the cytosol into the sarcoplasmic reticulum in order to maintain

calcium stores needed for muscle excitation and contraction91

. Mutations in this gene cause some

autosomal recessive forms of Brody disease, characterized by increasing impairment of muscular

relaxation during exercise. Calcium is also required for muscle growth and development92

and

SERCA1 null mutant mice died shortly after birth due to respiratory failure93

.

rs8049439 is located about 16 kb downstream, and rs4788102 and rs7498665 are located

about 15 kb to 25 kb upstream of mitochondrial Tu translation elongation factor (TUFM). TUFM is

involved in mitochondrial protein translation by promoting the binding of aminoacyl-tRNA to ribosomes.

Mutations in TUFM cause combined oxidative phosphorylation deficiency which results in lactic

acidosis and progressive fatal encephalopathy94

.

12

rs8049439 is located in intron 4 and rs4788102 and rs7498665 are located about 24 kb to 34

kb downstream of ataxin 2 like protein (ATXN2L). Although its function is unknown it has been

suggested to be a member of the cytokine signaling system95

. ATXN2L associates with Mpl but is

released when thrombopoietin (TPO) binds, which leads to the activation of Jak2 and Tyk2 which

initiates proliferative signaling during normal megakaryocyte and platelet development96

. ATXN2L has

similar domains as the ataxin type 2 gene and is therefore a member of the spinocerebellar ataxia

(SCAs) family, which is associated with a complex group of neurodegenerative disorders.

rs8049439, rs4788102 and rs7498665 are located about 90 kb to 136 kb downstream (relative

to the closer copy of the duplication) of EIF3C (also known as EIF3S8) is a member of a protein

complex responsible for the recruitment of the 40S ribosomal subunit to mRNA in order to initiate

translation97

. MacLaren et al observed, in a small sample, a decrease in EIF3C expression in insulin

resistant omental adipose from obese individuals when compared with non-obese and insulin sensitive

obese omental adipose98

. EIF3C is duplicated and another copy is located some 300 kb telomeric to

rs7498665.

rs8049439, rs4788102 and rs7498665 are located about 217 kb to 262 kb upstream of

sulfotransferase family cytosolic 1A1(SULT1A1) and 229 kb to 275 kb upstream of sulfotransferase

family cytosolic 1A2(SULT1A2), respectively. Sulfotransferase enzymes catalyze the sulfate

conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds99

. These

cytosolic enzymes are different in their tissue distributions and substrate specificities. SULT1A1 and

SULT1A2 encode the two phenol sulfotransferases with thermostable enzyme activity. Human

SULT1A1, SULT1A2, and SULT1A3 (and probably SULT1A4 also) genes have a high degree of

sequence homology, suggesting that these genes arose by gene duplication100

. SULT1A1 has been

implicated in numerous cancers including breast and colorectal. A fairly common allele of SULT1A1

(*2) codes for an allozyme with low enzyme activity and stability compared to the wildtype

(SULT1A1*1) enzyme. Therefore this genotype may increase susceptibility to mutations following

exposure to dietary and/or environmental toxins. The frequency of the SULT1A1*1 allele was higher in

older populations, suggesting an association of sulfation efficiency with protection against cell or tissue

damage during aging101

and furthermore, a significantly reduced risk of colorectal cancer102

was

associated with homozygosity for SULT1A1*1.

rs8049439, rs4788102 and rs7498665 are located about 327 kb to 373 kb downstream of the

apolipoprotein B48 receptor (APOB48R). APOB48R is a macrophage receptor that binds to the

apolipoprotein B48 of dietary triglyceride (TG)-rich lipoproteins103

. This receptor may provide essential

lipids, lipid-soluble vitamins and other nutrients to reticuloendothelial cells. If overwhelmed with

elevated plasma triglyceride, APOB48R may contribute to foam cell formation, endothelial dysfunction,

and atherothrombogenesis103

.

Several putative segmental duplications have been predicted in the region telomeric to

ATXN2L104

.

There are a number of other genes at this locus which will not be discussed.

16q12: rs8050136 and rs3751812 (r2=1 in CEU HapMap) are located in a well defined LD block with

rs6499640 in the adjacent LD block and all three situated in intron 1 of the fat mass and obesity

associated (FTO) gene. In a genome wide association study of type 2 diabetes, an association was

13

discovered between a sequence variant in the FTO gene and obesity related traits105

. Each additional

copy of the A allele of rs9939609 (r2 = 1 with rs8050136/rs3751812 in CEU HapMap) was found to be

associated with increased: risk of obesity, weight, waist circumference, and subcutaneous fat mass in

adults as well as increased risk of obesity in children106,107

. Using bioinformatics analysis, FTO was

shown to share sequence motifs with iron- and 2-oxoglutarate (2OG)-dependent oxygenases which

are involved in a wide range of processes including fatty acid metabolism, DNA repair and

posttranslational modifications108

. Mouse studies indicate that Fto is highly expressed in the

hypothalamic nuclei, which governs energy balance, and that mRNA levels in the arcuate nucleus are

regulated by feeding and fasting108

. In a recent publication carriers of the, rs9939609, AA or AT at risk

genotype showed suggestive evidence of increased energy intake, but not expenditure, when

compared to the TT wild-type109

.

rs8050136 and rs3751812 are located about 78 kb to 80 kb and rs6499640 is located about

32 kb upstream of the RPGRIP1-like gene (RPGRIP1L, also known as KIAA1005 and in mice as Ftm).

There are about 100bp between the first exons of FTO and RPGRIP1L. A mouse study revealed that

Rpgrip1l is located at the ciliary basal body and is necessary for developmental processes such as the

establishment of left-right asymmetry and patterning of the neural tube and the limbs and is also

involved in cilium related Hedgehog (Hh) signaling in response to Sonic Hedgehog (Shh)110

.

According to Frayling et al. RPGRIP1L and FTO are expressed in similar tissues (mainly brain and

pancreatic islets), at similar levels and may be jointly transcriptionally regulated105

. Similarly Nagase et

al. found RPGRIP1L expression in adult brain, with weak expression in kidney, ovary, and spinal cord,

but no expression in any other adult or fetal tissue they examined111

. Recent studies have revealed

missense and truncation mutations in RPGRIP1L linked to Cerebello-oculo-renal syndrome (CORS),

also called Joubert syndrome type B, and Meckel (MKS) syndrome which belongs to the group of

developmental autosomal recessive disorders that are associated with primary cilium

dysfunction112,113

.

18q21: rs12970134, rs1350341 and rs633265 are located about 153 to 207 kb, 2 LD blocks removed,

downstream of melanocortin 4 receptor (MC4R). The pro-opiomelanocortin (POMC) derived alpha-

melanocyte stimulating hormone (alpha-MSH) from the arcuate nucleus binds to MC4R, located in the

paraventricular nucleus of the hypothalamus, that activates the second messenger adenylyl cyclase

and is responsible for increase in energy expenditure and decrease in food intake. Studies in MC4R

gene inactivated mice, result in a maturity onset obesity syndrome associated with hyperphagia,

hyperinsulinemia, and hyperglycinemia114

. Several sequence variants have been observed in the

coding region of MC4R in severely obese children and adults with symptoms such as eating disorders,

hyperphagia, decreased lean mass and increased linear growth115-125

. With 1–2.5% of people with a

BMI greater than 30 kg/m2 being found to have pathogenic mutations in MC4R in UK and European

populations it is the most common cause of monogenic obesity126

. In two recent publications,

sequence variants, around 109-188 kb downstream of MC4R, were found to associate with obesity

related traits. Loos et. al. utilising a discovery cohort of 16,876 individuals and replicating in a further

60,352 individuals (all of European ancestry), found rs17782313 to be associated with fat mass,

weight, height and obesity risk127

; rs17782313 correlates with our most significantly associated SNP

rs12970134 (r2 = 0.81, D’ = 0.96 in CEU HapMap). Chambers et. al. found an association in 2,684

14

Indian Asian men between rs12970134 and waist circumference and insulin resistance128

, which they

replicate in a further 11,955 individuals of Indian Asian or European ancestry.

19q13: rs29941 is located about 4.4 kb downstream of the potassium channel tetramerisation domain

containing 15 gene (KCTD15). KCTD15 is a voltage gated potassium channel which has a BTB/POZ

domain and although its function has not been elucidated it may be a transcription factor from

sequence homology comparisons129,130

.

rs29941 located about 45.1 kb downstream of carbohydrate (N-acetylgalactosamine 4-0)

sulfotransferase 8 (CHST8, also known as GalNAc4ST). Sulfotransferases, like CHST8, carry out

sulfations of carbohydrates which confer highly specific functions on glycoproteins, glycolipids, and

proteoglycans and are critical for cell-cell interactions, signal transduction, and embryonic

development. CHST8 is expressed in the pituitary where it sulfates the pituitary glycoprotein

hormones131-133

. Mutations in one of the pituitary glycoprotein hormones, pro-opiomelanocortin

(POMC), has been implicated in obesity134,135

.

15

The 1p31 locus. (a) The pair-wise correlation structure in a 800 kb interval (72.1 – 72.9 Mb, NCBI B36) on chromosome 1. The upper plot shows pair-wise D’ for 666 common SNPs (with MAF > 5%) from the HapMap (v22) CEU dataset. The lower plot shows the corresponding r

2 values. (b) Estimated

recombination rates (saRR) in cM / Mb from the HapMap Phase II data136

. (c) Location of known genes in the region. (d) Schematic view of the association with weight (red dots) and BMI (blue dots) for all SNPs tested in the region in the combined genome-wide data.

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs2568958

saRR

NEGR1

rs3101336

rs1776012rs9424977

0

20

40

60

0

1

2

3

4

5

6

7

8

72.1 72.3 72.5 72.7 72.9

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs2568958

saRR

NEGR1

rs3101336

rs1776012rs9424977

0

20

40

60

0

1

2

3

4

5

6

7

8

72.1 72.3 72.5 72.7 72.9

16

The 1q25 locus. (a) The pair-wise correlation structure in a 500 kb interval (175.9 – 176.4 Mb, NCBI B36) on chromosome 1. The upper plot shows pair-wise D’ for 501 common SNPs (with MAF > 5%) from the HapMap (v22) CEU dataset. The lower plot shows the corresponding r



. (c) Location of known genes in the region. (d) Schematic view of the association with weight (red dots) and BMI (blue dots) for all SNPs tested in the region in the combined genome-wide data. A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs10913469

saRR

SEC16B RASAL2

0

20

40

60

80

100

0

1

2

3

4

5

6

7

175.9 176 176.1 176.2 176.3 176.4

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs10913469

saRR

SEC16B RASAL2

0

20

40

60

80

100

0

1

2

3

4

5

6

7

175.9 176 176.1 176.2 176.3 176.4

17


2 values. (b) Estimated recombination rates

(saRR) in cM / Mb from the HapMap Phase II data136


A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs2867125

TMEM18 LOC391343

rs4854344

rs7561317

saRR

0

20

40

60

0

1

2

3

4

5

6

7

8

9

10

0.4 0.5 0.6 0.7 0.8 0.9

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

rs2867125

TMEM18 LOC391343

rs4854344

rs7561317

saRR

0

20

40

60

saRR

0

20

40

60

0

1

2

3

4

5

6

7

8

9

10

0.4 0.5 0.6 0.7 0.8 0.9

18





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

SFRS10

rs7647305

ETV5

DGKG

0

20

40

60

80

0

1

2

3

4

5

6

187.1 187.2 187.3 187.4 187.5 187.6

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

SFRS10

rs7647305

ETV5

DGKG

0

20

40

60

80

0

1

2

3

4

5

6

187.1 187.2 187.3 187.4 187.5 187.6

19





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs2844479

HLA-B BAT1 LTB BAT3 LY6G5B LY6G6C C6orf26 HSPA1A

MICA ATP6V1G2 LST1 APOM LY6G5C C6orf25 C6orf27

HCP5 NFKBIL1 NCR3 C6orf47 BAT5 DDAH2 VARS

MICB LTA AIF1 BAT4 C6orf21 CLIC1 LSM2

MCCD1 TNF BAT2 CSNK2BLY6G6D MSH5 HSPA1L

rs2260000

rs1077393

rs1052486

0

5

10

15

20

0

1

2

3

4

5

6

7

8

9

31.4 31.5 31.6 31.7 31.8 31.9 32

EHMT2

HSPA1B ZBTB12

C6orf48

NEU1

SLC44A4

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs2844479

HLA-B BAT1 LTB BAT3 LY6G5B LY6G6C C6orf26 HSPA1A

MICA ATP6V1G2 LST1 APOM LY6G5C C6orf25 C6orf27

HCP5 NFKBIL1 NCR3 C6orf47 BAT5 DDAH2 VARS

MICB LTA AIF1 BAT4 C6orf21 CLIC1 LSM2

MCCD1 TNF BAT2 CSNK2BLY6G6D MSH5 HSPA1L

rs2260000

rs1077393

rs1052486

0

5

10

15

20

0

1

2

3

4

5

6

7

8

9

31.4 31.5 31.6 31.7 31.8 31.9 32

EHMT2

HSPA1B ZBTB12

C6orf48

NEU1

SLC44A4

20





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs925946

CCDC34 LIN7C

LGR4 BDNF

0

20

40

60

80

100

0

1

2

3

4

5

6

7

27.25 27.35 27.45 27.55 27.65 27.75 27.85

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs925946

CCDC34 LIN7C

LGR4 BDNF

0

20

40

60

80

100

0

1

2

3

4

5

6

7

27.25 27.35 27.45 27.55 27.65 27.75 27.85

21





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs7138803

PRPF40B KIAA1602

FMNL3

FAIM2 AQP6<

SMARCD1

LOC283331 AQP2<

AQP5<

RACGAP1 GPD1<

ACCN2TMBIM6 BCDIN3D

rs836964

0

20

40

60

0

1

2

3

4

5

6

7

48.3 48.4 48.5 48.6 48.7 48.8

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs7138803

PRPF40B KIAA1602

FMNL3

FAIM2 AQP6<

SMARCD1

LOC283331 AQP2<

AQP5<

RACGAP1 GPD1<

ACCN2TMBIM6 BCDIN3D

rs836964

0

20

40

60

0

1

2

3

4

5

6

7

48.3 48.4 48.5 48.6 48.7 48.8

22

The 16p11 locus. (a) The pair-wise correlation structure in a 1 Mb interval (28.0 – 29.0 Mb, NCBI B36) on chromosome 16. The upper plot shows pair-wise D’ for 232 common SNPs (with MAF > 5%) from the HapMap (v22) CEU dataset. The lower plot shows the corresponding r

2 values. (b) Estimated recombination rates

(saRR) in cM / Mb from the HapMap Phase II data136


A)

B)

C)

r 2

D’

saRR

rs7498665

IL27 LOC440350

SH2B1

CD19

LAT

APOB48R

LOC390688

ATXN2L

ATP2A1

NFATC2IP

CLN3

EIF3S8

TUFM

RABEP2

SPINL

rs8049439rs4788102

0

20

40

60

D)

-log P

Position (Mb)

0

1

2

3

4

5

6

28 28.1 28.2 28.3 28.4 28.5 28.6 28.7 28.8 28.9 29

LOC440350NUPR1LOC440350SBK1

XPO6

LOC440350 CCFC101 LOC390688

EIF3S8

SULT1A1

SULT1A2

A)

B)

C)

r 2

D’

saRR

rs7498665

IL27 LOC440350

SH2B1

CD19

LAT

APOB48R

LOC390688

ATXN2L

ATP2A1

NFATC2IP

CLN3

EIF3S8

TUFM

RABEP2

SPINL

rs8049439rs4788102

0

20

40

60

D)

-log P

Position (Mb)

0

1

2

3

4

5

6

28 28.1 28.2 28.3 28.4 28.5 28.6 28.7 28.8 28.9 29

LOC440350NUPR1LOC440350SBK1

XPO6

LOC440350 CCFC101 LOC390688

EIF3S8

SULT1A1

SULT1A2

23





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs3751812

RPGRIP1L FTO

12

16

20

24

rs8050136

rs6499640

rs7190492

rs8044769

0

20

40

60

80

100

0

4

8

12

16

20

24

52.1 52.2 52.3 52.4 52.5 52.6

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs3751812

RPGRIP1L FTO

12

16

20

24

rs8050136

rs6499640

rs7190492

rs8044769

0

20

40

60

80

100

0

4

8

12

16

20

24

52.1 52.2 52.3 52.4 52.5 52.6

24





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs12970134

MC4R

rs633265

rs1350341

020406080100120

0

1

2

3

4

5

6

55.75 55.85 55.95 56.05 56.15 56.25

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs12970134

MC4R

rs633265

rs1350341

020406080100120

0

1

2

3

4

5

6

55.75 55.85 55.95 56.05 56.15 56.25

25





A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs29941

KCDT15CHST8

0

20

40

60

0

1

2

3

4

5

6

38.8 38.9 39 39.1 39.2

A)

B)

C)

r 2

D’

D)

-log P

Position (Mb)

saRR

rs29941

KCDT15CHST8

0

20

40

60

0

1

2

3

4

5

6

38.8 38.9 39 39.1 39.2

26

Supplementary Tables

Supplementary Table 1: Summary of the sample sets used in the BMI and weight analysis. Summary of the number of individuals, the mean age, BMI and weight, for the sample sets used in the analysis. For information on the DGI sample set see ref.

137, and for information on the GIANT sample

set see ref.7. Note that for the Icelandic sample set information on height is missing for 186 individuals

from the whole set, and for 82 of the genotyped individuals, hence those were excluded from the BMI analysis. Likewise, information on height was missing for 25 individuals from the Dutch sample set.

Sample set Group N

(Males/Females) Mean Age (SD)

(years) Mean BMI (SD)

(kg/m2)

Mean Weight (SD) (kg)

Discovery sample sets

Iceland All 74,921 (25,370/49,551) 51.47 (17.43) 26.65 (5.05) 77.61 (17.00)

Genotyped 25,344 (8,454/16,890) 57.16 (18.02) 27.06 (5.20) 78.06 (17.22)

Dutch 2,998 (1857/1,141) 58.43 (10.28) 25.81 (4,16) 77.24 (13.40)

John Hopkins CAUC 1,890 (948/942) 47.13 (12.52) 28.63 (5.97) 83.87 (19.95)

AFAM 1,160 (444/716) 45.28 (11.75) 31.71 (7.65) 90.75 (22.43)

Follow-up sample sets

Denmark Inter99 5,586 (2,740/2,846) 47.17 (8.73) 26.26 (4.58) 77.93 (19.96)

Addition 5,450 (3,025/2,425) 60.10 (6.71) 28.25 (4.79) 82.70 (16.06)

27

Supplementary Table 2: Top signals from the combined GWA study on BMI and weight. All SNPs with a P < 10

-5 in the combined GWA analysis of either BMI or weight for the five groups that

were part of the discovery set: Iceland (ICE, n = 25,344 genotyped + 39,342 imputed), The Netherlands (DUT, n = 2,998), John Hopkins Americans of European descent (JHC, n = 1,890) and African-Americans (JHA, n = 1,160) and Diabetes Genetics Initiative (DGI, n = 3,025) when available. Included is the location of each of the SNPs in NCBI Build 36 coordinates, the variation and allele tested, the mean frequency in the four discovery sample sets, and the effect (in percentage of the standard deviation) and the standard error (se), and the combined P values for both BMI and weight.

Frequency BMI Weight

Locus SNP Position Var.

Allele tested ICE/DUT/JHC/JHA Effect (se) % P Effect (se) % P

1p32 rs3766431 54502624 C/T T 0.446/0.427/0.415/0.423 3.87 (0.90) 1.6×10-5 4.23 (0.96) 9.5×10

-6

1p31 rs1776012 72490331 A/G A 0.455/0.469/0.525/0.311 3.69 (0.83) 8.9×10-6 3.70 (0.91) 4.5×10

-5

" rs9424977 72497932 C/T T 0.458/0.468/0.526/0.454 3.71 (0.81) 4.6×10-6 3.76 (0.88) 1.7×10

-5

" rs3101336 72523773 A/G G 0.582/0.592/0.634/0.528 4.56 (0.86) 1.1×10-7 4.00 (0.90) 8.7×10

-6

" rs2568958 72537704 A/G A 0.581/0.587/0.634/0.528 4.66 (0.87) 9.9×10-8 4.14 (0.92) 6.9×10

-6

1p21 rs1973993 96716582 C/T C 0.625/0.598/0.593/0.254 3.67 (0.84) 1.3×10-5 3.57 (0.80) 7.9×10

-6

" rs10783050 96809671 C/T C 0.358/0.357/0.356/0.083 4.21 (0.90) 2.8×10-6 3.84 (0.91) 2.5×10

-5

1q25 rs10913469 176180142 C/T C 0.200/0.199/0.203/0.255 4.29 (0.93) 4.2×10-6 4.87 (0.96) 4.3×10

-7

2p25 rs2867125 612827 A/G G 0.836/0.834/0.814/0.891 6.83 (1.06) 1.1×10-10

6.87 (1.10) 3.6×10-10

" rs4854344 628144 G/T T 0.839/0.825/0.815/0.777 6.33 (1.00) 2.9×10-10

6.46 (1.05) 8.6×10-10

" rs7561317 634953 A/G G 0.837/0.832/0.814/0.760 6.42 (1.01) 2.4×10-10

6.59 (1.07) 6.2×10-10

3q27 rs7647305 187316984 C/T C 0.772/0.803/0.769/0.622 4.66 (1.00) 3.1×10-6 4.34 (1.01) 1.7×10

-5

5q21 rs467650 97997353 C/T T 0.700/0.670/0.666/0.354 4.14 (0.90) 4.2×10-6 4.00 (0.95) 2.3×10

-5

5q32 rs1047440 122709733 A/G G 0.570/0.560/0.563/0.667 2.51 (0.75) 0.00084 4.03 (0.79) 3.7×10-7

" rs2115172 122713027 A/G A 0.565/0.556/0.562/0.653 2.45 (0.74) 0.00097 4.09 (0.80) 3.2×10-7

6p21 rs2844479 31680935 G/T T 0.676/0.660/0.630/0.686 3.64 (0.91) 6.1×10-5 5.88 (0.97) 1.2×10

-9

" rs2260000 31701455 C/T T 0.672/0.632/0.614/0.912 2.75 (0.78) 0.00046 4.37 (0.90) 1.4×10-6

" rs1077393 31718508 C/T T 0.563/0.518/0.491/0.657 2.94 (0.84) 0.00047 4.80 (0.95) 5.0×10-7

8p23 rs17069257 4030923 C/T C 0.133/0.170/0.164/0.212 3.91 (0.95) 3.6×10-5 4.89 (1.01) 1.3×10

-6

9q31 rs6477693 110958186 A/C C 0.308/0.273/0.260/0.281 3.13 (0.82) 0.00015 3.99 (0.85) 2.3×10-6

9q33 rs867559 128505146 A/G G 0.217/0.182/0.195/0.326 5.07 (1.13) 7.0×10-6 4.82 (1.14) 2.5×10

-5

11p14 rs7481311 27539705 C/T T 0.237/0.233/0.233/0.305 5.01 (1.10) 4.9×10-6 5.16 (1.14) 5.8×10

-6

" rs4074134 27603861 A/G G 0.844/0.789/0.804/0.825 5.77 (1.21) 1.8×10-6 4.86 (1.20) 5.4×10

-5

" rs4923461 27613486 A/G A 0.845/0.788/0.804/0.822 5.89 (1.21) 1.1×10-6 4.98 (1.21) 3.8×10

-5

" rs925946 27623778 G/T T 0.335/0.295/0.305/0.254 4.90 (0.94) 2.0×10-7 4.84 (1.01) 1.5×10

-6

" rs10501087 27626684 C/T T 0.844/0.789/0.806/0.914 5.68 (1.23) 4.2×10-6 4.79 (1.25) 0.00012

" rs6265 27636492 A/G G 0.853/0.802/0.825/0.941 5.67 (1.26) 7.2×10-6 5.05 (1.24) 4.9×10

-5

" rs10835211 27657941 A/G A 0.264/0.251/0.253/0.114 4.11 (0.95) 1.5×10-5 4.53 (1.00) 6.3×10

-6

12q13 rs7138803 48533735 A/G A 0.373/0.376/0.375/0.184 4.89 (1.00) 9.6×10-7 4.19 (0.93) 7.3×10

-6

" rs836964 48556162 C/T T 0.893/0.910/0.882/0.756 6.24 (1.32) 2.2×10-6 6.48 (1.37) 2.3×10

-6

13q12 rs7336332 26956404 A/G G 0.154/0.160/0.156/0.269 5.02 (1.11) 6.3×10-6 5.73 (1.23) 3.5×10

-6

16p11 rs8049439 28745016 C/T C 0.437/0.400/0.388/0.425 3.92 (0.87) 6.0×10-6 3.90 (0.92) 2.1×10

-5

" rs4788102 28780899 A/G A 0.436/0.390/0.386/0.261 4.03 (0.87) 3.5×10-6 4.09 (0.92) 8.2×10

-6

" rs7498665 28790742 A/G G 0.438/0.390/0.390/0.263 4.25 (0.89) 1.7×10-6 4.35 (0.93) 3.2×10

-6

16q12 rs6499640 52327178 A/G A 0.647/0.613/0.599/0.635 5.55 (1.02) 6.0×10-8 4.76 (1.05) 5.3×10

-6

" rs8050136 52373776 A/C A 0.408/0.387/0.413/0.427 8.28 (0.82) 4.4×10-24

7.15 (0.81) 1.6×10-18

" rs3751812 52375961 G/T T 0.407/0.387/0.410/0.106 8.92 (0.88) 3.3×10-24

8.06 (0.88) 6.9×10-20

" rs7190492 52386253 A/G G 0.621/0.587/0.655/0.779 6.85 (0.97) 2.0×10-12

5.74 (0.96) 2.1×10-9

" rs8044769 52396636 C/T C 0.518/0.506/0.544/0.759 6.85 (0.85) 7.9×10-16

6.00 (0.83) 5.7×10-13

18q21 rs633265 55982448 A/C A 0.464/0.463/0.425/0.771 3.14 (0.80) 8.9×10-5 3.47 (0.78) 9.1×10

-6

" rs1350341 55993513 C/T T 0.461/0.462/0.424/0.769 3.14 (0.79) 6.4×10-5 3.51 (0.77) 5.7×10

-6

" rs12970134 56035730 A/G A 0.299/0.282/0.257/0.159 4.23 (0.90) 2.6×10-6 4.45 (0.94) 2.3×10

-6

19q13 rs29941 39001372 C/T C 0.691/0.682/0.684/0.791 4.25 (0.94) 5.6×10-6 4.13 (0.98) 2.3×10

-5

28

Supplementary Table 3: Association with BMI for the individual study groups in the discovery set for the select 43 SNPs. Shown is the association with BMI for the 43 SNPs with a combined P < 10

-5 in the GWA study of

either BMI or weight. Shown is the location of the SNPs, the P values and effect (in percentage of the standard deviation) for the five groups, Iceland (ICE), The Netherlands (DUT), John Hopkins Americans of European descent (JHC) and African-Americans (JHA) and Diabetes Genetics Initiative (DGI), used in the GW analysis, and P values for the four groups of European descent combined and for all five groups combined, respectively. All P values have been adjusted using the method of genomic control.

ICE DUT JHC JHA DGI CAUC All

Locus SNP Eff (%) P Eff (%) P Eff (%) P Eff (%) P Eff (%) P P P

1p32 rs3766431 3.5 0.0014 4.2 0.13 7.8 0.046 5.7 0.23 4.1 0.13 3.0×10-5 1.6×10

-5

1p31 rs1776012 3.1 0.0010 10.0 0.00020 -2.1 0.58 10.3 0.042 3.6×10-5 8.9×10

-6

" rs9424977 3.0 0.0010 9.6 0.00033 -2.2 0.57 14.3 0.0022 4.5×10-5 4.6×10

-6

" rs3101336 4.3 8.5×10-6 8.7 0.0013 -4.5 0.26 13.2 0.0059 1.1×10

-6 1.1×10

-7

" rs2568958 4.5 7.3×10-6 8.6 0.0015 -4.5 0.25 13.2 0.0059 9.7×10

-7 9.9×10

-8

1p21 rs1973993 4.1 3.5×10-5 5.2 0.058 -1.1 0.79 4.0 0.46 1.2 0.6 1.7×10

-5 1.3×10

-5

" rs10783050 4.5 6.8×10-6 4.4 0.12 4.0 0.33 11.9 0.17 -1.2 0.73 6.3×10

-6 2.8×10

-6

1q25 rs10913469 4.9 2.9×10-6 1.4 0.68 3.8 0.43 7.8 0.14 0.9 0.86 1.0×10

-5 4.2×10

-6

2p25 rs2867125 6.5 1.4×10-7 10.0 0.0049 4.3 0.38 9.9 0.19 7.2 0.036 2.7×10

-10 1.1×10

-10

" rs4854344 6.0 2.7×10-7 9.5 0.0069 4.8 0.33 6.7 0.24 7.2 0.036 5.7×10

-10 2.9×10

-10

" rs7561317 6.2 1.6×10-7 9.6 0.0063 4.5 0.35 4.8 0.39 7.2 0.036 3.4×10

-10 2.4×10

-10

3q27 rs7647305 4.6 6.3×10-5 3.4 0.31 9.6 0.033 0.8 0.88 4.6 0.15 2.5×10

-6 3.1×10

-6

5q21 rs467650 3.8 0.00025 2.6 0.36 4.7 0.24 12.2 0.013 5.1 0.11 2.4×10-5 4.2×10

-6

5q32 rs1047440 2.0 0.025 5.6 0.037 -2.3 0.56 2.3 0.65 6.8 0.0077 0.00092 0.00084

" rs2115172 1.9 0.030 5.7 0.033 -1.9 0.63 2.0 0.70 6.8 0.0077 0.0010 0.00097

6p21 rs2844479 4.1 9.5×10-5 1.9 0.50 2.8 0.49 7.6 0.13 0.8 0.88 0.00015 6.1×10

-5

" rs2260000 3.2 0.00032 3.7 0.19 0.3 0.94 -0.4 0.96 0.5 0.97 0.00036 0.00046

" rs1077393 3.8 5.6×10-5 2.1 0.44 0.5 0.90 -10.5 0.035 7.4×10

-5 0.00047

8p23 rs17069257 3.5 0.00077 3.9 0.28 2.3 0.67 7.7 0.18 7.2 0.056 7.8×10-5 3.6×10

-5

9q31 rs6477693 2.9 0.0021 5.9 0.049 6.1 0.16 0.8 0.88 2.0 0.48 0.00013 0.00015

9q33 rs867559 4.3 0.0011 10.1 0.0038 8.3 0.086 5.5 0.27 1.3×10-5 7.0×10

-6

11p14 rs7481311 5.6 2.2×10-5 7.7 0.017 1.0 0.83 -4.6 0.37 3.6 0.32 1.5×10

-6 4.9×10

-6

" rs4074134 5.8 8.1×10-5 7.3 0.028 0.4 0.94 16.6 0.0069 2.8 0.47 1.3×10

-5 1.8×10

-6

" rs4923461 6.0 5.6×10-5 7.3 0.029 0.5 0.91 16.8 0.0058 2.8 0.47 8.9×10

-6 1.1×10

-6

" rs925946 5.1 3.0×10-6 4.7 0.12 4.9 0.23 5.5 0.32 2.8 0.36 3.4×10

-7 2.0×10

-7

" rs10501087 5.8 8.1×10-5 7.3 0.029 -0.4 0.94 16.4 0.045 2.6 0.49 1.6×10

-5 4.2×10

-6

" rs6265 6.2 4.0×10-5 7.5 0.030 -3.1 0.55 8.0 0.40 3.5 0.36 1.0×10

-5 7.2×10

-6

" rs10835211 4.4 0.00011 6.0 0.056 4.4 0.33 -9.0 0.22 4.7 0.16 3.7×10-6 1.5×10

-5

12q13 rs7138803 5.4 7.2×10-6 5.4 0.051 5.2 0.20 0.1 0.99 1.8 0.57 6.4×10

-7 9.6×10

-7

" rs836964 6.4 2.6×10-5 10.9 0.022 6.0 0.32 -0.7 0.91 3.1 0.47 1.4×10

-6 2.2×10

-6

13q12 rs7336332 5.0 0.00014 0.0 1.00 7.4 0.16 4.0 0.46 9.3 0.0062 8.3×10-6 6.3×10

-6

16p11 rs8049439 3.9 6.7×10-5 -2.9 0.29 3.8 0.34 12.2 0.010 7.3 0.0089 3.6×10

-5 6.0×10

-6

" rs4788102 4.0 4.0×10-5 -2.4 0.39 3.9 0.33 12.2 0.024 7.3 0.0089 1.7×10

-5 3.5×10

-6

" rs7498665 4.2 2.5×10-5 -2.3 0.42 4.4 0.27 12.6 0.020 7.3 0.0089 8.9×10

-6 1.7×10

-6

16q12 rs6499640 5.5 2.7×10-6 4.4 0.11 10.6 0.0071 1.7 0.73 5.0×10

-8 6.0×10

-8

" rs8050136 9.2 2.0×10-22

6.7 0.015 9.9 0.011 -1.1 0.82 5.0 0.078 5.2×10-25

4.4×10-24

" rs3751812 9.5 1.1×10-22

6.5 0.018 10.2 0.0086 -0.3 0.97 4.6×10-25

3.3×10-24

" rs7190492 7.6 4.1×10-12

4.7 0.087 7.0 0.083 -4.1 0.48 2.9×10-13

2.0×10-12

" rs8044769 7.1 5.6×10-14

5.9 0.028 12.4 0.0012 -4.4 0.43 6.7×10-17

7.9×10-16

18q21 rs633265 3.5 9.2×10-5 0.1 0.97 7.3 0.061 1.7 0.77 0.9 0.71 8.5×10

-5 8.9×10

-5

" rs1350341 3.5 9.0×10-5 0.0 0.99 7.1 0.068 2.1 0.71 1.6 0.53 6.5×10

-5 6.4×10

-5

" rs12970134 4.3 1.3×10-5 0.3 0.93 9.4 0.032 13.5 0.033 0.9 0.74 1.2×10

-5 2.6×10

-6

19q13 rs29941 4.3 0.00022 9.2 0.0014 -4.8 0.24 7.8 0.19 3.6 0.2 1.2×10-5 5.6×10

-6

29

Supplementary Table 4: Association with weight for the individual study groups in the discovery set for the select 43 SNPs. Shown is the association with weight for the 43 SNPs with a combined P < 10

-5 in the GWA study of

either BMI or weight. Shown is the location of the SNPs, the P values and effect (in percentage of the standard deviation) for the five groups, Iceland (ICE), The Netherlands (DUT), John Hopkins Americans of European descent (JHC) and African-Americans (JHA) and Diabetes Genetics Initiative (DGI), used in the GW analysis, and P values for the four groups of European descent combined and for all five groups combined, respectively. All P values have been adjusted using the method of genomic control.

ICE DUT JHC JHA DGI CAUC All

Locus SNP Eff (%) P Eff (%) P Eff (%) P Eff (%) P Eff (%) P P P

1p32 rs3766431 3.7 0.0026 5.5 0.045 5.3 0.18 8.4 0.076 5.5 0.044 2.9×10-5 9.5×10

-6

1p31 rs1776012 4.0 9.9×10-5 5.7 0.034 -4.7 0.23 4.2 0.40 6.5×10

-5 4.5×10

-5

" rs9424977 3.9 9.0×10-5 5.5 0.038 -4.9 0.21 9.4 0.045 6.5×10

-5 1.7×10

-5

" rs3101336 4.6 7.5×10-6 4.2 0.12 -7.6 0.061 8.6 0.075 2.8×10

-5 8.7×10

-6

" rs2568958 4.8 5.5×10-6 4.2 0.12 -7.7 0.058 8.6 0.075 2.2×10

-5 6.9×10

-6

1p21 rs1973993 3.8 4.3×10-5 4.6 0.093 -1.2 0.77 6.8 0.21 2.0 0.36 1.6×10

-5 7.9×10

-6

" rs10783050 4.0 8.4×10-5 3.8 0.18 2.4 0.56 10.3 0.24 0.5 0.78 4.8×10

-5 2.5×10

-5

1q25 rs10913469 5.1 3.1×10-6 4.5 0.18 3.5 0.48 11.0 0.039 1.9 0.69 1.9×10

-6 4.3×10

-7

2p25 rs2867125 6.2 1.9×10-6 12.9 0.00025 5.2 0.30 9.1 0.23 7.0 0.051 7.6×10

-10 3.6×10

-10

" rs4854344 5.7 4.5×10-6 12.2 0.00051 5.3 0.29 9.2 0.11 7.0 0.051 2.8×10

-9 8.6×10

-10

" rs7561317 5.9 2.7×10-6 12.2 0.00049 5.2 0.29 7.8 0.16 7.0 0.051 1.6×10

-9 6.2×10

-10

3q27 rs7647305 4.2 0.00041 5.4 0.11 12.6 0.0064 -2.0 0.69 2.5 0.41 9.1×10-6 1.7×10

-5

5q21 rs467650 4.2 0.00019 3.0 0.31 3.7 0.36 7.6 0.12 2.5 0.43 6.0×10-5 2.3×10

-5

5q32 rs1047440 3.2 0.00076 8.1 0.0024 -0.8 0.85 3.0 0.56 10.0 0.00010 4.2×10-7 3.7×10

-7

" rs2115172 3.3 0.00068 8.0 0.0027 -0.1 0.97 2.4 0.63 10.0 0.00010 3.3×10-7 3.2×10

-7

6p21 rs2844479 6.2 5.5×10-8 5.3 0.061 4.5 0.26 10.5 0.036 2.5 0.45 6.7×10

-9 1.2×10

-9

" rs2260000 4.8 5.1×10-6 3.7 0.18 4.1 0.30 1.0 0.90 3.0 0.39 1.1×10

-6 1.4×10

-6

" rs1077393 5.7 8.1×10-8 1.0 0.70 6.4 0.099 -7.3 0.15 6.8×10

-8 5.0×10

-7

8p23 rs17069257 4.5 8.0×10-5 6.7 0.057 5.9 0.28 9.2 0.10 4.5 0.27 3.9×10

-6 1.3×10

-6

9q31 rs6477693 3.8 7.0×10-5 5.0 0.091 4.6 0.30 2.8 0.59 5.0 0.12 2.6×10

-6 2.3×10

-6

9q33 rs867559 3.6 0.0090 13.5 8.7×10-5 6.4 0.20 7.1 0.15 5.8×10

-5 2.5×10

-5

11p14 rs7481311 6.3 2.9×10-6 5.7 0.076 0.1 0.99 -4.4 0.40 1.5 0.68 1.9×10

-6 5.8×10

-6

" rs4074134 5.0 0.00069 5.5 0.10 -0.7 0.89 19.2 0.0017 1.0 0.77 0.00041 5.4×10-5

" rs4923461 5.1 0.00056 5.5 0.10 -0.4 0.94 19.6 0.0013 1.0 0.77 0.00032 3.8×10-5

" rs925946 5.6 1.5×10-6 2.0 0.50 4.1 0.33 9.3 0.095 0.0 0.95 4.6×10

-6 1.5×10

-6

" rs10501087 4.9 0.00073 5.5 0.096 -1.0 0.85 19.0 0.020 1.0 0.86 0.00049 0.00012

" rs6265 5.5 0.00024 7.2 0.034 -3.9 0.45 10.3 0.28 2.5 0.48 8.4×10-5 4.9×10

-5

" rs10835211 5.1 1.9×10-5 4.4 0.16 4.9 0.28 -4.0 0.58 3.0 0.36 2.7×10

-6 6.3×10

-6

12q13 rs7138803 4.5 5.7×10-5 5.3 0.054 5.1 0.22 -1.5 0.81 2.0 0.48 4.2×10

-6 7.3×10

-6

" rs836964 7.1 9.6×10-6 10.4 0.028 6.4 0.30 -0.4 0.94 0.5 0.92 1.5×10

-6 2.3×10

-6

13q12 rs7336332 6.0 5.8×10-5 1.7 0.64 6.5 0.23 6.7 0.22 6.5 0.055 7.1×10

-6 3.5×10

-6

16p11 rs8049439 4.0 0.00019 -2.3 0.40 5.7 0.17 9.4 0.048 6.0 0.024 7.5×10-5 2.1×10

-5

" rs4788102 4.0 0.00014 -1.5 0.58 5.9 0.15 11.8 0.029 6.0 0.024 3.5×10-5 8.2×10

-6

" rs7498665 4.3 6.1×10-5 -1.5 0.59 6.4 0.12 12.0 0.027 6.0 0.024 1.5×10

-5 3.2×10

-6

16q12 rs6499640 4.6 0.00011 3.2 0.25 10.1 0.012 3.5 0.48 6.8×10-6 5.3×10

-6

" rs8050136 8.3 4.6×10-19

4.1 0.14 8.8 0.028 -2.4 0.62 3.0 0.30 1.9×10-19

1.6×10-18

" rs3751812 8.7 2.6×10-19

3.9 0.15 9.1 0.023 3.9 0.61 3.7×10-20

6.9×10-20

" rs7190492 6.6 8.6×10-10

2.4 0.37 6.0 0.15 -4.1 0.48 4.7×10-10

2.1×10-9

" rs8044769 6.5 1.5×10-12

3.4 0.20 10.4 0.0081 -4.4 0.42 6.8×10-14

5.7×10-13

18q21 rs633265 3.7 3.1×10-5

1.5 0.58 8.9 0.026 2.2 0.70 1.0 0.60 9.0×10-6 9.1×10

-6

" rs1350341 3.6 2.9×10-5 1.3 0.63 8.8 0.027 2.8 0.62 2.0 0.39 6.1×10

-6 5.7×10

-6

" rs12970134 4.6 7.4×10-6 -1.4 0.65 11.3 0.012 12.9 0.041 1.5 0.63 9.5×10

-6 2.3×10

-6

19q13 rs29941 4.1 0.00058 5.9 0.038 -7.3 0.083 12.5 0.034 6.0 0.037 8.9×10-5 2.3×10

-5

30

Supplementary Table 5: Follow-up of top 43 signals in Danish samples. Follow-up of the top 43 variants selected from the GWA study on BMI and weight in 5,586 Danish individuals from the Inter99 study. For three variants data on an additional 5,450 Danish individuals from the ADDITION study were included in the analysis. Effects and P values in the Danish group are shown for the top signals together with effects, standard errors and P values for the Danish results combined with the results for the genome-wide study. All effects are shown in percentage of the standard deviation. Also included is the frequency of the tested allele in the Danish sample set.

BMI Weight

Denmark Combined Denmark Combined

Locus SNP Frq Effect P Effect (se) P Effect P Effect (se) P

1p32 rs3766431 0.468 -0.22 0.92 3.24 (0.87) 2.1×10-4 0.24 0.91 3.55 (0.95) 1.9×10

-4

1p31 rs1776012 0.477 1.58 0.4 3.44 (0.78) 1.2×10-5 1.65 0.38 3.40 (0.84) 4.7×10

-5

" rs9424977 0.476 1.49 0.43 3.42 (0.76) 7.3×10-6 1.55 0.41 3.43 (0.81) 2.2×10

-5

" rs3101336 0.590 0.18 0.93 3.86 (0.80) 1.2×10-6 -0.06 0.98 3.32 (0.83) 5.9×10

-5

" rs2568958 0.589 0.62 0.74 4.02 (0.81) 6.8×10-7 0.57 0.77 3.55 (0.85) 2.7×10

-5

1p21 rs1973993 0.582 1.18 0.53 3.49 (0.81) 1.8×10-5 1.83 0.33 3.44 (0.78) 1.0×10

-5

" rs10783050 0.332 4.41 0.028 4.67 (0.85) 4.0×10-8 5.16 0.011 4.32 (0.87) 6.1×10

-7

1q25 rs10913469 0.214 5.66 0.013 4.73 (0.88) 7.8×10-8 5.78 0.012 5.25 (0.91) 9.0×10

-9

2p25 rs2867125 0.827 8.86 0.0004 7.19 (1.03) 2.4×10-12

7.93 0.0017 7.15 (1.06) 1.9×10-11

" rs4854344 0.831 9.15 0.00027 6.78 (0.98) 4.5×10-12

7.91 0.0018 6.76 (1.03) 4.7×10-11

" rs7561317 0.831 9.41 0.00018 6.92 (0.99) 2.9×10-12

8.18 0.0013 6.93 (1.04) 2.6×10-11

3q27 rs7647305* 0.809 5.55 0.0012 4.89 (0.89) 4.3×10-8 5.21 0.0024 4.70 (0.90) 1.9×10

-7

5q21 rs467650* 0.687 1.46 0.32 3.29 (0.78) 2.7×10-5 1.44 0.32 3.36 (0.83) 4.7×10

-5

5q32 rs1047440 0.556 -0.42 0.83 1.75 (0.75) 0.02 -0.15 0.94 2.95 (0.79) 2.0×10-4

" rs2115172 0.560 1.00 0.6 1.94 (0.74) 0.0093 0.73 0.7 3.15 (0.80) 8.4×10-5

6p21 rs2844479 0.662 -0.35 0.87 3.27 (0.86) 0.00015 1.95 0.37 5.58 (0.93) 1.8×10-9

" rs2260000 0.630 1.33 0.49 2.72 (0.75) 0.00029 3.62 0.062 4.35 (0.85) 2.9×10-7

" rs1077393 0.520 1.58 0.41 2.70 (0.77) 0.00043 2.66 0.17 4.36 (0.85) 2.7×10-7

8p23 rs17069257 0.173 -3.81 0.13 2.36 (0.85) 0.0054 -3.92 0.12 3.48 (0.95) 0.00023

9q31 rs6477693* 0.272 0.64 0.67 2.55 (0.75) 0.00064 -0.57 0.71 2.66 (0.74) 3.3×10-4

9q33 rs867559 0.197 1.89 0.43 4.60 (1.04) 1.0×10-5 1.48 0.54 4.39 (1.07) 4.4×10

-5

11p14 rs7481311 0.238 0.45 0.84 4.42 (1.06) 3.0×10-5 0.71 0.75 4.75 (1.09) 1.4×10

-5

" rs4074134 0.783 6.78 0.0028 6.20 (1.11) 2.3×10-8 7.06 0.0021 5.56 (1.10) 4.7×10

-7

" rs4923461 0.783 7.00 0.0021 6.36 (1.11) 1.2×10-8 6.49 0.0048 5.56 (1.11) 5.5×10

-7

" rs925946 0.311 5.92 0.0036 5.23 (0.89) 3.6×10-9 5.43 0.0081 5.27 (0.92) 1.2×10

-8

" rs10501087 0.782 7.09 0.0019 6.19 (1.13) 4.3×10-8 7.10 0.0021 5.51 (1.13) 1.0×10

-6

" rs6265 0.795 6.77 0.0035 6.08 (1.16) 1.7×10-7 6.02 0.01 5.50 (1.16) 2.2×10

-6

" rs10835211 0.266 1.86 0.38 3.74 (0.91) 4.2×10-5 2.93 0.17 4.40 (0.95) 3.9×10

-6

12q13 rs7138803 0.403 6.79 0.00033 5.46 (0.91) 2.1×10-9 7.89 3.7×10

-5 5.00 (0.87) 7.7×10

-9

" rs836964 0.900 5.08 0.1 6.38 (1.28) 5.9×10-7 6.77 0.031 7.09 (1.32) 7.7×10

-8

13q12 rs7336332 0.169 0.51 0.84 3.83 (1.06) 3.0×10-4 1.91 0.45 4.95 (1.18) 2.6×10

-5

16p11 rs8049439 0.414 1.72 0.37 3.16 (0.80) 8.2×10-5 1.09 0.57 3.13 (0.86) 2.6×10

-4

" rs4788102 0.409 1.42 0.45 3.21 (0.81) 6.6×10-5 1.11 0.56 3.32 (0.86) 1.2×10

-4

" rs7498665 0.407 1.47 0.44 3.42 (0.83) 3.4×10-5 1.19 0.54 3.57 (0.88) 4.9×10

-5

16q12 rs6499640 0.627 7.58 9.3×10-5 5.88 (0.90) 5.2×10

-11 8.82 6.6×10

-6 5.44 (0.90) 1.6×10

-9

" rs8050136 0.412 11.36 3.5×10-9 9.03 (0.78) 4.3×10

-31 10.01 2.7×10

-7 7.90 (0.77) 1.8×10

-24

" rs3751812 0.410 10.75 2.4×10-8 9.22 (0.80) 6.6×10

-31 9.55 9.1×10

-7 8.25 (0.80) 4.3×10

-25

" rs7190492 0.624 9.85 6.5×10-7 7.34 (0.87) 2.4×10

-17 7.68 1.2×10

-4 6.03 (0.86) 1.9×10

-12

" rs8044769 0.533 10.13 1.5×10-7 7.40 (0.78) 1.8×10

-21 8.76 7.1×10

-6 6.42 (0.76) 3.6×10

-17

18q21 rs633265 0.439 1.81 0.34 3.03 (0.75) 5.4×10-5 3.41 0.072 3.59 (0.74) 1.4×10

-6

" rs1350341 0.442 1.70 0.36 2.96 (0.74) 5.8×10-5 3.05 0.1 3.48 (0.73) 1.8×10

-6

" rs12970134 0.281 5.67 0.0066 4.64 (0.84) 3.5×10-8 7.11 0.00072 4.98 (0.87) 8.4×10

-9

19q13 rs29941 0.679 2.50 0.21 4.13 (0.92) 7.0×10-6 2.86 0.16 3.85 (0.95) 5.5×10

-5

* Data on 5,450 individuals from the Addition study included in the analysis of this variant. Restricted to individuals from the Inter99 study the P values for BMI (weight) are 0.25 (0.19), 0.35 (0.73) and 0.20 (0.17), for rs7647305, rs6477693 and rs467650, respectively.

31

Supplementary Table 6: Comparison of top signals with results from GIANT. Comparison of the 43 variants selected from the GWA study on BMI and weight with results from the

GIANT consortium (n ≈ 32,000). Shown are the GIANT results (effect and P values) for the 43 variants, the P value for the two follow-up groups combined, and combined analysis of the GWA association study, the Danish results and the GIANT results (effect, standard error and P values). Note that results from the DGI study are included in the combined GIANT results and have been excluded from the discovery samples before combining the results. All effects are shown in percentage of the standard deviation.

BMI Weight

GIANT Replic. Combined GIANT Replic. Combined

Locus SNP Eff % P P Eff (se) % P Eff % P P Eff (se) % P

1p32 rs3766431 1.11 0.21 0.23 2.12 (0.60) 0.00048 1.74 0.034 0.044 2.60 (0.63) 4.0×10-5

1p31 rs1776012 1.99 0.0038 0.0018 2.70 (0.52) 1.7×10-7 1.68 0.06 0.038 2.56 (0.61) 2.4×10

-5

" rs9424977 1.55 0.023 0.013 2.47 (0.51) 1.4×10-6 1.03 0.22 0.15 2.21 (0.57) 0.00012

" rs3101336 3.49 1.2×10-5 1.8×10

-5 3.67 (0.55) 2.5×10

-11 3.16 0.00024 0.00072 3.24 (0.60) 5.4×10

-8

" rs2568958 3.53 9.8×10-6 1.0×10

-5 3.77 (0.56) 1.2×10

-11 3.20 0.00020 0.00039 3.37 (0.60) 2.2×10

-8

1p21 rs1973993 1.20 0.057 0.037 2.31 (0.52) 1.1×10-5 2.03 0.014 0.0082 2.71 (0.56) 1.3×10

-6

" rs10783050 0.60 0.28 0.06 2.60 (0.56) 3.6×10-6 0.88 0.3 0.053 2.57 (0.61) 2.2×10

-5

1q25 rs10913469 2.02 0.026 0.002 3.36 (0.62) 6.2×10-8 2.43 0.019 0.0017 3.82 (0.67) 1.2×10

-8

2p25 rs2867125 5.04 8.1×10-6 1.5×10

-8 6.11 (0.74) 1.7×10

-16 5.69 1.9×10

-7 1.7×10

-9 6.43 (0.76) 3.1×10

-17

" rs4854344 5.31 2.8×10-6 3.2×10

-9 6.05 (0.72) 6.8×10

-17 6.00 9.3×10

-9 7.9×10

-11 6.38 (0.73) 2.9×10

-18

" rs7561317 5.31 2.6×10-6 2.3×10

-9 6.12 (0.73) 4.2×10

-17 6.01 8.7×10

-9 5.8×10

-11 6.47 (0.74) 1.6×10

-18

3q27 rs7647305 3.87 0.00043 1.5×10-6 4.42 (0.68) 7.2×10

-11 3.20 0.0024 3.3×10

-5 4.00 (0.68) 4.2×10

-9

5q21 rs467650 0.76 0.4 0.21 2.08 (0.57) 0.00029 0.69 0.42 0.23 2.08 (0.60) 0.00047

5q32 rs1047440 0.81 0.3 0.35 1.25 (0.52) 0.017 2.28 0.0052 0.011 2.59 (0.57) 4.8×10-6

" rs2115172 0.83 0.28 0.22 1.37 (0.52) 0.0091 2.31 0.0046 0.0057 2.71 (0.57) 1.9×10-6

6p21 rs2844479 0.34 0.63 0.67 1.73 (0.58) 0.003 1.75 0.046 0.029 3.58 (0.64) 2.1×10-8

" rs2260000 0.42 0.93 0.73 1.54 (0.59) 0.0099 1.84 0.029 0.0063 3.06 (0.60) 2.6×10-7

" rs1077393 1.07 0.51 0.34 1.87 (0.63) 0.0032 1.99 0.014 0.0052 3.15 (0.59) 8.7×10-8

8p23 rs17069257 1.00 0.14 0.4 1.62 (0.54) 0.0027 1.30 0.24 0.63 2.31 (0.69) 0.00074

9q31 rs6477693 0.97 0.29 0.24 1.78 (0.55) 0.0013 0.58 0.54 0.74 1.67 (0.55) 0.0025

9q33 rs867559 1.55 0.2 0.13 3.04 (0.75) 5.8×10-5 1.37 0.21 0.16 2.85 (0.76) 0.00017

11p14 rs7481311 1.99 0.035 0.034 3.15 (0.70) 7.8×10-6 2.29 0.024 0.028 3.50 (0.75) 3.2×10

-6

" rs4074134 3.85 0.00034 4.2×10-6 5.01 (0.76) 4.4×10

-11 2.56 0.012 0.00043 4.09 (0.76) 8.3×10

-8

" rs4923461 3.74 0.00041 4.4×10-6 5.03 (0.76) 3.2×10

-11 2.44 0.017 0.00095 4.02 (0.77) 1.5×10

-7

" rs925946 2.52 0.0071 0.00021 3.85 (0.63) 8.5×10-10

2.38 0.0078 0.00052 3.80 (0.64) 3.7×10-9

" rs10501087 3.64 0.0004 4.0×10-6 4.90 (0.75) 8.7×10

-11 2.63 0.0079 0.00028 4.06 (0.76) 9.7×10

-8

" rs6265 3.57 0.00064 9.9×10-6 4.58 (0.77) 5.1×10

-10 2.54 0.013 0.001 4.00 (0.78) 3.4×10

-7

" rs10835211 2.50 0.0077 0.0035 3.09 (0.64) 1.3×10-6 2.87 0.0024 0.00087 3.61 (0.67) 6.9×10

-8

12q13 rs7138803 1.15 0.14 0.0051 3.28 (0.62) 1.2×10-7 1.40 0.12 0.0022 3.27 (0.62) 1.6×10

-7

" rs836964 1.31 0.32 0.11 3.79 (0.90) 2.5×10-5 2.52 0.052 0.0087 4.76 (0.92) 2.6×10

-7

13q12 rs7336332 2.17 0.16 0.15 2.96 (0.83) 0.00039 3.15 0.006 0.0047 4.01 (0.82) 1.0×10-6

16p11 rs8049439 3.70 9.6×10-6 3.7×10

-6 3.42 (0.56) 1.4×10

-9 3.79 5.1×10

-6 9.5×10

-6 3.45 (0.60) 6.7×10

-9

" rs4788102 3.83 5.6×10-6 2.8×10

-6 3.51 (0.57) 6.4×10

-10 3.82 4.9×10

-6 8.9×10

-6 3.56 (0.60) 2.7×10

-9

" rs7498665 3.87 5.4×10-6 2.6×10

-6 3.63 (0.58) 3.2×10

-10 3.85 4.4×10

-6 7.6×10

-6 3.69 (0.60) 1.0×10

-9

16q12 rs6499640 4.64 0.00051 9.2×10-7 5.25 (0.73) 4.0×10

-13 5.60 7.5×10

-6 1.4×10

-9 5.50 (0.73) 6.1×10

-14

" rs8050136 7.04 1.4×10-17

7.6×10-26

8.04 (0.55) 1.1×10-47

6.19 5.0×10-14

4.2×10-19

7.05 (0.56) 4.5×10-36

" rs3751812 7.00 2.4×10-17

5.3×10-25

8.09 (0.56) 4.1×10-47

6.20 4.3×10-14

8.0×10-19

7.21 (0.57) 1.3×10-36

" rs7190492 4.66 1.6×10-7 3.6×10

-12 5.98 (0.61) 8.1×10

-23 4.60 1.2×10

-7 2.0×10

-10 5.30 (0.61) 3.0×10

-18

" rs8044769 5.46 5.6×10-11

8.1×10-17

6.41 (0.55) 7.6×10-31

5.12 5.5×10-10

9.8×10-14

5.76 (0.56) 5.3×10-25

18q21 rs633265 2.62 0.0012 0.00045 2.81 (0.54) 1.6×10-7 2.81 0.00056 0.00011 3.19 (0.55) 5.1×10

-9

" rs1350341 2.55 0.0016 0.00064 2.74 (0.53) 2.4×10-7 2.75 0.00081 0.0002 3.11 (0.54) 1.0×10

-8

" rs12970134 4.11 1.4×10-5 1.6×10

-7 4.38 (0.62) 1.2×10

-12 4.30 8.5×10

-6 5.8×10

-8 4.66 (0.64) 4.5×10

-13

19q13 rs29941 4.26 7.0×10-7 1.3×10

-7 4.18 (0.61) 7.3×10

-12 3.64 2.2×10

-5 8.3×10

-6 3.73 (0.64) 4.9×10

-9

32

Supplementary Table 7: Pair-wise correlation between SNPs. Pair-wise correlation for SNPs in eight out of the eleven BMI or weight associated loci where more than one variant was selected for follow-up. The tables include estimates of D’ (lower left corner) and r2 (upper right corner) based on genotypes for the 90 HapMap CEU samples

138.

(a) 1p31

-

rs1776012

rs9424977

rs3101336

rs2568958

rs1776012 - 0.9 0.53 0.54

rs9424977 0.97 - 0.56 0.58

rs3101336 0.95 1 - 1

rs2568958 0.95 1 1 -

D 'r2

(b) 2p25

-

rs2867125

rs4854344

rs7561317

rs2867125 - 1 1

rs4854344 1 - 1

rs7561317 1 1 -

D 'r2

(c) 6p21

-

rs2844479

rs2260000

rs1077393

rs2844479 - 0.58 0.39

rs2260000 0.83 - 0.73

rs1077393 0.8 1 -

D 'r2

(d) 11p14

rs7481311

rs4074134

rs4923461

rs925946

rs10501087

rs6265

rs10835211

rs7481311 - 0.08 0.08 0.56 0.08 0.07 0.66

rs4074134 1 - 1 0.14 1 0.85 0.11

rs4923461 1 1 - 0.14 1 0.85 0.11

rs925946 1 1 1 - 0.14 0.12 0.7

rs10501087 1 1 1 1 - 0.85 0.11

rs6265 1 1 1 1 1 - 0.09

rs10835211 0.95 1 1 0.96 1 1 -

D 'r2

33

Supplementary Table 7: Pair-wise correlation between SNPs (cont.) (e) 12q13

-

rs7138803

rs836964

rs7138803 - 0.12

rs836964 1 -

D 'r2

(f) 16p11

-

rs8049439

rs4788102

rs7498665

rs8049439 - 0.96 0.96

rs4788102 1 - 1

rs7498665 1 1 -

D 'r2

(g) 16q12

-

rs6499640

rs8050136

rs3751812

rs7190492

rs8044769

rs6499640 - 0.18 0.18 0.36 0.14

rs8050136 0.64 - 1 0.34 0.64

rs3751812 0.64 1 - 0.34 0.64

rs7190492 0.69 1 1 - 0.49

rs8044769 0.44 1 1 0.95 -

D 'r2

(h) 18q21

-

rs633265

rs1350341

rs12970134

rs633265 - 1 0.31

rs1350341 1 - 0.31

rs12970134 0.78 0.78 -

D 'r2

34

Supplementary Table 8: Pair-wise conditional analysis. Conditional analysis of the association with BMI and weight for SNPs at eight loci with multiple SNPs from the discovery analysis. For each SNP the correlation to BMI and weight is tested conditional on the observed association of each of the other SNPs at that locus. The conditional analysis is done for the four discovery samples sets, ICE, DUT, JHC and JHA and the Danish replication sample set. Each table shows the combined P value for the pair-wise adjustment for SNPs at one locus and for BMI and weight separately. The SNPs tested are listed in the first column and the SNP that is adjusted for is listed in the top rows of each table.

BMI Weight

(a) 1p31

rs1776012

rs9424977

rs3101336

rs2568958

rs1776012

rs9424977

rs3101336

rs2568958

rs1776012 - 0.76 0.66 0.63 - 0.82 0.26 0.26

rs9424977 0.63 - 0.56 0.49 0.73 - 0.18 0.15

rs3101336 0.0072 0.011 - 0.44 0.083 0.11 - 0.31

rs2568958 0.022 0.045 0.36 - 0.12 0.19 0.39 -

(b) 2p25

rs2867125

rs4854344

rs7561317

rs2867125

rs4854344

rs7561317

rs2867125 - 0.1 0.13 - 0.13 0.24

rs4854344 0.85 - 0.58 0.92 - 0.47

rs7561317 0.93 0.23 - 0.78 0.16 -

(c) 6p21

rs2844479

rs2260000

rs1077393

rs2844479

rs2260000

rs1077393

rs2844479 - 0.013 0.044 - 5.5E-05 4.9×10

-5

rs2260000 0.71 - 0.98 0.85 - 0.61

rs1077393 0.11 0.088 - 0.043 0.0084 -

(d) 11p14

rs7481311

rs4074134

rs4923461

rs925946

rs10501087

rs6265

rs10835211

rs7481311

rs4074134

rs4923461

rs925946

rs10501087

rs6265

rs10835211

rs7481311 - 0.0048 0.0052 0.74 0.0053 0.005 0.14 - 5.7×10-4 5.2×10

-4 0.5 5.9×10

-4 4.8×10

-4 0.21

rs4074134 2.9×10-5

- 0.86 0.00073 0.59 0.27 4.9×10-5

0.00085 - 0.79 0.011 0.62 0.23 0.0016

rs4923461 0.00028 0.62 - 0.00081 0.58 0.22 0.00023 0.0089 0.55 - 0.019 0.61 0.58 0.008

rs925946 0.039 0.00011 0.00015 - 8.9×10-5 8.2×10

-5 0.0062 0.045 1.8×10

-5 2.7×10

-5 - 1.5×10

-5 1.8×10

-5 0.023

rs10501087 0.00052 0.77 0.87 0.0018 - 0.28 0.00048 0.015 0.72 0.98 0.037 - 0.7 0.016

rs6265 0.00011 0.38 0.36 0.0017 0.47 - 0.00018 0.0042 0.19 0.5 0.03 0.34 - 0.0068

rs10835211 0.96 0.0028 0.0031 0.26 0.0023 0.012 - 0.6 2.1×10-4 2.2×10

-4 0.79 1.5×10

-4 1.8×10

-4 -

35

Supplementary Table 8: Pair-wise conditional analysis (cont.). BMI Weight

(e) 12q13

rs7138803

rs836964

rs7138803

rs836964

rs7138803 - 0.00004 - 0.0018

rs836964 0.0034 - 0.0007 -

(f) 16p11

rs8049439

rs4788102

rs7498665

rs8049439

rs4788102

rs7498665

rs8049439 - 0.59 0.59 - 0.26 0.35

rs4788102 0.23 - 0.26 0.095 - 0.29

rs7498665 0.079 0.2 - 0.29 0.23 -

(g) 16q12

rs8050136

rs3751812

rs6499640

rs7190492

rs8044769

rs8050136

rs3751812

rs6499640

rs7190492

rs8044769

rs8050136 - 0.5 1.7×10-15

7.4×10-9 1.0×10

-7 - 0.45 8.0×10

-12 2.2×10

-7 4.1×10

-6

rs3751812 0.59 - 1.5×10-15

1.1×10-8 1.3×10

-7 0.51 - 2.8×10

-12 1.2×10

-7 2.3×10

-6

rs6499640 0.00039 0.00049 - 7.1×10-5 6.9×10

-5 0.0023 0.0029 - 4.9×10

-4 5.6×10

-4

rs7190492 0.026 0.024 9.810-12

- 0.0023 0.16 0.18 5.1×10-8 - 0.031

rs8044769 0.5 0.53 4.610-13

0.00035 - 0.62 0.7 5.1×10-10

5.1×10-4 -

(h) 18q21

rs633265

rs1350341

rs12970134

rs633265

rs1350341

rs12970134

rs633265 - 0.78 0.19 - 0.83 0.06

rs1350341 0.87 - 0.17 0.81 - 0.12

rs12970134 0.0027 0.0027 - 0.004 0.0043 -

36

Supplementary Table 9: Pair-wise correlation between selected 6p21 SNPs. Pair-wise correlation between rs2844479, at the 6p21 locus, and SNPs that have previously been associated with obesity or obesity related traits; rs1061581 in HSPA1B, rs1041981 in LTA, promoter rs1800629 and intronic rs1800610, in TNF . The table includes estimates of D’ (lower left) and r

2

(upper right) based on genotypes for the 90 HapMap CEU samples138

.

D' \ r2 rs1041981 rs1800629 rs1800610 rs1061581

rs2844479 0.29 \ 0.02 0.56 \ 0.04 1 \ 0.096 ND

Position (NCBI Build 36) and the minor allele frequency (MAF) of the five SNPs based on HapMap CEU when available, otherwise other CEU samples (see the NCBI’s dbSNP database for more details).

Ref SNP Pos NCBI B36 Minor Allele MAF Sample sex

rs1041981 31648763 A 0.358 HapMap CEU

rs1800629 31651010 A 0.217 HapMap CEU

rs1800610 31651806 A 0.04 HapMap CEU

rs2844479 31680935 G 0.317 HapMap CEU

rs1061581* 31892565 G 0.289 non-HapMap CEU

*Multiple position in the genome

37

Supplementary Table 10: Genes located at the eleven GWS loci List of potential and verified genes and cDNA clones at the eleven loci showing GWS association to either BMI or weight.

Gene (alias) EntrezGene Chr Strand NCBI36-start NCBI36-stop Description

NEGR1 257194 1p31 - 71641212 72520993 Neuronal growth regulator 1

SEC16B (LZTR2) 89866 1q25 - 176164111 176258426 SEC16 homolog B (Leucine zipper transcription regulator 2)

AK124464 1q25 - 176327265 176329358 Homo sapiens cDNA FLJ42473 fis, clone BRACE2030884.

CR597233 1q25 - 176327265 176329751 Homo sapiens cDNA FLJ42473 fis, clone BRACE2030884.

RASAL2 9462 1q25 + 176330252 176710180 RAS protein activator like 2

TMEM18 129787 2p25 - 657972 667439 Transmembrane protein 18

CR598144 2p25 + 667185 672802 full-length cDNA clone CS0DL002YB02 of B cells (Ramos cell line) Cot 25-normalized of humans

LOC391343 391343 2p25 - 892823 896011 Hypothetical protein LOC391343; similar to CG2839-PA

SFRS10 6434 3q27 - 187117228 187138450 Splicing factor, arginine/serine-rich 10

ETV5 2119 3q27 - 187246803 187309571 ETS variant gene 5

DGKG 1608 3q27 - 187347683 187562717 Diacylglycerol kinase gamma

HLA-B 3106 6p21 - 31429628 31432968 Major histocompatibility complex class I B

MICA 4276 6p21 + 31475539 31491069 MHC class I polypeptide-related sequence A

HCP5 10866 6p21 + 31538937 31541461 HLA complex P5

MICB 4277 6p21 + 31573944 31586880 MHC class I polypeptide-related sequence B

MCCD1 401250 6p21 + 31604717 31605987 Mitochondrial coiled-coil domain 1

BAT1 7919 6p21 - 31605974 31622606 HLA-B associated transcript 1 variant protein

ATP6V1G2 534 6p21 - 31620218 31622606 ATPase, H+ transporting, lysosomal, V1 subunit

NFKBIL1 4795 6p21 + 31623350 31634585 Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1

LTA 4049 6p21 + 31647718 31650077 Lymphotoxin alpha (TNF superfamily, member 1)

TNF 7124 6p21 + 31651328 31654091 Tumor necrosis factor alpha

LTB 4050 6p21 - 31656314 31658181 Lymphotoxin beta

LST1 7940 6p21 + 31661949 31664665 Leukocyte specific transcript 1

NCR3 259197 6p21 - 31664650 31668741 Natural cytotoxicity triggering receptor 3

AIF1 199 6p21 + 31691011 31692777 Allograft inflammatory factor 1

BAT2 7916 6p21 + 31696575 31713516 HLA-B associated transcript 2

BAT3 7917 6p21 - 31714796 31728434 HLA-B associated transcript 3

APOM 55937 6p21 + 31728199 31733966 Apolipoprotein M

C6orf47 57827 6p21 - 31734053 31736528 G4 protein (chromosome 6 open reading frame 47)


CSNK2B 1460 6p21 + 31741635 31748206 Casein kinase 2, beta polypeptide

LY6G5B 58496 6p21 + 31746706 31748206 Lymphocyte antigen 6 complex G5B

LY6G5C 80741 6p21 - 31752439 31759796 Lymphocyte antigen 6 complex G5C


C6orf21 259215 6p21 + 31782662 31786351 G6f protein (chromosome 6 open reading frame 21)

LY6G6D 58530 6p21 + 31791111 31793560 Lymphocyte antigen 6 complex G6D

LY6G6C 80740 6p21 - 31794403 31797489 Lymphocyte antigen 6 complex G6C

C6orf25 80739 6p21 + 31799139 31800830 G6B protein (chromosome 6 open reading frame 25)

DDAH2 23564 6p21 - 31802795 31806018 Dimethylarginine dimethylaminohydrolase 2

CLIC1 1192 6p21 - 31806336 31813074 Chloride intracellular channel 1

MSH5 4439 6p21 + 31815752 31840607 mutS homolog 5

C6orf26 401251 6p21 + 31838752 31840603 Hypothetical protein LOC401251 (chromosome 6 open reading frame 26)

C6orf27 80737 6p21 - 31841494 31852550 NG37 protein (chromosome 6 open reading frame 27)

VARS 7407 6p21 - 31853275 31871691 Valyl-tRNA synthetase

LSM2 57819 6p21 - 31873152 31882722 LSM2 homolog, U6 small nuclear RNA associated

HSPA1L 3305 6p21 - 31885374 31890814 Heat shock 70kDa protein 1-like

HSPA1A 3303 6p21 + 31891298 31893698 Heat shock 70kDa protein 1A

HSPA1B 3304 6p21 + 31903502 31906010 Heat shock 70kDa protein 1B

C6orf48 50854 6p21 + 31910671 31915520 G8 protein (chromosome 6 open reading frame 48)

RDBP 7936 6p21 - 32027842 32034843 Homo sapiens cDNA clone IMAGE:3050953, **** WARNING: chimeric clone ****, RD RNA-binding protein

38

Supplementary Table 10: Genes located at the eleven GWS loci (cont.)

Gene (alias) EntrezGene Chr Strand NCBI36-start NCBI36-stop Description

BBOX1 8424 11p14 + 27019085 27105930 Gamma-butyrobetaine dioxygenase

CCDC34 91057 11p14 - 27316636 27341371 Coiled-coil domain containing 34

LGR4 55366 11p14 - 27344083 27450869 Leucine-rich repeat-containing G protein-coupled

LIN7C 55327 11p14 - 27472698 27484879 LIN-7 homolog C

BDNF 627 11p14 - 27633017 27699872 Brain-derived neurotrophic factor

PRPF40B (HYPC) 25766 12q13 + 48303670 48324716 PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae); Huntingtin interacting protein C

FMNL3 91010 12q13 - 48317990 48387464 Formin-like 3

TMBIM6 (TEGT) 7009 12q13 + 48421606 48444762 Testis enhanced gene transcript (BAX inhibitor 1)

CR623040 7009 12q13 + 48443347 48444983 Homo sapiens cDNA: FLJ22952 fis, clone KAT09742

KIAA1602 57701 12q13 - 48471195 48477052 Homo sapiens mRNA for KIAA1602 protein, partial cds

LOC283331 283331 12q13 - 48482317 48485440 Homo sapiens cDNA FLJ36581 fis, clone TRACH2012918.,hypothetical protein LOC283331

BC014925 12q13 + 48508592 48521204 Homo sapiens cDNA FLJ30580 fis, clone BRAWH2006996

BCDIN3D 144233 12q13 - 48517824 48523142 BCDIN3 domain containing

FAIM2 23017 12q13 - 48546946 48584032 Fas apoptotic inhibitory molecule 2 (lifeguard)

AX747994 12q13 - 48588942 48591907 Homo sapiens cDNA FLJ35896 fis, clone TESTI2009462

BC034605 12q13 + 48592002 48606389 Homo sapiens cDNA clone IMAGE:4838146

AQP2 359 12q13 + 48630795 48638931 Aquaporin 2

AQP5 362 12q13 + 48641545 48645227 Aquaporin 5

AQP6 363 12q13 + 48647243 48657189 Aquaporin 6

RACGAP1 29127 12q13 - 48669211 48705488 Rac GTPase activating protein 1

ACCN2 41 12q13 + 48737753 48763661 Amiloride-sensitive cation channel 2, neuronal

SMARCD1 6602 12q13 + 48765250 48780761 SWI/SNF-related matrix-associated

GPD1 2819 12q13 + 48784068 48791360 Glycerol-3-phosphate dehydrogenase 1 (soluble)

CLN3 1201 16p11 - 28396101 28411124 Ceroid-lipofuscinosis neuronal 3

APOB48R 55911 16p11 + 28413494 28417783 Apolipoprotein B48 receptor

IL27 246778 16p11 - 28418184 28425656 Interleukin 27

NUPR1 26471 16p11 - 28456163 28457996 Nuclear protein 1

CCDC101 112869 16p11 + 28472758 28510610 Coiled-coil domain containing 101

SULT1A2 6799 16p11 - 28510767 28515302 Sulfotransferase family cytosolic 1A

SULT1A1 6817 16p11 - 28524417 28528150 Sulfotransferase family cytosolic 1A

LOC440350 440350 16p11 + 28563411 28576505 Hypothetical protein LOC440350; similar to nuclear pore complex interacting protein; hits to multiple locations

LOC390688 390688 16p11 - 28618998 28620433 CDC37-like; hits to multiple locations

EIF3C (EIF3S8) 8663 16p11 + 28630283 28654551 Eukaryotic translation initiation factor 3; hits to multiple locations

LOC440350 440350 16p11 + 28677526 28690630 Hypothetical protein LOC440350; similar to nuclear pore complex interacting protein; hits to multiple locations

AK125489 16p11 + 28721597 28736650 Homo sapiens cDNA FLJ43500 fis, clone PEBLM2002887, weakly similar to ZINC FINGER PROTEIN 195

ATXN2L (A2LP) 11273 16p11 + 28741914 28756059 Ataxin 2 related protein

TUFM 7284 16p11 - 28761612 28765144 Tu translation elongation factor, mitochondrial

SH2B1 25970 16p11 + 28782815 28793027 SH2B adaptor protein 1

ATP2A1 (SERCA1) 487 16p11 + 28797309 28823331 ATPase, Ca++ transporting, fast twitch 1

RABEP2 79874 16p11 - 28823242 28844033 Rabaptin, RAB GTPase binding effector protein 2

CD19 930 16p11 + 28850760 28858164 CD19 antigen

NFATC2IP 84901 16p11 + 28869628 28885268 Nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein

SPNS1 (SPIN1) 83985 16p11 + 28893593 28904339 Spindlin, spinster homolog 1 (Drosophila)

LAT 27040 16p11 + 28903026 28909605 Linker for activation of T cells

AKTIP 64400 16q12 - 52082693 52094671 AKT interacting protein

RPGRIP1L 23322 16q12 - 52191318 52295272 RPGRIP1-like

FTO 79068 16q12 + 52295375 52705882 Fat mass and obesity associated gene

MC4R 4160 18q21 - 56189543 56190981 Melanocortin 4 receptor

CHST8 64377 19q13 + 38804716 38956254 Carbohydrate (N-acetylgalactosamine4-0) sulfotransferase 8

KCTD15 79047 19q13 + 38979606 38996986 BTB/POZ domain-containing protein, potassium channel tetramerisation domain

39

Supplementary Table 11: Genotype specific mean BMI and weight for variants at the eleven GWS loci.

BMI (kg/m

2)

Weight (kg)

Locus SNP

Genot

ICE

DUT

JHA

JHC

DEN

ICE

DUT

JHA

JHC

DEN

1p31

rs2568958

GG

26.8

4 (

0.0

8)

25.4

5 (

0.1

5)

29.0

3 (

0.3

7)

31.2

6 (

0.5

2)

26.3

9 (

0.1

5)

77.2

0 (

0.2

5)

77.0

7 (

0.5

2)

85.1

1 (

1.1

7)

90.6

4 (

1.5

0)

78.2

0 (

0.5

0)

GA

27.0

1 (

0.0

5)

25.9

3 (

0.1

8)

28.8

9 (

0.2

1)

31.2

6 (

0.3

1)

26.1

3 (

0.0

9)

77.9

7 (

0.1

6)

76.9

7 (

0.3

6)

85.0

6 (

0.6

9)

89.2

8 (

0.9

0)

77.6

6 (

0.3

1)

AA

27.2

5 (

0.0

6)

26.2

7 (

0.1

9)

28.2

1 (

0.2

0)

32.9

3 (

0.4

2)

26.3

7 (

0.1

1)

78.6

7 (

0.1

9)

77.7

3 (

0.4

4)

82.1

2 (

0.7

1)

93.6

3 (

1.2

6)

78.2

1 (

0.3

8)

1q25

rs10913469

TT

26.9

6 (

0.0

4)

26.0

9 (

0.1

6)

28.5

0 (

0.1

7)

31.4

8 (

0.2

9)

26.1

3 (

0.0

8)

77.7

5 (

0.1

3)

77.2

1 (

0.3

1)

83.7

2 (

0.5

7)

89.7

6 (

0.8

6)

77.5

2 (

0.2

7)

TC

27.2

1 (

0.0

6)

25.7

1 (

0.1

3)

28.7

7 (

0.2

6)

31.6

7 (

0.3

9)

26.4

6 (

0.1

1)

78.5

4 (

0.1

9)

77.1

6 (

0.4

3)

83.9

8 (

0.8

2)

91.0

5 (

1.1

0)

78.7

1 (

0.3

9)

CC

27.4

6 (

0.1

8)

26.1

3 (

0.3

3)

29.5

4 (

0.7

3)

33.8

1 (

0.9

0)

26.4

3 (

0.2

8)

79.3

5 (

0.5

7)

78.9

8 (

1.2

2)

85.1

4 (

2.2

8)

97.1

2 (

2.6

7)

78.1

7 (

0.9

1)

2p25

rs7561317

AA

26.4

6 (

0.1

8)

25.6

5 (

0.4

8)

28.1

0 (

0.6

4)

30.3

2 (

0.9

1)

25.8

3 (

0.3

2)

76.0

6 (

0.6

2)

75.4

9 (

1.5

3)

81.5

0 (

2.2

3)

88.4

6 (

2.7

1)

76.1

2 (

1.2

0)

AG

26.8

5 (

0.0

6)

25.6

0 (

0.1

9)

28.4

6 (

0.2

6)

31.7

3 (

0.3

6)

25.9

3 (

0.1

1)

77.4

9 (

0.2

0)

76.3

7 (

0.4

7)

83.4

5 (

0.8

8)

89.7

5 (

1.0

6)

77.1

8 (

0.3

9)

GG

27.1

6 (

0.0

4)

26.1

3 (

0.1

4)

28.7

4 (

0.1

7)

31.8

3 (

0.3

0)

26.4

1 (

0.0

8)

78.3

5 (

0.1

3)

77.6

9 (

0.2

9)

84.1

8 (

0.5

6)

91.6

1 (

0.8

8)

78.3

2 (

0.2

7)

3q27

rs7647305

TT

26.6

4 (

0.1

3)

25.1

5 (

0.3

4)

27.2

8 (

0.3

9)

32.2

3 (

0.5

7)

26.9

5 (

0.2

3)

77.3

1 (

0.4

3)

75.1

4 (

1.0

9)

78.5

9 (

1.4

0)

92.9

6 (

1.7

5)

79.2

4 (

0.8

0)

TC

26.9

1 (

0.0

5)

26.1

5 (

0.2

5)

28.3

2 (

0.2

2)

31.3

6 (

0.3

2)

27.0

4 (

0.0

8)

77.5

4 (

0.1

8)

77.2

7 (

0.4

6)

83.0

5 (

0.7

5)

89.8

1 (

0.9

4)

79.7

9 (

0.2

8)

CC

27.1

8 (

0.0

4)

25.9

4 (

0.1

2)

28.9

4 (

0.1

9)

32.0

0 (

0.3

8)

27.3

6 (

0.0

6)

78.4

4 (

0.1

4)

77.4

1 (

0.3

0)

84.8

5 (

0.6

2)

91.1

7 (

1.0

9)

80.5

9 (

0.2

0)

6p21

rs2844479

GG

26.7

4 (

0.1

0)

25.6

3 (

0.1

8)

28.2

8 (

0.3

5)

30.6

3 (

0.6

6)

26.2

9 (

0.2

0)

76.6

9 (

0.3

2)

75.9

3 (

0.6

3)

82.4

3 (

1.2

0)

86.0

5 (

1.7

6)

77.3

1 (

0.6

9)

GT

27.0

2 (

0.0

5)

25.9

8 (

0.1

8)

28.5

7 (

0.2

0)

31.5

0 (

0.3

3)

26.2

8 (

0.1

0)

77.7

7 (

0.1

6)

77.2

2 (

0.3

7)

83.9

7 (

0.6

6)

90.1

8 (

0.9

5)

78.0

3 (

0.3

6)

TT

27.1

7 (

0.0

5)

26.0

4 (

0.1

7)

28.8

3 (

0.2

3)

32.1

4 (

0.3

5)

26.2

1 (

0.1

0)

78.6

9 (

0.1

6)

77.6

1 (

0.3

8)

84.2

8 (

0.7

5)

92.2

8 (

1.0

3)

78.0

3 (

0.3

5)

" rs

925946

GG

26.9

0 (

0.0

5)

25.9

1 (

0.1

8)

28.5

7 (

0.2

0)

31.3

6 (

0.2

9)

26.1

1 (

0.0

9)

77.4

7 (

0.1

6)

76.9

7 (

0.3

4)

83.4

9 (

0.6

7)

89.5

6 (

0.8

5)

77.3

5 (

0.3

1)

GT

27.1

3 (

0.0

5)

26.1

0 (

0.1

5)

28.5

6 (

0.2

1)

32.1

1 (

0.3

9)

26.3

1 (

0.1

0)

78.3

9 (

0.1

7)

77.8

2 (

0.3

8)

83.8

4 (

0.6

9)

91.9

9 (

1.1

1)

78.2

5 (

0.3

3)

TT

27.3

8 (

0.1

0)

25.6

8 (

0.2

6)

29.3

2 (

0.4

2)

32.3

7 (

0.8

7)

26.7

7 (

0.2

1)

79.1

1 (

0.3

2)

76.1

0 (

0.8

8)

86.0

0 (

1.4

7)

93.5

7 (

2.6

6)

79.2

7 (

0.7

0)

11p14

rs6265

AA

26.4

7 (

0.2

0)

25.3

0 (

0.3

8)

29.4

9 (

0.7

6)

30.1

6 (

1.7

2)

26.0

0 (

0.2

9)

76.2

4 (

0.6

8)

75.8

8 (

1.1

7)

88.2

2 (

2.7

5)

84.9

5 (

6.0

3)

77.9

2 (

1.0

5)

AG

26.8

8 (

0.0

6)

25.8

4 (

0.2

1)

28.7

0 (

0.2

7)

31.1

0 (

0.6

9)

26.0

5 (

0.1

1)

77.5

6 (

0.2

1)

76.6

9 (

0.4

0)

84.2

3 (

0.8

6)

88.9

2 (

2.0

3)

77.1

5 (

0.3

8)

GG

27.1

4 (

0.0

4)

26.0

8 (

0.1

4)

28.5

7 (

0.1

6)

31.8

0 (

0.2

4)

26.3

9 (

0.0

8)

78.2

9 (

0.1

3)

77.6

8 (

0.3

2)

83.5

2 (

0.5

5)

91.0

1 (

0.7

0)

78.3

8 (

0.2

7)

12q13

rs7138803

GG

26.8

4 (

0.0

5)

25.7

4 (

0.1

5)

28.4

9 (

0.2

3)

31.8

4 (

0.2

8)

26.0

3 (

0.1

0)

77.4

9 (

0.1

7)

76.8

0 (

0.3

8)

83.1

1 (

0.7

4)

91.0

6 (

0.8

2)

77.1

7 (

0.3

4)

GA

27.1

5 (

0.0

5)

26.0

1 (

0.1

6)

28.7

0 (

0.2

0)

31.3

0 (

0.3

8)

26.2

7 (

0.0

9)

78.2

7 (

0.1

6)

77.2

9 (

0.3

5)

84.4

4 (

0.6

7)

89.5

4 (

1.1

0)

78.0

3 (

0.3

3)

AA

27.3

8 (

0.0

9)

26.4

3 (

0.4

1)

28.8

0 (

0.3

6)

33.8

4 (

1.7

2)

26.7

0 (

0.1

5)

79.0

2 (

0.3

0)

78.4

5 (

0.7

4)

84.0

4 (

1.2

1)

97.5

4 (

5.4

4)

79.2

5 (

0.5

4)

16p11

rs7498665

AA

26.8

5 (

0.0

6)

26.1

4 (

0.2

2)

28.2

3 (

0.2

2)

31.2

7 (

0.3

1)

26.1

6 (

0.1

0)

77.4

9 (

0.1

9)

77.6

3 (

0.4

1)

82.4

7 (

0.7

5)

89.3

9 (

0.9

1)

77.5

1 (

0.3

6)

AG

27.1

0 (

0.0

5)

25.9

0 (

0.1

5)

28.8

8 (

0.2

1)

32.2

3 (

0.3

6)

26.3

1 (

0.0

9)

78.1

5 (

0.1

6)

76.9

9 (

0.3

5)

84.5

5 (

0.6

7)

92.5

1 (

1.0

3)

78.1

9 (

0.3

2)

GG

27.3

0 (

0.0

8)

25.7

6 (

0.2

0)

28.7

5 (

0.3

7)

32.8

4 (

0.9

3)

26.2

7 (

0.1

5)

78.8

7 (

0.2

5)

76.9

9 (

0.6

4)

84.7

1 (

1.2

0)

93.1

8 (

2.9

1)

77.8

7 (

0.5

2)

16q12

rs6499640

GG

26.8

5 (

0.0

9)

25.4

3 (

0.1

6)

27.7

4 (

0.3

1)

31.1

8 (

0.5

3)

25.9

1 (

0.1

7)

77.4

2 (

0.2

9)

76.7

0 (

0.5

7)

81.3

1 (

1.0

5)

89.2

1 (

1.5

1)

76.6

0 (

0.5

8)

GA

26.9

0 (

0.0

5)

25.9

6 (

0.1

6)

28.5

3 (

0.2

0)

31.7

8 (

0.3

3)

26.1

2 (

0.0

9)

77.6

5 (

0.1

6)

77.0

7 (

0.3

7)

83.6

9 (

0.6

8)

90.8

5 (

0.9

8)

77.4

3 (

0.3

0)

AA

27.3

0 (

0.0

5)

26.2

0 (

0.2

1)

29.1

7 (

0.2

4)

31.8

3 (

0.3

6)

26.5

5 (

0.1

0)

78.7

4 (

0.1

7)

77.6

4 (

0.4

1)

85.2

6 (

0.7

7)

91.1

8 (

1.0

8)

79.0

6 (

0.3

6)

" rs

8050136

CC

26.6

3 (

0.0

5)

25.8

7 (

0.1

9)

28.1

1 (

0.2

3)

31.8

4 (

0.4

3)

25.8

5 (

0.1

0)

76.8

4 (

0.1

8)

76.8

5 (

0.4

0)

82.5

9 (

0.7

8)

91.7

0 (

1.2

4)

76.7

2 (

0.3

5)

CA

27.1

4 (

0.0

5)

25.8

6 (

0.1

1)

28.8

7 (

0.2

0)

31.7

2 (

0.3

0)

26.2

7 (

0.0

9)

78.2

7 (

0.1

6)

77.6

0 (

0.3

6)

84.2

6 (

0.6

5)

90.4

0 (

0.8

8)

77.9

4 (

0.3

1)

AA

27.7

0 (

0.0

9)

26.5

6 (

0.4

5)

29.0

2 (

0.3

4)

31.4

7 (

0.5

3)

26.9

9 (

0.1

6)

80.0

4 (

0.2

8)

77.2

4 (

0.6

1)

85.3

7 (

1.1

7)

90.0

3 (

1.5

9)

80.1

0 (

0.5

6)

18q21

rs12970134

GG

26.9

3 (

0.0

5)

25.8

2 (

0.1

3)

28.2

9 (

0.1

8)

31.4

2 (

0.2

7)

26.1

2 (

0.0

8)

77.6

1 (

0.1

5)

77.1

7 (

0.3

5)

82.4

7 (

0.5

9)

89.9

7 (

0.7

9)

77.4

0 (

0.3

0)

GA

27.1

6 (

0.0

5)

26.2

2 (

0.2

2)

28.9

3 (

0.2

4)

32.3

2 (

0.4

5)

26.4

2 (

0.1

0)

78.3

3 (

0.1

7)

77.5

7 (

0.3

8)

84.9

8 (

0.7

7)

92.1

8 (

1.2

6)

78.5

0 (

0.3

4)

AA

27.2

9 (

0.1

1)

25.5

4 (

0.2

4)

29.7

4 (

0.5

5)

33.5

5 (

1.2

3)

26.4

9 (

0.2

2)

79.2

9 (

0.3

7)

75.9

2 (

0.9

0)

89.1

0 (

1.9

5)

96.9

6 (

3.6

7)

78.9

2 (

0.8

1)

19q13

rs29941

TT

26.7

3 (

0.1

0)

25.5

7 (

0.2

3)

28.7

6 (

0.3

8)

29.9

0 (

0.9

5)

25.9

6 (

0.1

8)

76.8

8 (

0.3

3)

76.4

6 (

0.8

6)

85.0

6 (

1.3

7)

83.4

5 (

3.0

8)

76.7

3 (

0.6

2)

TC

26.9

9 (

0.0

5)

25.9

6 (

0.2

1)

28.8

5 (

0.2

2)

31.5

9 (

0.3

8)

26.2

7 (

0.0

9)

77.8

6 (

0.1

6)

77.1

0 (

0.3

6)

84.2

2 (

0.7

0)

89.9

6 (

1.0

8)

77.9

4 (

0.3

3)

CC

27.1

9 (

0.0

5)

26.0

7 (

0.1

4)

28.4

3 (

0.2

0)

31.8

9 (

0.2

9)

26.3

4 (

0.0

9)

78.4

9 (

0.1

6)

77.6

0 (

0.3

6)

83.3

4 (

0.6

8)

91.6

2 (

0.8

6)

78.3

0 (

0.3

2)

40

Supplementary Table 12: Obese compared to normal weight individuals.

Associa

tion t

est, O

R a

nd P

va

lue,

com

paring th

e f

requ

ency o

f th

e o

besity a

sso

cia

ted v

ari

ants

in o

bese ind

ivid

ua

ls (

BM

I ≥ 3

0)

with t

he f

reque

ncy in ind

ivid

ua

ls w

ith

norm

al w

eig

ht (1

8.5

< B

MI

< 2

5).

This

is d

on

e f

or

SN

Ps a

t th

e e

leven

associa

ted lo

ci th

at

sho

w s

tron

gest corr

ela

tion w

ith B

MI a

nd w

eig

ht. F

or

two loci, 1

1p

14 a

nd

16q1

2,

where

there

is e

vid

ence f

or

multip

le s

ign

als

, re

sults f

or

two S

NP

s a

re s

ho

wn. T

he a

naly

sis

is d

on

e o

n the

sam

ple

sets

fro

m Icela

nd (

ICE

; 9,2

55 n

orm

al

weig

ht /

5,9

96 o

bese),

the N

eth

erl

an

ds (

DU

T; 1,4

32

/ 3

31),

Denm

ark

(D

EN

; 2,4

13 / 9

49),

and t

he A

mericans o

f E

uro

pe

an d

escent (J

HC

; 47

2 / 5

91)

and A

fric

an

-A

merican (

JH

A; 21

3 / 6

25)

sam

ple

sets

fro

m J

ohn H

op

kin

s, U

SA

. A

lso s

ho

wn

are

the r

esu

lts f

or

all

five s

am

ple

sets

com

bin

ed u

sin

g t

he M

ante

l-H

aen

ze

l m

eth

od.

For

the f

our

sam

ple

sets

th

at

were

inclu

ded in t

he g

en

om

e-w

ide a

na

lysis

, th

e P

valu

es w

ere

adju

ste

d u

sin

g t

he m

eth

od o

f ge

nom

ic c

ontr

ol. T

he C

hi2

adju

stm

ent

facto

rs w

ere

1.4

1 f

or

ICE

, 1

.03 f

or

DU

T, 1.2

8 f

or

JH

C a

nd 1

.15 f

or

JH

A.

ICE

DUT

DAN

JHC

JHA

Combined

Loci

SNP

Allele OR P

OR

P

OR P

OR

P

OR

P

OR (95% CI)

P

1p

31

rs

25

68

958

A

1

.08

0

.00

38

1

.26

0

.01

3

1.0

0

0.9

6

0.8

1

0.0

45

1

.21

0

.11

1

.07

(1.0

2-1

.12

) 0

.00

46

1q

25

rs

10

91

346

9

C

1.1

1

0.0

024

1

.07

0

.55

1

.17

0

.02

1

.06

0

.61

1

.09

0

.52

1

.11

(1.0

5-1

.18

) 0

.00

01

1

2p

25

rs

75

61

317

G

1

.16

5

.9×1

0-5

1

.34

0

.01

7

1.3

6

3.9×1

0-5

1

.04

0

.74

1

.23

0

.14

1

.20

(1.1

3-1

.27

) 2

.6×1

0-9

3q

27

rs

76

47

305

C

1

.14

6

.3×1

0-5

1

.11

0

.38

1

.02

0

.77

1

.12

0

.32

0

.94

0

.6

1.1

1 (

1.0

5-1

.17

) 0

.00

01

8

6p

21

rs

28

44

479

T

1

.09

0

.00

53

1

.07

0

.45

0

.98

0

.69

1

.08

0

.47

1

.06

0

.65

1

.07

(1.0

2-1

.12

) 0

.00

93

11

p1

4

rs6

265

G

1

.15

0

.00

03

1

.09

0

.43

1

.14

0

.04

6

0.8

4

0.1

8

0.9

9

0.9

7

1.1

2 (

1.0

6-1

.19

) 0

.00

02

2

" rs

92

59

46

T

1

.11

0

.00

04

6

1.0

9

0.3

6

1.1

2

0.0

59

1

.07

0

.5

1.0

6

0.6

5

1.1

1 (

1.0

5-1

.16

) 3

.5×1

0-5

12

q1

3

rs7

138

803

A

1

.14

4

.3×1

0-6

1

.06

0

.52

1

.20

0

.00

09

2

1.0

7

0.4

9

1.0

6

0.7

3

1.1

4 (

1.0

9-1

.19

) 2

.5×1

0-8

16

p1

1

rs7

498

665

G

1

.10

0

.00

1

1.0

3

0.7

7

1.0

3

0.6

2

0.9

9

0.9

1

1.4

1

0.0

16

1

.08

(1.0

3-1

.13

) 0

.00

07

6

16

q1

2

rs6

499

640

A

1

.14

4

.0×1

0-6

1

.14

0

.17

1

.22

0

.00

05

6

1.3

0

0.0

11

0

.95

0

.71

1

.16

(1.1

0-1

.21

) 1

.1×1

0-9

" rs

80

50

136

A

1

.28

9

.1×1

0-2

0

1.1

3

0.1

8

1.3

6

4.1×1

0-8

1

.29

0

.01

1

0.9

4

0.6

2

1.2

7 (

1.2

1-1

.32

) 3

.0×

10

-26

18

q2

1

rs1

297

013

4

A

1.1

0

0.0

018

1

.05

0

.64

1

.15

0

.02

3

1.2

5

0.0

47

1

.43

0

.03

4

1.1

2 (

1.0

6-1

.17

) 1

.0×1

0-5

19

q1

3

rs2

994

1

C

1.1

0

0.0

009

9

1.2

8

0.0

11

1

.09

0

.13

0

.82

0

.05

8

1.1

5

0.3

5

1.1

0 (

1.0

4-1

.15

) 0

.00

02

1

41

Supplementary Table 13: Association of the BMI and weight variants at the eleven loci with T2D.

The a

ssocia

tio

n w

ith T

2D

for

thirte

en S

NP

s loca

ted in t

he e

leve

n loci th

at sho

w s

ignific

ant

associa

tio

n w

ith w

eig

ht or

BM

I. F

or

each

locu

s the S

NP

that

sho

ws th

e

most sig

nific

ant

associa

tion

is teste

d e

xcept fo

r 11

p1

4 a

nd 1

6q

12 w

here

tw

o S

NP

s, possib

ly r

epre

sentin

g t

wo d

istinct sig

na

ls o

f associa

tion

, are

se

lecte

d. In

all

cases the a

llele

tha

t corr

ela

tes w

ith incre

ased w

eig

ht/

BM

I is

teste

d. T

he a

ssocia

tio

n is teste

d in s

am

ple

sets

fro

m Icela

nd (

1,4

05 T

2D

cases a

nd 2

3,1

90 c

ontr

ols

) and f

rom

Denm

ark

(2,4

71 T

2D

cases a

nd 4

,841co

ntr

ols

), a

nd th

e r

esults, O

R’s

and P

-valu

es, are

com

bin

ed u

sin

g a

Ma

nte

l-H

ae

nzel m

odel. A

lso

inclu

ded a

re

results f

or

the a

ssocia

tion w

ith T

2D

, O

Radj a

nd P

adj,

adju

ste

d f

or

BM

I b

y inclu

din

g s

tand

ard

ize

d a

ge a

nd s

ex a

dju

ste

d B

MI

va

lues a

s c

ovari

ate

s in t

he lo

gis

tic

regre

ssio

n. F

or

a m

eanin

gfu

l com

parison, b

oth

associa

tio

n tests

are

restr

icte

d to c

ases a

nd c

on

trols

for

whic

h B

MI in

form

ation is a

vaila

ble

. T

he P

va

lues p

resente

d

for

the Icela

nd

ic s

am

ple

sets

were

adju

ste

d u

sin

g t

he m

eth

od o

f genom

ic c

ontr

ol.

Iceland (

1,4

05

/23

,190

)

Denmark

(2.4

71/4

,84

1)

Combined (

3,8

76

/28

,031

)

Loci

SNP

Allele

OR

P

ORadj

Padj

OR P

ORadj Padj

OR (95% CI)

P

ORadj (95% CI)

Padj

1p

31

rs

25

68

958

A

1

.07

0

.15

1

.04

0

.35

1.0

6

0.1

3

1.0

4

0.2

7

1

.06

(1.0

0-1

.12

) 0

.03

8

1.0

4 (

0.9

9-1

.10

) 0

.15

1q

25

rs

10

91

346

9

C

1.0

1

0.8

6

0.9

8

0.7

3

0

.99

0

.73

0

.95

0

.25

0.9

9 (

0.9

3-1

.06

) 0

.87

0

.96

(0.9

0-1

.03

) 0

.27

2p

25

rs

75

61

317

G

0

.99

0

.86

0

.95

0

.43

1.0

8

0.0

94

1

.04

0

.41

1.0

5 (

0.9

7-1

.13

) 0

.22

1

.00

(0.9

3-1

.08

) 0

.9

3q

27

rs

76

47

305

C

1

.07

0

.19

1

.04

0

.45

1.0

8

0.1

0

1.0

3

0.5

6

1

.08

(1.0

0-1

.15

) 0

.03

6

1.0

3 (

0.9

6-1

.11

) 0

.35

6p

21

rs

28

44

479

T

1

.00

0

.96

0

.98

0

.59

0.9

1

0.0

21

0

.89

0

.01

1

0

.95

(0.9

0-1

.01

) 0

.11

0

.93

(0.8

7-0

.99

) 0

.02

8

11

p1

4

rs6

265

G

1

.15

0

.03

3

1.1

1

0.1

2

0

.92

0

.04

6

0.8

7

0.0

027

0.9

8 (

0.9

2-1

.06

) 0

.64

0

.94

(0.8

8-1

.02

) 0

.12

" rs

92

59

46

T

1

.08

0

.12

1

.05

0

.32

1.0

2

0.5

6

0.9

9

0.7

0

1

.04

(0.9

8-1

.11

) 0

.15

1

.01

(0.9

5-1

.07

) 0

.73

12

q1

3

rs7

138

803

A

1

.09

0

.04

9

1.0

6

0.1

8

1

.12

0

.00

17

1

.09

0

.02

3

1

.11

(1.0

5-1

.17

) 0

.00

02

3

1.0

8 (

1.0

2-1

.14

) 0

.00

9

16

p1

1

rs7

498

665

G

0

.97

0

.50

0

.94

0

.20

1.1

1

0.0

046

1

.10

0

.01

1

1

.05

(1.0

0-1

.11

) 0

.06

9

1.0

3 (

0.9

8-1

.09

) 0

.25

16

q1

2

rs6

499

640

A

1

.05

0

.34

1

.01

0

.79

1.0

8

0.0

39

1

.03

0

.49

1.0

7 (

1.0

1-1

.13

) 0

.02

7

1.0

2 (

0.9

6-1

.08

) 0

.48

" rs

80

50

136

A

1

.11

0

.02

1

1.0

5

0.3

2

1

.14

0

.00

02

1

.05

0

.16

1.1

3 (

1.0

7-1

.19

) 1

.6×1

0-5

1

.05

(0.9

9-1

.11

) 0

.08

6

18

q2

1

rs1

297

013

4

A

1.0

2

0.6

7

1.0

0

0.9

1

1

.05

0

.17

1

.01

0

.79

1.0

4 (

0.9

8-1

.10

) 0

.18

1

.00

(0.9

5-1

.06

) 0

.91

19

q1

3

rs2

994

1

C

1.0

2

0.6

3

1.0

0

0.9

9

1

.00

0

.92

1

.00

0

.96

1.0

1 (

0.9

5-1

.07

) 0

.70

1

.00

(0.9

3-1

.07

) 0

.96

42

Supplementary Table 14: Correlation with expression. Correlation between the BMI and weight association variants and the expression of genes located at each of the eleven loci that pass the genome-wide significance threshold in the correlation to weight or BMI. The correlation was tested both for adipose tissue from 603 individuals and for blood from 745 individuals. For each locus the variant that shows the strongest association with BMI or weight is used, except for 11p14 and 16q12 where two variants are tested. As many expression traits were tested at each locus, results are only shown for correlation tests with P < 0.005. The correlation tested by regressing with the MLR values for each trait on the number of copies of allele tested for each SNP. The effect of age and sex, and for blood, the differential blood cell count, is taken into account by including them as explanatory variables in the regression. Adjusting for weight of the individuals did not lead to any substantial change in the correlation observed. The NM prefixed names in parentheses next to the gene names are NCBI Accession numbers and the number in parentheses for NEGR1 is a GenBank Accession number.

Locus Variant Gene Tissue Effect (%)

P Comment

1p31 rs2568958 A NEGR1 (AI912975) Blood 12.1 4.2×10-13

No other variant with stronger correlation to NEGR1

1q25 rs10913469 C No significant correlation with expression

2p25 rs7561317 G TMEM18 (NM_152834) Adipose 2.7 0.0037 Not significant after adjusting for rs2867137

3q27 rs7647305 C No significant correlation with expression

6p21 rs2844479 T CSNK2B (NM_001320) Adipose 11.9 < 10-60

" " " Blood 11.3 < 10-26

No other variant with stronger correlation to CSNK2B

" " NCR3 (NM_147130) Blood 9.1 1.1×10-6 Not significant after adjusting for rs6916921

" " BAT3 (NM_080703) Adipose -2.3 9.3×10-5

" " " Blood -2.2 0.00079 Not significant after adjusting for rs3115662

11p14 rs6265 G No significant correlation with expression

" rs925946 T LIN7C (NM_018362) Adipose 8.1 2.8×10-16

Less significant after adjusting for rs10835180 (P = 0.006)

" rs925946 T LIN7C (NM_018362) Blood 6.6 5.1×10-8 Less significant after adjusting for rs10835180 (P = 0.015)

12q13 rs7138803 A TMBIM6 (NM_003217) Adipose -1.9 0.0033 rs297924 (r

2 = 0.5 with rs7138803) has stronger correlation

with the expression of TMBIM6

16p11 rs7498665 G TUFM (NM_003321) Blood 14.9 < 10-41

No other variant with stronger correlation to TUFM

" SULT1A2 (NM_001054)

Adipose 25.3 1.8×10-20

" " Blood 7.4 6.8×10-10

No other variant with stronger correlation to SULT1A2

" SULT1A1(NM_001055) Adipose 17.8 2.9×10-16

" " Blood 6.1 1.6×10-6

No other variant with stronger correlation to SULT1A1

" SH2B1 (NM_015503) Adipose -4.0 1.4×10-12

No other variant with stronger correlation to SH2B1

" EIF3C (NM_003752) Adipose 9.1 1.6×10-10

" " Blood 5.8 0.0012 No other variant with stronger correlation to EIF3C

" APOB48R (NM_018690)

Adipose 6.0 8.4×10-7 No other variant with stronger correlation to APOB48R

16q12 rs6499640 A No significant correlation with expression

" rs8050136 A No significant correlation with expression

18q21 rs12970134 A No significant correlation with expression

19q13 rs29941 C KCTD15 (NM_024076) Adipose -3.3 0.0059 Not significant after adjusting for rs287104

43

Supplementary Figures

Supplementary Figure 1: A Q-Q plot of the GWA results. a) A Quantile-Quantile plot of the 305,846 adjusted Chi

2-statistics from a GWA analysis of BMI for the

four groups of European descent (Iceland, The Netherlands, European Americans and DGI) combined (blue dots) and for all five groups combined (red dots). The equiangular line (black line) is included in the plot for reference purpose. The dashed horizontal line indicates the threshold for genome-wide significance assuming a Bonferroni correction for the 305,846 SNPs tested. b) Same as a), except for weight. c) and d) show the corresponding Q-Q plots for BMI and weight, respectively, after excluding 138 SNPs in a 1 Mb region around the FTO gene on chromosome 16.

a)

Chi2 expected

Chi2observed

b)

Chi2 expected

Chi2observed

c)

Chi2 expected

Chi2observed

d)

Chi2 expected

Chi2observed

a)

Chi2 expected

Chi2observed

a)

Chi2 expected

Chi2observed

b)

Chi2 expected

Chi2observed

b)

Chi2 expected

Chi2observed

c)

Chi2 expected

Chi2observed

c)

Chi2 expected

Chi2observed

d)

Chi2 expected

Chi2observed

d)

Chi2 expected

Chi2observed

44

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