GIANT consortium data files

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We are releasing the summary data from our meta-analyses of Genome-Wide Association Studies (GWAS) in order to enable other researchers to examine particular variants or loci for their evidence of association with anthropometric traits. The files include p-values and direction of effect at over 2 million directly genotyped or imputed single nucleotide polymorphisms (SNPs). To prevent the possibility of identification of individuals from these summary results, we are not releasing allele frequency data from our samples.

2018 WHR Exome for Public Release

File Name Structure: PublicRelease.WHRadjBMI.*.*.*.txt.gz

Abbreviations in filenames:

C-Combined Sexes

M-Men

W-Women

All- All Ancestries

Eur- European descent only

Add- Additive genetic model

Rec- Recessive genetic model


File headers:

1. snpname - dbSNP rsID

2. chr - chromosome

3. pos - position

4. markername - chr:pos

5. ref - reference allele (hg19 + strand)

6. alt - alternate allele (hg19 + strand)

7. beta - beta

8. se - standard error

9. pvalue - P value

10. n - sample size

11. gmaf/eur_maf - alternate allele frequency in 1000 Genome Combined/European Ancestries

12. exac_maf/exac_nfe_maf -alternate allele frequency in ExAC Combined/Non-Finnish European Ancestries


2018 Exome Array Summary Statistics

WHR Exome Array Summary Statistics

Download WHR Exome Array Data File Description


WHR Data Files:


BMI Exome Array Summary Statistics

BMI Data Files:

If you use these data, please cite: Turcot V, Lu Y, Highland HM, Schurmann C, Justice AE, Fine RS, Bradfield JP, Esko T, Giri A, Graff M, Guo X, Hendricks AE, et al. (2018). Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity. Nat Genet. 2018 Jan;50(1):26-41. doi: 10.1038/s41588-017-0011-x. Epub 2017 Dec 22. PMID: 29273807


Height Exome Array Summary Statistics

Download Height Exome Array Data File Description


Height Data Files:


2018 GIANT and UK BioBank Meta-analysis

WHR GIANT and UK BioBank Meta-analysis Summary Statistics

WHR UK BioBank Meta Analysis for Public Release:

Access link for GWAS data for all ~27M sites: https://zenodo.org/record/1251813#.XCLJ7vZKhE4 DOI (10.5281/zenodo.1251813)


BMI and Height GIANT and UK BioBank Meta-analysis Summary Statistics

Please Note: We discovered that the BMI files for the meta-analysis of UK Biobank and GIANT originally uploaded did not reflect the full sample size and have now been corrected. If you downloaded these files prior to June 25, 2018, please download them again. Our apologies for any inconvenience.

If you use these data, please cite: Yengo L, Sidorenko J, Kemper KE, Zheng Z, Wood AR, Weedon MN, Frayling TM, Hirschhorn J, Yang J, Visscher PM, GIANT Consortium. (2018). Meta-analysis of genome-wide association studies for height and body mass index in ~700,000 individuals of European ancestry. Biorxiv.


2017 Gene x Environment Summary Statistics

Summary Statistics for Models Adjusting for Smoking Status

Download Models Adjusting for Smoking Status Data File Description


BMI:


WCadjBMI:


WHRadjBMI:


Summary Statistics for Smoking Stratified Models

Download Smoking Stratified Models Data File Description


BMI:


WCadjBMI:


WHRadjBMI:


Summary Statistics for Gene x Physical Activity

Download Gene x Physical Activity Data File Description


BMI Data Files:


WAISTadjBMI Data Files:


WHRadjBMI Data Files:


GIANT Consortium 2016 Exome Array Data is Available Here for Download

2016 Data File Description:

Each file consists of the following information for each SNP and its association to the specified trait based on meta-analysis in the respective publication. Significant digits for the p values, betas and standard errors are limited to two digits to further limit the possibility of identifiability.

  • Column 1. CHR: chromosome
  • Column 2. POS: position of the variant (hg19)
  • Column 3. REF: reference allele (hg19 + strand)
  • Column 4. ALT: alternate allele (hg19 + strand)
  • Column 5. SNPNAME: dbSNP name of the genetic marker
  • Column 6. (one among these)
    • GMAF: Non-reference allele and frequency of existing variant in 1000 Genomes
    • AFR_MAF: Non-reference allele and frequency of existing variant in 1000 Genomes combined African population
    • AMR_MAF: Non-reference allele and frequency of existing variant in 1000 Genomes combined American population
    • EUR_MAF: Non-reference allele and frequency of existing variant in 1000 Genomes combined European population
    • EAS_MAF: Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population
    • SAS_MAF: Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population
  • Column 7. (one among these)
    • ExAC_MAF: Frequency of existing variant in ExAC combined population
    • ExAC_AFR_MAF: Frequency of existing variant in ExAC African/American population
    • ExAC_AMR_MAF: Frequency of existing variant in ExAC American population
    • ExAC_EAS_MAF: Frequency of existing variant in ExAC East Asian population
    • ExAC_NFE_MAF: Frequency of existing variant in ExAC Non-Finnish European population
    • ExAC_SAS_MAF: Frequency of existing variant in ExAC South Asian population
  • Column 8. beta: beta
  • Column 9. se: standard error
  • Column 10. Pvalue: p-value after meta-analysis using regression coefficients (beta and standard error)


GIANT Consortium 2012-2015 GWAS Summary Statistics

Download 2012-2015 GIANT GWAS Summary Statistics Data File Description


GWAS Age-/Sex-Stratified 2015 BMI and WHR Summary Statistics

If you use these data, please cite: Winkler TW*, Justice AE*, Graff M*, Barata L*, Feitosa MF, Chu S, Czajkowski J, Esko T, Fall T, Kilpeläinen TO, Lu Y, Mägi R et al. (2015). The influence of age and sex on genetic associations with adult body size and shape: a large-scale genome-wide interaction study. PLoS Genetics. In press.


GWAS Anthropometric 2015 BMI Summary Statistics

If you use these BMI data, please cite: Locke AE, Kahali B, Berndt SI, Justice AE, Pers TH, Day FR, Powell C, Vedantam S, Buchkovich ML, Yang J, Croteau-Chonka DC, Esko T et al. (2015). Genetic studies of body mass index yield new insights for obesity biology. Nature 518, 197-206.


GWAS Anthropometric 2015 Waist Summary Statistics

HIP:

HIPadjBMI:

WC:

WCadjBMI:

WHR:

WHRadjBMI:

If you use these Waist data, please cite: Shungin D, Winkler TW, Croteau-Chonka DC, Ferreira T, Locke AE, Magi R, Strawbridge R, Pers TH, Fischer K, Justice AE, Workalemahu T, Wu JM, et al. (2015). New genetic loci link adipose and insulin biology to body fat distribution. Nature 518: 187-196.


GWAS Anthropometric 2014 Height Summary Statistics

If you use these Height data, please cite: Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S et al. (2014). Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics 11:1173-86.


Variability in BMI and Height Summary Statistics

If you use these Body Mass Index or Height data, please cite: Yang J, Loos RJ, Powell JE, Medland SE, Speliotes EK, Chasman DI, Rose LM, Thorleifsson G, Steinthorsdottir V, Mägi R, et al. (2012). FTO genotype is associated with phenotypic variability of body mass index. Nature 490:267-272.


Sex Stratified Anthropometrics Summary Statistics

If you use these data, please cite: Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S, et al. (2013). Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet 9: e1003500.


Extremes of Anthropometric Traits Summary Statistics

If you use these data, please cite: Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, et al. (2013). Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics 45:501-512.

GIANT Consortium 2010 GWAS Summary Statistics

Download GIANT Consortium 2010 GWAS Summary Statistics Data File Description


GWAS 2010 BMI Summary Statistics

If you use these Body Mass Index data, please cite: Speliotes, E.K., Willer, C.J., Berndt, S.I., Monda, K.L., Thorleifsson, G., Jackson, A.U., Allen, H.L., Lindgren, C.M., Luan, J., Magi, R., et al. (2010). Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42, 937-948.


GWAS 2010 Height Summary Statistics

If you use these Height data, please cite: Lango Allen, H., Estrada, K., Lettre, G., Berndt, S.I., Weedon, M.N., Rivadeneira, F., Willer, C.J., Jackson, A.U., Vedantam, S., Raychaudhuri, S., et al. (2010). Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832-838.


GWAS 2010 WHRadjBMI Summary Statistics

If you use these waist-hip ratio adjusted for BMI data, please cite: Heid, I.M., Jackson, A.U., Randall, J.C., Winkler, T.W., Qi, L., Steinthorsdottir, V., Thorleifsson, G., Zillikens, M.C., Speliotes, E.K., Magi, R., et al. (2010). Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet 42, 949-960.

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