GIANT consortium data files
We are releasing the summary data from our 2010-2013 meta-analyses of Genome-wide Association (GWA) data, 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.
Contents
GIANT Consortium 2010 GWAS Metadata is Available Here for Download
2010 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. SNPs where N < 50% of the maximum have been excluded.
- MarkerName: The dbSNP name of the genetic marker
- Allele1: The first allele, by definition the trait-increasing allele (hg18 + strand)
- Allele2: The second allele (hg18 + strand)
- Freq.Allele1.HapMapCEU: The allele frequency of Allele1 in the HapMap CEU population
- P: P value after meta-analysis using regression coefficients (beta and standard error), and after correction for inflation of test statistics using genomic control both at the individual study level and again after meta-analysis
- N: Number of observations
BMI (download GZIP)
MD5 (GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.txt -- 79 MB; 2,471,517 lines) = 38c836542807a3830101bcf48bb34472
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.
Height (download GZIP)
MD5 (GIANT_HEIGHT_LangoAllen2010_publicrelease_HapMapCeuFreq.txt -- 82 MB; 2,469,636 lines) = b51b4c4ff1f03bd33c4b2dfd6b10cb82
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.
WHRadjBMI (download GZIP)
MD5 (GIANT_WHRadjBMI_Heid2010_publicrelease_HapMapCeuFreq.txt -- 75 MB; 2,483,326 lines) = 8f7e2ca61c33a120db9e7bfe51e3c053
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.
GIANT consortium 2012-2014 GWAS Metadata is Available Here for Download
2012-2014 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.
- MarkerName: The dbSNP name of the genetic marker
- Allele1: The first allele (hg19 + strand). Where the regression coefficients (betas) are provided, the first allele is the effect allele. Where betas are not provided (typically the 2010 data), the first allele is the trait-increasing allele.
- Allele2: The second allele (hg19 + strand)
- Freq.Allele1.HapMapCEU: The allele frequency of Allele1 in the HapMap CEU population
- b: beta
- SE: standard error
- p: p-value after meta-analysis using regression coefficients (beta and standard error), and after correction for inflation of test statistics using genomic control both at the individual study level and again after meta-analysis
- N: Number of observations
For the Height DEPICT Gene Set Enrichment Analysis file, the columns are as follows:
- A: the ID of the predefined gene set (before reconstitution by DEPICT);
- B: the name of the gene set;
- C: the DEPICT P-value for enrichment;
- D: the false discovery rate for enrichment;
- E: the genes in the gene set that overlap height-associated loci
GWAS Anthropometric 2014 BMI
If you use these BMI data, please cite:
GWAS Anthropometric 2014 Height
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 (2014). Nature Genetics.
Variability in BMI and Height
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
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
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.
