GIANT consortium data files

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= [[Main Page|GIANT consortium]] GWAS metadata is available here for download. =
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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.  
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= GIANT Consortium 2010 GWAS Metadata is Available Here for Download =
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We are releasing the summary data from our 2010 meta-analyses of 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. A manuscript describing the rationale for releasing association data but not frequency data is in preparation.
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===2010 Data File Description:===
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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.
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*'''MarkerName''': The [http://www.ncbi.nlm.nih.gov/SNP/ dbSNP] name of the genetic marker
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*'''Allele1''': The first allele, by definition the trait-increasing allele (hg18 + strand)
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*'''Allele2''': The second allele (hg18 + strand)
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*'''Freq.Allele1.HapMapCEU''': The allele frequency of Allele1 in the [http://www.hapmap.org HapMap] CEU population
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*'''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
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*'''N''': Number of observations
== BMI ([[Media:GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.txt.gz|download GZIP]]) ==
== BMI ([[Media:GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.txt.gz|download GZIP]]) ==
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If you use these '''Body Mass Index''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20935630 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 <strong>42</strong>, 937-948.
If you use these '''Body Mass Index''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20935630 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 <strong>42</strong>, 937-948.
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== Height ([[Media:GIANT_HEIGHT_LangoAllen2010_publicrelease_HapMapCeuFreq.txt.gz ‎|download GZIP]]) ==
== Height ([[Media:GIANT_HEIGHT_LangoAllen2010_publicrelease_HapMapCeuFreq.txt.gz ‎|download GZIP]]) ==
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If you use these '''height''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20881960 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 <strong>467</strong>, 832-838.
If you use these '''height''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20881960 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 <strong>467</strong>, 832-838.
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== WHRadjBMI ([[Media:GIANT WHRadjBMI Heid2010 publicrelease HapMapCeuFreq.txt.gz |download GZIP]]) ==
== WHRadjBMI ([[Media:GIANT WHRadjBMI Heid2010 publicrelease HapMapCeuFreq.txt.gz |download GZIP]]) ==
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If you use these '''waist-hip ratio adjusted for BMI''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20935629 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 <strong>42</strong>, 949-960.
If you use these '''waist-hip ratio adjusted for BMI''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=20935629 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 <strong>42</strong>, 949-960.
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= GIANT consortium 2012-2013 GWAS Metadata is Available Here for Download =
 +
 +
===2012-2013 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 [http://www.ncbi.nlm.nih.gov/SNP/ 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.
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*'''Allele2''': The second allele (hg19 + strand)
 +
*'''Freq.Allele1.HapMapCEU''': The allele frequency of Allele1 in the [http://www.hapmap.org HapMap] CEU population
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*'''b''': beta
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*'''SE''': standard error
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*'''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
 +
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==Variability in BMI and Height==
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*[[Media:GIANT_Yang2012Nature_publicrelease_HapMapCeuFreq_BMI.txt.gz|Download BMI GZIP]]
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*[[Media:GIANT_Yang2012Nature_publicrelease_HapMapCeuFreq_Height.txt.gz|Download Height GZIP]]
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If you use these '''Body Mass Index''' or '''Height''' data, please cite: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=22982992 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 <strong>490</strong>, 267-272.
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==Sex Stratified Anthropometrics==
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_BMI_MEN_N.txt|Download BMI Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_BMI_WOMEN_N.txt|Download BMI Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HEIGHT_MEN_N.txt|Download HEIGHT Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HEIGHT_WOMEN_N.txt| Download HEIGHT Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HIP_MEN_N.txt|Download HIP Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HIP_WOMEN_N.txt|Download HIP Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HIPadjBMI_MEN_N.txt|Download HIPadjBMI Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_HIPadjBMI_WOMEN_N.txt|Download HIPadjBMI Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WC_MEN_N.txt|Download WC Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WC_WOMEN_N.txt|Download WC Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WCadjBMI_MEN_N.txt| Download WCadjBMI Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WCadjBMI_WOMEN_N.txt|Download WCadjBMI Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WEIGHT_MEN_N.txt|Download WEIGHT Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WEIGHT_WOMEN_N.txt|Download WEIGHT Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WHR_MEN_N.txt|Download WHR Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WHR_WOMEN_N.txt|Download WHR Women]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WHRadjBMI_MEN_N.txt|Download WHRadjBMI Men]]
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*[[Media:GIANT_Randall2013PlosGenet_stage1_publicrelease_HapMapCeuFreq_WHRadjBMI_WOMEN_N.txt|Download WHRadjBMI Women]]
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If you use these data, please cite: [http://www.ncbi.nlm.nih.gov/pubmed/23754948?dopt=Citation 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 <strong>9</strong>: e1003500.
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==Extremes of Anthropometric Traits==
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*[[Media:GIANT_EXTREME_BMI_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz|Download Extreme BMI Stage 1 GZIP]]
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*[[Media:GIANT_EXTREME_HEIGHT_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz| Download Extreme Height Stage 1 GZIP]]
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*[[Media: GIANT_EXTREME_WHR_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz | Download Extreme WHR Stage 1 GZIP]]
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*[[Media:GIANT_OBESITY_CLASS1_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz | Download Obesity Class 1 Stage 1 GZIP]]
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*[[Media:GIANT_OBESITY_CLASS2_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz | Download Obesity Class 2 Stage1 GZIP]]
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*[[Media:GIANT_OBESITY_CLASS3_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz | Download Obesity Class 3 Stage1 GZIP]]
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*[[Media:GIANT_OVERWEIGHT_Stage1_Berndt2013_publicrelease_HapMapCeuFreq.txt.gz | Download Overweight Stage 1 GZIP]]
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If you use these data, please cite: [http://www.ncbi.nlm.nih.gov/pubmed/23563607?dopt=Citation 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 <strong>45</strong>:501-512.

Latest revision as of 18:41, 10 February 2014

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.

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 2012-2013 GWAS Metadata is Available Here for Download

2012-2013 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.

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.

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