GWAS Catalog Track Settings
 
NHGRI Catalog of Published Genome-Wide Association Studies   (All Phenotype and Literature tracks)

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Data last updated: 2014-06-10

Description

This track displays single nucleotide polymorphisms (SNPs) identified by published Genome-Wide Association Studies (GWAS), collected in the Catalog of Published Genome-Wide Association Studies at the National Human Genome Research Institute (NHGRI). Some abbreviations are used above.

From http://www.genome.gov/gwastudies/:

The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports and occasional comparisons with an existing database of GWAS literature (HuGE Navigator).

Methods

From http://www.genome.gov/gwastudies/:

SNP-trait associations listed here are limited to those with p-values < 1.0 x 10-5 (see full methods for additional details). Multipliers of powers of 10 in p-values are rounded to the nearest single digit; odds ratios and allele frequencies are rounded to two decimals. Standard errors are converted to 95 percent confidence intervals where applicable. Allele frequencies, p-values and odds ratios derived from the largest sample size, typically a combined analysis (initial plus replication studies), are recorded below if reported; otherwise, statistics from the initial study sample are recorded. For quantitative traits, information on % variance explained, SD increment, or unit difference is reported where available. Odds ratios (OR) < 1 in the original paper are converted to OR > 1 for the alternate allele. Where results from multiple genetic models are available, we prioritized effect sizes (ORs or beta-coefficients) as follows: 1) genotypic model, per-allele estimate; 2) genotypic model, heterozygote estimate; 3) allelic model, allelic estimate.

Gene regions corresponding to SNPs were identified from the UCSC Genome Browser. Gene names and risk alleles are those reported by the authors in the original paper. Only one SNP within a gene or region of high linkage disequilibrium is recorded unless there was evidence of independent association.

Occasionally, the term "pending" is used to denote one or more studies that were identified as an eligible GWAS, but for which SNP information has not yet been extracted; studies of CNVs are also noted as pending.

References

Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PNAS. 2009 Jun 9;106(23):9362-7.