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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

We have developed an online catalog of SNP-trait associations from published genome-wide association studies for use in investigating genomic characteristics of trait/disease-associated SNPs (TASs). Reported TASs were common [median risk allele frequency 36%, interquartile range (IQR) 21%-53%] and were associated with modest effect sizes [median odds ratio (OR) 1.33, IQR 1.20-1.61]. Among 20 genomic annotation sets, reported TASs were significantly overrepresented only in nonsynonymous sites [OR = 3.9 (2.2-7.0), p = 3.5 x 10(-7)] and 5kb-promoter regions [OR = 2.3 (1.5-3.6), p = 3 x 10(-4)] compared to SNPs randomly selected from genotyping arrays. Although 88% of TASs were intronic (45%) or intergenic (43%), TASs were not overrepresented in introns and were significantly depleted in intergenic regions [OR = 0.44 (0.34-0.58), p = 2.0 x 10(-9)]. Only slightly more TASs than expected by chance were predicted to be in regions under positive selection [OR = 1.3 (0.8-2.1), p = 0.2]. This new online resource, together with bioinformatic predictions of the underlying functionality at trait/disease-associated loci, is well-suited to guide future investigations of the role of common variants in complex disease etiology.

Pubmed ID: 19474294


  • Hindorff LA
  • Sethupathy P
  • Junkins HA
  • Ramos EM
  • Mehta JP
  • Collins FS
  • Manolio TA


Proceedings of the National Academy of Sciences of the United States of America

Publication Data

June 9, 2009

Associated Grants

  • Agency: Intramural NIH HHS, Id:

Mesh Terms

  • Disease
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Humans
  • Polymorphism, Genetic
  • Polymorphism, Single Nucleotide