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

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Hindorff, Lucia A., Sethupathy, Praveen, Junkins, Heather A., Ramos, Erin M., Mehta, Jayashri P., Collins, Francis S., Manolio, Teri A.·2009·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.0903103106PMC PMC2687147

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Abstract

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 × 10 −7 ] and 5kb-promoter regions [OR = 2.3 (1.5−3.6), p = 3 × 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 × 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.

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Authors: Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A.
Affiliations: National Institutes of Health (US)
National Human Genome Research Institute (US)
ORCID: Hindorff, Lucia A.
Sethupathy, Praveen
Ramos, Erin M.
Collins, Francis S.
Manolio, Teri A.
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2009-06-09
Volume: 106
Issue: 23
Pages: 9362-9367
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.0903103106
PMC: PMC2687147
OpenAlex: W2117446594
Cited by: 4,013
References: 22
Citations by year: 2026: 42 · 2025: 91 · 2024: 89 · 2023: 102 · 2022: 147 · 2021: 184 · 2020: 176 · 2019: 166 · 2018: 206 · 2017: 223 · 2016: 268 · 2015: 344 · 2014: 438 · 2013: 480 · 2012: 433
FWCI: 205.13
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Human Genome Research Institute
U.S. National Library of Medicine
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords: genome-wide association study, single nucleotide polymorphisms, disease-associated SNPs, SNP-trait association, genome annotation, non-synonymous mutations, promoter, intronic SNPs, intergenic regions, positive selection, common genetic variants, OPAC
MeSH terms: Disease, Humans, Polymorphism, Genetic, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study

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

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