Properties of structural variants and short tandem repeats associated with gene expression and complex traits
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Published:2020-06-10
Issue:1
Volume:11
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Jakubosky David, D’Antonio MatteoORCID, Bonder Marc Jan, Smail Craig, Donovan Margaret K. R., Young Greenwald William W., Matsui Hiroko, Bonder Marc J., Cai Na, Carcamo-Orive Ivan, D’Antonio Matteo, Frazer Kelly A., Young Greenwald William W., Jakubosky David, Knowles Joshua W., Matsui Hiroko, McCarthy Davis J., Mirauta Bogdan A., Montgomery Stephen B., Quertermous Thomas, Seaton Daniel D., Smail Craig, Smith Erin N., Stegle Oliver, D’Antonio-Chronowska Agnieszka, Stegle Oliver, Smith Erin N., Montgomery Stephen B.ORCID, DeBoever ChristopherORCID, Frazer Kelly A.ORCID,
Abstract
AbstractStructural variants (SVs) and short tandem repeats (STRs) comprise a broad group of diverse DNA variants which vastly differ in their sizes and distributions across the genome. Here, we identify genomic features of SV classes and STRs that are associated with gene expression and complex traits, including their locations relative to eGenes, likelihood of being associated with multiple eGenes, associated eGene types (e.g., coding, noncoding, level of evolutionary constraint), effect sizes, linkage disequilibrium with tagging single nucleotide variants used in GWAS, and likelihood of being associated with GWAS traits. We identify a set of high-impact SVs/STRs associated with the expression of three or more eGenes via chromatin loops and show that they are highly enriched for being associated with GWAS traits. Our study provides insights into the genomic properties of structural variant classes and short tandem repeats that are associated with gene expression and human traits.
Funder
California Institute for Regenerative Medicine U.S. Department of Health & Human Services | National Institutes of Health U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry
Reference52 articles.
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