Properties of structural variants and short tandem repeats associated with gene expression and complex traits
Open Access
- 10 June 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 11 (1), 1-15
- https://doi.org/10.1038/s41467-020-16482-4
Abstract
Structural 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.Funding Information
- California Institute for Regenerative Medicine (GC1R-06673)
- U.S. Department of Health & Human Services | National Institutes of Health (HG008118, HL107442, DK105541, DK112155, U01HG009431)
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- 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 (T15LM011271)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (F31HL142151)
- U.S. Department of Health & Human Services | National Institutes of Health
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