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Currin KW, Erdos MR, Narisu N, Rai V, Vadlamudi S, Perrin HJ, Idol JR, Yan T, Albanus RD, Broadaway KA, Etheridge AS, Bonnycastle LL, Orchard P, Didion JP, Chaudhry AS, Innocenti F, Schuetz EG, Scott LJ, Parker SCJ, Collins FS, Mohlke KL. Genetic effects on liver chromatin accessibility identify disease regulatory variants. Am J Hum Genet 2021; 108:1169-1189. [PMID: 34038741 PMCID: PMC8323023 DOI: 10.1016/j.ajhg.2021.05.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 05/04/2021] [Indexed: 02/02/2023] Open
Abstract
Identifying the molecular mechanisms by which genome-wide association study (GWAS) loci influence traits remains challenging. Chromatin accessibility quantitative trait loci (caQTLs) help identify GWAS loci that may alter GWAS traits by modulating chromatin structure, but caQTLs have been identified in a limited set of human tissues. Here we mapped caQTLs in human liver tissue in 20 liver samples and identified 3,123 caQTLs. The caQTL variants are enriched in liver tissue promoter and enhancer states and frequently disrupt binding motifs of transcription factors expressed in liver. We predicted target genes for 861 caQTL peaks using proximity, chromatin interactions, correlation with promoter accessibility or gene expression, and colocalization with expression QTLs. Using GWAS signals for 19 liver function and/or cardiometabolic traits, we identified 110 colocalized caQTLs and GWAS signals, 56 of which contained a predicted caPeak target gene. At the LITAF LDL-cholesterol GWAS locus, we validated that a caQTL variant showed allelic differences in protein binding and transcriptional activity. These caQTLs contribute to the epigenomic characterization of human liver and help identify molecular mechanisms and genes at GWAS loci.
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Affiliation(s)
- Kevin W Currin
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Rai
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Hannah J Perrin
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jacqueline R Idol
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tingfen Yan
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - K Alaine Broadaway
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Amy S Etheridge
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lori L Bonnycastle
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Orchard
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - John P Didion
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarjit S Chaudhry
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Federico Innocenti
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erin G Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
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