Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation
Open accessAbstract
We apply integrative approaches to expression quantitative loci (eQTLs) from 44 tissues from the Genotype-Tissue Expression project and genome-wide association study data. About 60% of known trait-associated loci are in linkage disequilibrium with a cis-eQTL, over half of which were not found in previous large-scale whole blood studies. Applying polygenic analyses to metabolic, cardiovascular, anthropometric, autoimmune, and neurodegenerative traits, we find that eQTLs are significantly enriched for trait associations in relevant pathogenic tissues and explain a substantial proportion of the heritability (40-80%). For most traits, tissue-shared eQTLs underlie a greater proportion of trait associations, although tissue-specific eQTLs have a greater contribution to some traits, such as blood pressure. By integrating information from biological pathways with eQTL target genes and applying a gene-based approach, we validate previously implicated causal genes and pathways, and propose new variant and gene associations for several complex traits, which we replicate in the UK BioBank and BioVU.
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In parallel, efforts to connect trait-associated regulatory variants to the genes and processes they regulate in disease-relevant cell types have been scaled.
“In parallel, there has been a scaling of efforts to connect trait-associated regulatory variants to the genes and processes that they regulate in cell types relevant to the disease of interest110,111.”
From A brief history of human disease genetics (2020) · cites this paper as [110]
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- Authors
- GTEx Consortium, Gamazon, E. R., Segrè, A. V., van de Bunt, M., Wen, X., Xi, H. S., Hormozdiari, F., Ongen, H., Konkashbaev, A., Derks, E. M., Aguet, F., Quan, J., Nicolae, D. L., Eskin, E., Kellis, M., Getz, G., McCarthy, M. I., Dermitzakis, E. T., Cox, N. J., & Ardlie, K. G.
- Affiliations
- University of Cambridge (GB)
- Broad Institute (US)
- University of Michigan (US)
- Pfizer (United States) (US)
- Harvard University (US)
- University of Geneva (CH)
- Vanderbilt University Medical Center (US)
- QIMR Berghofer Medical Research Institute (AU)
- University of Chicago (US)
- University of California, Los Angeles (US)
- Centre for Human Genetics (GB)
- Corresponding author
- Gamazon, Eric R.
- Segrè, Ayellet V.
- ORCID
- Venue
- Nature Genetics
- Published
- 2018-06-28
- Volume
- 50
- Issue
- 7
- Pages
- 956-967
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC6248311
- OpenAlex
- W2811205482
- Cited by
- 412
- References
- 58
- Citations by year
- 2026: 22 · 2025: 25 · 2024: 37 · 2023: 49 · 2022: 47 · 2021: 74 · 2020: 81 · 2019: 68 · 2018: 9
- FWCI
- 8.15
- Type
- journal article
- Language
- en
- Open access
- green
- pure.amsterdamumc.nl
- Licence
- other-oa
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (098381, 090532, 203141, 106130/Z/14/Z, 106130)
- National Institutes of Health (UL1TR000445)
- Medical Research Council (MC_PC_17228)
- National Heart, Lung, and Blood Institute (U19HL065962)
- National Institute of Mental Health (R01MH101814, R01MH090937, R01MH101782, R01MH101820, R01MH113362)
- National Human Genome Research Institute (U01HG007610, R01HG007022, U01HG006378, U01HG004798, U01HG009088)
- National Cancer Institute (R01CA157823)
- National Institute of General Medical Sciences (P50GM115305, RC2GM092618)
- National Institute of Diabetes and Digestive and Kidney Diseases (U01DK105535)
- National Institute of Neurological Disorders and Stroke (R01NS032830)
- National Institute of Environmental Health Sciences (R01ES022282)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR042742)
- National Center for Research Resources (S10RR025141, UL1RR024975)
- National Center for Advancing Translational Sciences
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD074711)
- 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
- expression quantitative trait loci, cis-eQTL, tissue-specific gene regulation, polygenic heritability, complex traits, disease-associated loci, linkage disequilibrium, blood pressure, metabolic phenotypes, cardiovascular traits, anthropometric traits, pathway enrichment, causal genes, GTEx, UK Biobank, BioVU
- MeSH terms
- Disease, Gene Expression Regulation, Genotype, Humans, Phenotype, Gene Expression, Quantitative Trait, Heritable, Polymorphism, Single Nucleotide, Gene Expression Profiling, Quantitative Trait Loci, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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