Patterns of Cis Regulatory Variation in Diverse Human Populations
Open accessAbstract
The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs) after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.
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The overall genetic architecture of the CSF pQTLs was similar to findings reported for plasma pQTLs, gene expression QTLs, and a recent study on CSF pQTLs.
“The overall genetic architecture of the CSF pQTLs was similar to findings reported for plasma pQTLs (Sun et al, 2018), gene expression QTLs (Stranger et al, 2012), and a recent study on CSF pQTLs (Yang et al, 2021).”
From The genetic regulation of protein expression in cerebrospinal fluid (2023) · cites this paper as Stranger et al, 2012
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- Authors
- Stranger, B. E., Montgomery, S. B., Dimas, A. S., Parts, L., Stegle, O., Ingle, C. E., Sekowska, M., Smith, G. D., Evans, D., Gutierrez-Arcelus, M., Price, A., Raj, T., Nisbett, J., Nica, A. C., Beazley, C., Durbin, R., Deloukas, P., & Dermitzakis, E. T.
- Affiliations
- Broad Institute (US)
- University of Geneva (CH)
- Wellcome Sanger Institute (GB)
- Max Planck Institute for Developmental Biology (DE)
- University of Bristol (GB)
- Corresponding author
- Dermitzakis, Emmanouil T.
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-04-19
- Volume
- 8
- Issue
- 4
- Pages
- e1002639
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3330104
- OpenAlex
- W2085459418
- Cited by
- 470
- References
- 2
- Citations by year
- 2026: 13 · 2025: 7 · 2024: 16 · 2023: 14 · 2022: 14 · 2021: 21 · 2020: 28 · 2019: 22 · 2018: 21 · 2017: 36 · 2016: 51 · 2015: 60 · 2014: 85 · 2013: 67 · 2012: 13
- FWCI
- 40.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Explore Bristol Research (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Brigham and Women's Hospital
- Wellcome Trust
- Louis-Jeantet Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- National Institutes of Health
- National Institute of Mental Health
- 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 › Forensic and Genetic Research
- Keywords
- cis-regulatory variation, expression quantitative trait loci, genetic differentiation, ancestry, lymphoblastoid cell lines, gene expression variation, functional pathways
- MeSH terms
- Cell Line, Gene Expression Regulation, Genetics, Population, Humans, Regulatory Sequences, Nucleic Acid, Genome, Human, Polymorphism, Single Nucleotide, Transcription Initiation Site, Quantitative Trait Loci, Black People, White People, Asian People, HapMap Project
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