Cited by 339Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

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Grubert, Fabian, Zaugg, Judith B., Kasowski, Maya, Ursu, Oana, Spacek, Damek V., Martin, Alicia R., Greenside, Peyton, Srivas, Rohith, Phanstiel, Doug H., Pekowska, Aleksandra, Heidari, Nastaran, Euskirchen, Ghia, Huber, Wolfgang, Pritchard, Jonathan K., Bustamante, Carlos D., Steinmetz, Lars M., Kundaje, Anshul, Snyder, Michael·2015·Cell

DOI 10.1016/j.cell.2015.07.048PMC PMC4556133

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Abstract

Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.

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Authors: Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., Heidari, N., Euskirchen, G., Huber, W., Pritchard, J. K., Bustamante, C. D., Steinmetz, L. M., Kundaje, A., & Snyder, M.
Affiliations: Stanford Medicine (US)
European Molecular Biology Laboratory (DE)
Howard Hughes Medical Institute (US)
Corresponding author: Snyder, Michael
ORCID: Zaugg, Judith B.
Kasowski, Maya
Ursu, Oana
Martin, Alicia R.
Srivas, Rohith
Huber, Wolfgang
Pritchard, Jonathan K.
Bustamante, Carlos D.
Steinmetz, Lars M.
Kundaje, Anshul
Snyder, Michael
Venue: Cell
Publisher: Elsevier BV
Published: 2015-08
Volume: 162
Issue: 5
Pages: 1051-1065
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2015.07.048
PMC: PMC4556133
OpenAlex: W2112673809
Cited by: 319
References: 56
Citations by year: 2026: 12 · 2025: 13 · 2024: 18 · 2023: 21 · 2022: 25 · 2021: 23 · 2020: 37 · 2019: 39 · 2018: 48 · 2017: 39 · 2016: 36 · 2015: 8
FWCI: 18.95
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 392 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: Howard Hughes Medical Institute
National Heart, Lung, and Blood Institute (R01HL122887, U01HL107393)
National Human Genome Research Institute (U41HG007000, U54HG006996, R00HG008662, K99HG008662, U41-HG007000-02S1, P50HG007735, U01HG007919, P01HG000205, T32HG000044)
National Institute of General Medical Sciences (T32GM007790, T32GM007205)
National Institute of Environmental Health Sciences (R01ES025009)
U.S. National Library of Medicine (LM 07033, T15LM007033)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
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
Keywords: histone modifications, chromatin state, long-range chromatin interactions, topologically associating domains, non-coding variants, gene expression regulation, lymphoblastoid cell lines, Hi-C, ChIA-PET
MeSH terms: Cell Line, Chromatin, Chromosomes, Human, Female, Histones, Humans, Lymphocytes, Male, Cohort Studies, Human Genome Project, Quantitative Trait Loci, Regulatory Elements, Transcriptional, Gene Regulatory Networks, Genome-Wide Association Study

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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

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