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Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions
Open accessAbstract
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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“Mapping interactions between enhancers and promoters in disease-relevant cells improves the accuracy of the assignment (Grubert et al., 2015; McGeachie et al., 2016; Pomerantz et al., 2009), but this is not always feasible.”
From Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control (2016) · cites this paper as Grubert et al., 2015
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Meta-Analysis of 74,046 Individuals Identifies 11 New Susceptibility Loci for Alzheimer’s Disease
(EADI), E. A. D. I., Lambert, J.-C., (GERAD), G. A. E. R. I. A. D., Alzheimer's Disease Genetic Consortium (ADGC), (CHARGE), C. F. H. A. A. R. I. G. E., Ibrahim-Verbaas, C. A., Harold, D., Naj, A. C., Sims, R., Bellenguez, C., et al. (2013) · Nature Genetics · doi:10.1038/ng.2802 · Cited by 4,336
Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903103106 · Cited by 4,013
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Items 301–339 of 339
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11981370
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11981367
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11981358
Improved chromatin quantitative trait loci mapping with CACTIPreprint
Wang, L., Qi, Z., & Liu, X. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.06.657866
Structural Variants at Intronic CTCF Loop Anchors Drive Differential Exon UsagePreprint
Moskwa, N. L., Kim, M., Syed, S. A., & Lee, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.29.667294 · Cited by 1
A combined genomic arrhythmia propensity score delineates cumulative risk
Monroe, T. O., Puckelwartz, M. J., Pesce, L. L., Kearns, S. D., Page, P., Ibrahim, N., Weber, Z., Ugwor, E. I., Nóbrega, M. A., Kannankeril, P. J., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.102455
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26333222
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.26667909
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.25001748
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.25001607
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750699
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750702
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.26667918
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.26667915
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26333392
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750705
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750696
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11981343
Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616741
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750711
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.26667912
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750693
Gorkin, D. U., Qiu, Y., Hu, M., Fletez‐Brant, K., Liu, T., Schmitt, A. D., Noor, A., Chiou, J., Gaulton, K. J., Sebat, J. L., et al. (2020) · Figshare · doi:10.6084/m9.figshare.11981346
Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616747
Prowse-Wilkins, C., Lopdell, T., Xiang, R., Vander-Jagt, C. J., Littlejohn, M. D., Chamberlain, A. J., & Goddard, M. E. (2023) · Figshare · doi:10.6084/m9.figshare.22616744
Pushkarev, O., van Mierlo, G., Kribelbauer, J. F., Saelens, W., Gardeux, V., & Deplancke, B. (2024) · Figshare · doi:10.6084/m9.figshare.26750708
Pettie, K. P., Mumbach, M. R., Lea, A. J., Ayroles, J. F., Chang, H. Y., Kasowski, M. M., & Fraser, H. B. (2024) · Figshare · doi:10.6084/m9.figshare.26667906
Multivariate genetic architecture of poor sleep quality
Wang, Q., Gao, L., Yang, X., Chen, B., Li, W., & Wang, H. R. (2026) · Frontiers in Neuroscience · doi:10.3389/fnins.2025.1647046
Halu, A., Moll, M. R., Zhang, C., Martini, L., Bakke, P. S., Bowler, R. P., Castaldi, P. J., Cho, M. H., DeMeo, D. L., Glass, K., et al. (2026) · medRxiv · doi:10.64898/2026.01.22.26344654 · Cited by 1
The functional and spatial organization of chromatin during Thymocyte development
Zouari, Y. B. (2018) · theses.fr (ABES) · doi:10.70675/1386d580z2888z41aaz8840z58384a36037b
Analyse à haute résolution de la structure spatiale des chromosomes eucaryotes
Carron, L. (2019) · theses.fr (ABES) · doi:10.70675/54e488fdzb7afz40cazaa57z583979c137f4
Gervásio, I. C., Brito, L. F., Araujo, A. C., Fanalli, S. L., Silva‐Vignato, B., Rocha, A. O., Benfica, L. F., de Oliveira, L. F., Felício, A., Moreira, G. C. M., et al. (2026) · Frontiers in Genetics · doi:10.3389/fgene.2026.1779847
Multivariate genetic architecture of age-related eye disease
Gao, L., Wang, Q., & Zhu, C. (2026) · PLoS ONE · doi:10.1371/journal.pone.0349199
Exploring the oasis of plant genomes: From genetic variations to function and beyond
Han, X., Zong, Z., Ning, W., Zhang, Y., Tan, Z., Liu, Y., Song, Y., Long, Q., Xiang, Y., Lu, S., et al. (2026) · Molecular Plant · doi:10.1016/j.molp.2026.05.014
Dashtiahangar, M., & Siggers, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.20.726379
Muhammad, F., Asselstine, V., Baes, C. F., Miglior, F., Schenkel, F. S., & Cánovas, Á. (2026) · Journal of Dairy Science · doi:10.3168/jds.2025-28092
Zhao, M., Li, A., Zhang, K., Wang, W., Zhang, G., & Li, L. (2026) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2026.101913
Banno, S., Sanosaka, T., Tomooka, R., Mizota, N., Tokunaga, A., Okano, H., & Kohyama, J. (2026) · iScience · doi:10.1016/j.isci.2026.117332
Metadata
- 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
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-08
- Volume
- 162
- Issue
- 5
- Pages
- 1051-1065
- ISSN
- 0092-8674 (ISSN-L)
- 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
- 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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