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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Open accessAbstract
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers. Promoter interactomes reflect lineage relationships of the hematopoietic tree, consistent with dynamic remodeling of nuclear architecture during differentiation. Interacting regions are enriched in genetic variants linked with altered expression of genes they contact, highlighting their functional role. We exploit this rich resource to connect non-coding disease variants to putative target promoters, prioritizing thousands of disease-candidate genes and implicating disease pathways. Our results demonstrate the power of primary cell promoter interactomes to reveal insights into genomic regulatory mechanisms underlying common diseases.
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“Capture Hi-C analyses in multiple cell types consistently detect enhancer–promoter contacts that cross TAD boundaries [141, 243].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“PCHi-C showed that active promoters contacted a median of two active enhancers in human primary blood cells [243].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“A similar network of contacts is also detectable between the active promoters of multiple histone genes in many mammalian cell types [243, 279, 471, 492].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“the number of enhancers correlates with the expression level of a gene across cell types [243, 278, 279, 349].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“These enrichment methods have detected multitudes of enhancer–promoter loops in many human and mouse cell types [243, 286–291].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“Enhancers vastly outnumber promoters in human and mouse genomes [131], and consistently promoters often contact more than one enhancer in the same cell type [141, 243, 278, 279].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [243]
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“disease-associated SNPs in non-coding areas of the genome influence genes associated with diseases including Alzheimer’s Disease (AD)”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [50]
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Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationAn integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationHeinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
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
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
The Reactome pathway Knowledgebase
Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605
Genetic studies of body mass index yield new insights for obesity biology
Study, T. L. C., Locke, A. E., The ADIPOGen Consortium, The AGEN-BMI Working Group, The CARDIOGRAMplusC4D Consortium, The CKDGen Consortium, The, G. L. G. C., The, I. C. B. P., The MAGIC Investigators, The MuTHER Consortium, et al. (2015) · Nature · doi:10.1038/nature14177 · Cited by 4,534
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Võsa, U., Claringbould, A., Westra, H.-J., Bonder, M. J., Deelen, P., Zeng, B., Kirsten, H., Saha, A., Kreuzhuber, R., Yazar, S., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00913-z · Cited by 2,607
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Sun, B. B., Maranville, J. C., Peters, J. E., Stacey, D., Staley, J. R., Blackshaw, J., Burgess, S., Jiang, T., Paige, E., Surendran, P., et al. (2018) · Nature · doi:10.1038/s41586-018-0175-2 · Cited by 2,268
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Bonev, B., Mendelson Cohen, N., Szabo, Q., Fritsch, L., Papadopoulos, G. L., Lubling, Y., Xu, X., Lv, X., Hugnot, J.-P., Tanay, A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.043 · Cited by 1,338
Complex genetic signatures in immune cells underlie autoimmunity and inform therapy
Orrù, V., Steri, M., Sidore, C., Marongiu, M., Serra, V., Olla, S., Sole, G., Lai, S., Dei, M., Mulas, A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0684-4 · Cited by 1,246
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Corces, M. R., Granja, J. M., Shams, S., Louie, B. H., Seoane, J. A., Zhou, W., Silva, T. C., Groeneveld, C., Wong, C. K., Cho, S. W., et al. (2018) · Science · doi:10.1126/science.aav1898 · Cited by 1,230
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Self-citationMonaco, G., Lee, B., Xu, W., Mustafah, S., Hwang, Y. Y., Carré, C., Burdin, N., Visan, L., Ceccarelli, M., Poidinger, M., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.01.041 · Cited by 958
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Robertson, C. C., Inshaw, J. R. J., Onengut-Gumuscu, S., Chen, W.-M., Santa Cruz, D. F., Yang, H., Cutler, A. J., Crouch, D. J. M., Farber, E., Bridges, S. L., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00880-5 · Cited by 302
Self-citationMiguel-Escalada, I., Bonàs‐Guarch, S., Cebola, I., Ponsa-Cobas, J., Mendieta-Esteban, J., Atla, G., Javierre, B. M., Rolando, D., Farabella, I., Morgan, C. C., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0457-0 · Cited by 269
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Lyons, P., Peters, J. E., Alberici, F., Liley, J., Coulson, R., Astle, W. J., Baldini, C., Bonatti, F., Cid, M. C., Elding, H., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12515-9 · Cited by 287
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Malaria Genomic Epidemiology Network, Band, G., Le, S. Q., Clarke, G. M., Kivinen, K., Hubbart, C., Jeffreys, A. E., Rowlands, K., Leffler, E. M., Jallow, M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-13480-z · Cited by 182
López‐Isac, E., Acosta‐Herrera, M., Kerick, M., Assassi, S., Satpathy, A. T., Granja, J. M., Mumbach, M. R., Beretta, L., Simeón‐Aznar, C. P., Carreira, P. E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12760-y · Cited by 188
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Gazal, S., Weissbrod, O., Hormozdiari, F., Dey, K. K., Nasser, J., Jagadeesh, K. A., Weiner, D. J., Shi, H., Fulco, C. P., O’Connor, L. J., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01087-y · Cited by 181
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Lu, L., Liu, X., Huang, W., Giusti‐Rodríguez, P., Cui, J., Zhang, S., Xu, W., Wen, Z., Ma, S., Rosen, J. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.007 · Cited by 175
Thiecke, M. J., Wutz, G., Muhar, M., Tang, W., Bevan, S., Malysheva, V., Stocsits, R., Neumann, T., Zuber, J., Fraser, P., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107929 · Cited by 177
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Bertero, A., Fields, P., Ramani, V., Bonora, G., Yardımcı, G. G., Reinecke, H., Pabon, L., Noble, W. S., Shendure, J., & Murry, C. E. (2019) · Nature Communications · doi:10.1038/s41467-019-09483-5 · Cited by 168
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Waage, J., collaborators, A., Standl, M., Curtin, J. A., Jessen, L. E., Thorsen, J., Tian, C., Schoettler, N., Flores, C., Abdellaoui, A., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0157-1 · Cited by 172
Hawe, J. S., Wilson, R., Schmid, K., Zhou, L., Lakshmanan, L. N., Lehne, B. C., Kühnel, B., Scott, W. R., Wielscher, M., Yew, Y. W., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-00969-x · Cited by 170
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Stankey, C. T., Bourges, C., Haag, L.-M., Turner‐Stokes, T., Piedade, A. P., Palmer-Jones, C., Papa, I., dos Santos, M. S., Zhang, Q., Cameron, A. J., et al. (2024) · Nature · doi:10.1038/s41586-024-07501-1 · Cited by 163
Self-citationChesi, A., Wagley, Y., Johnson, M. E., Manduchi, E., Su, C., Lu, S., Leonard, M. E., Hodge, K. M., Pippin, J. A., Hankenson, K. D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09302-x · Cited by 158
Gazal, S., Loh, P.-R., Finucane, H. K., Ganna, A., Schoech, A., Sunyaev, S., & Price, A. L. (2018) · Nature Genetics · doi:10.1038/s41588-018-0231-8 · Cited by 154
Cell-type-specific 3D epigenomes in the developing human cortex
Song, M., Pebworth, M.-P., Yang, X., Abnousi, A., Fan, C., Wen, J., Rosen, J. D., Choudhary, M. N. K., Cui, X., Jones, I. R., et al. (2020) · Nature · doi:10.1038/s41586-020-2825-4 · Cited by 145
Li, B., & Ritchie, M. D. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.713230 · Cited by 155
Westra, H.-J., Martínez‐Bonet, M., Önengüt-Gümüşcü, S., Lee, A., Luo, Y., Teslovich, N. C., Worthington, J., Martin, J. J., Huizinga, T. W. J., Klareskog, L., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0216-7 · Cited by 147
Self-citationA promoter interaction map for cardiovascular disease genetics
Montefiori, L. E., Sobreira, D. R., Sakabe, N. J., Aneas, I., Joslin, A. C., Hansen, G. T., Bozek, G., Moskowitz, I. P., McNally, E. M., & Nóbrega, M. A. (2018) · eLife · doi:10.7554/elife.35788 · Cited by 145
Vilarrasa‐Blasi, R., Soler-Vila, P., Verdaguer-Dot, N., Russiñol, N., Stefano, M. D., Chapaprieta, V., Clot, G., Farabella, I., Cuscó, P., Kulis, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20849-y · Cited by 146
Self-citationInferring Interaction Networks From Multi-Omics Data
Hawe, J. S., Theis, F. J., & Heinig, M. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00535 · Cited by 148
Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells
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Grassi, L., Pourfarzad, F., Ullrich, S., Merkel, A., Were, F., Pau, E. C. D. S., Yi, G., Hiemstra, I. H., Tool, A. T. J., Mul, E. P. J., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.018 · Cited by 142
Self-citationHuang, Y., An, J., Sircar, S., Bergis, C., Lopes, C. D., He, X., Costa, B. D., Tan, F., Bazin, J., Antúnez-Sánchez, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36227-3 · Cited by 141
Deniz, Ö., Ahmed, M., Todd, C. D., Rio‐Machín, A., Dawson, M. A., & Branco, M. R. (2020) · Nature Communications · doi:10.1038/s41467-020-17206-4 · Cited by 145
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Li, W., Wong, W. H., & Jiang, R. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz167 · Cited by 133
McKeown, M. R., Corces, M. R., Eaton, M. L., Fiore, C., Lee, E., Lopez, J. T., Chen, M. W., Smith, D., Chan, S. M., Koenig, J. L., et al. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-17-0399 · Cited by 134
Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development
Alavattam, K. G., Maezawa, S., Sakashita, A., Khoury, H., Barski, A., Kaplan, N., & Namekawa, S. H. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0189-y · Cited by 141
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Chen, L., Morris, D. L., & Vyse, T. J. (2017) · Current Opinion in Rheumatology · doi:10.1097/bor.0000000000000411 · Cited by 132
The three-dimensional genome: regulating gene expression during pluripotency and development
Andrey, G., & Mundlos, S. (2017) · Development · doi:10.1242/dev.148304 · Cited by 134
A practical view of fine-mapping and gene prioritization in the post-genome-wide association era
Broekema, R., Bakker, O. B., & Jonkers, I. H. (2020) · Open Biology · doi:10.1098/rsob.190221 · Cited by 141
Dileep, V., Boix, C. A., Mathys, H., Marco, A., Welch, G. M., Meharena, H. S., Loon, A., Jeloka, R., Peng, Z., Bennett, D. A., et al. (2023) · Cell · doi:10.1016/j.cell.2023.08.038 · Cited by 130
Capture Hi-C identifies putative target genes at 33 breast cancer risk loci
Baxter, J. S., Leavy, O. C., Dryden, N. H., Maguire, S. L., Johnson, N., Fedele, V., Simigdala, N., Martin, L., Andrews, S., Wingett, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03411-9 · Cited by 123
Self-citationGutiérrez‐Arcelus, M., Baglaenko, Y., Arora, J., Hannes, S. K., Luo, Y., Amariuta, T., Teslovich, N. C., Rao, D. A., Ermann, J., Jonsson, A. H., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0579-4 · Cited by 119
Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants
Chandra, V., Bhattacharyya, S., Schmiedel, B. J., Madrigal, A., Gonzalez-Colin, C., Fotsing, S., Crinklaw, A., Seumois, G., Mohammadi, P., Kronenberg, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00745-3 · Cited by 122
Chromatin conformation analysis of primary patient tissue using a low input Hi-C method
Díaz, N., Kruse, K., Erdmann, T., Staiger, A. M., Ott, G., Lenz, G., & Vaquerizas, J. M. (2018) · Nature Communications · doi:10.1038/s41467-018-06961-0 · Cited by 129
Ferreira, M. A. R., Gamazon, E. R., Al‐Ejeh, F., Aittomäki, K., Andrulis, I. L., Anton‐Culver, H., Arason, A., Arndt, V., Aronson, K. J., Arun, B., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08053-5 · Cited by 127
Odhams, C. A., Roberts, A. L., Vester, S. K., Duarte, C., Beales, C. T., Clarke, A. J., Lindinger, S., Daffern, S. J., Zito, A., Chen, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10106-2 · Cited by 124
Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis
Liu, M., Cao, S., He, L., Gao, J., Arab, J. P., Cui, H., Xuan, W., Gao, Y., Sehrawat, T. S., Hamdan, F. H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24843-w · Cited by 120
Cook, P. R., & Marenduzzo, D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky763 · Cited by 117
Metadata
- Authors
- Javierre, B. M., Burren, O. S., Wilder, S. P., Kreuzhuber, R., Hill, S. M., Sewitz, S., Cairns, J., Wingett, S. W., Várnai, C., Thiecke, M. J., Burden, F., Farrow, S., Cutler, A. J., Rehnström, K., Downes, K., Grassi, L., Kostadima, M., Freire-Pritchett, P., Wang, F., Martens, J. H., Kim, B., Sharifi, N., Janssen-Megens, E. M., Yaspo, M.-L., Linser, M., Kovacsovics, A., Clarke, L., Richardson, D., Datta, A., Flicek, P., Stunnenberg, H. G., Todd, J. A., Zerbino, D. R., Stegle, O., Ouwehand, W. H., Frontini, M., Wallace, C., Spivakov, M., & Fraser, P.
- Affiliations
- Babraham Institute (GB)
- University of Cambridge (GB)
- European Bioinformatics Institute (GB)
- National Health Service (GB)
- MRC Biostatistics Unit (GB)
- Radboud University Nijmegen (NL)
- Corresponding author
- Frontini, Mattia
- Wallace, Chris
- Spivakov, Mikhail
- Fraser, Peter
- ORCID
- Javierre, Biola M.
- Burren, Oliver S.
- Wilder, Steven P.
- Kreuzhuber, Roman
- Sewitz, Sven
- Cairns, Jonathan
- Wingett, Steven W.
- Várnai, Csilla
- Thiecke, Michiel J.
- Burden, Frances
- Cutler, Antony J.
- Downes, Kate
- Grassi, Luigi
- Kostadima, Myrto
- Freire-Pritchett, Paula
- Wang, Fan
- Martens, Joost H.
- Yaspo, Marie-Laure
- Clarke, Laura
- Richardson, David
- Datta, Avik
- Flicek, Paul
- Stunnenberg, Hendrik G.
- Zerbino, Daniel R.
- Stegle, Oliver
- Ouwehand, Willem H.
- Frontini, Mattia
- Wallace, Chris
- Spivakov, Mikhail
- Fraser, Peter
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2016-11
- Volume
- 167
- Issue
- 5
- Pages
- 1369-1384.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5123897
- OpenAlex
- W2553838260
- Cited by
- 1,046
- References
- 87
- Citations by year
- 2026: 59 · 2025: 84 · 2024: 102 · 2023: 113 · 2022: 116 · 2021: 135 · 2020: 126 · 2019: 130 · 2018: 117 · 2017: 59 · 2016: 4
- FWCI
- 53.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Radboud Repository (Radboud University) (submittedVersion, other-oa)
- Apollo (cc-by)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/J004480/1)
- National Institute for Health Research (PG-0310-1002)
- Wellcome Trust (107212, 107881, 089989, 091157, 095908, 100140)
- Seventh Framework Programme (282510, 241447)
- European Research Council
- Medical Research Council (MC_UP_1302/3, MC_UP_1302/5, MC_UP_1302/1, MR/L007150/1)
- European Molecular Biology Laboratory
- British Heart Foundation (RG/09/12/28096)
- Juvenile Diabetes Research Foundation United States of America (5-SRA-2015-130, 9-2011-253)
- 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 › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- enhancer-promoter interactions, long-range chromatin interactions, promoter capture Hi-C, hematopoietic lineage, enhancers, transcriptional regulation
- MeSH terms
- Blood Cells, Cell Separation, Chromatin, Disease, Enhancer Elements, Genetic, Hematopoiesis, Humans, Promoter Regions, Genetic, Cell Lineage, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study, Epigenomics
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