Histone modification ChIP-seq peaks from ENCODE, Blueprint, ROADMAP, and CEEHRC, spanning primary cells, cell lines, tissues, and stem cells. Coverage is extensive across adult, embryonic, and fetal samples, with strong representation of blood, brain, digestive, and lung tissues across all major biological systems.
Data in this track hub were uniformly downloaded, processed, and harmonized by FILER2. Raw files were obtained from each source repository, converted to BED/bigBed format, lifted to the target genome assembly where necessary, and annotated with standardized metadata including cell type, tissue category, and assay type.
Source: https://www.encodeproject.org
Publication: An integrated encyclopedia of DNA elements in the human genome
Citation: ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247
Funding: The Consortium is funded by grants from the NHGRI as follows: Production Grants: U54HG004570 (Bernstein); U01HG004695 (Birney); U54HG004563 (Crawford); U54HG004557 (Gingeras); U54HG004555 (Hubbard); U41HG004568 (Kent); U54HG004576 (Myers); U54HG004558 (Snyder); U54HG004592 (Stamatoyannopoulos). Pilot Grants: R01HG003143 (Dekker); RC2HG005591 and R01HG003700 (Giddings); R01HG004456-03 (Ruan); U01HG004571 (Tenenbaum); U01HG004561 (Weng); RC2HG005679 (White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541, U01HG004561, RC2HG005679 and R01HG003988 (PI: Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (Elnitski, ZIAHG200323; Margulies, ZIAHG200341). Research in the Pennachio lab was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
Publication: Data navigation on the ENCODE portal
Citation: Kagda MS, Lam B, Litton C, et al. Data navigation on the ENCODE portal. Nat Commun. 2025;16(1):9592. Published 2025 Oct 30. doi:10.1038/s41467-025-64343-9
Funding: All the figures in the manuscript are prepared using the free academic licence version of Tableau Desktop 2023.1. The authors would like to thank Salesforce for providing us with a free academic version. In addition, we would like to thank all the past and present members of the ENCODE and affiliated consortia. National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Publication: New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
Citation: Luo Y, Hitz BC, Gabdank I, et al. New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. Nucleic Acids Res. 2020;48(D1):D882-D889. doi:10.1093/nar/gkz1062
Funding: National Human Genome Research Institute, National Institutes of Health [U24 HG009397]. The content is solely theresponsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health. The funders had no role in design, data processing, implementation, decision to publish, or preparation of the manuscript. Funding for open access charge: National Human Genome Research Institute, National Institutes of Health [U24 HG009397].
Source: http://homer.ucsd.edu/iholtman/Nuclei_project/interaction/MAPS/
Publication: Brain cell type-specific enhancer-promoter interactome maps and disease-risk association
Citation: Nott A, Holtman IR, Coufal NG, et al. Brain cell type-specific enhancer-promoter interactome maps and disease-risk association. Science. 2019;366(6469):1134-1139. doi:10.1126/science.aay0793
Funding: Support was provided by NIH grants R01 NS096170, RF1 AG061060-01, R01 AG056511-01A1, R01 AG057706-01, a Cure Alzheimer’s Fund Gifford Neuroinflammation Consortium, and UCSD Shiley-Marcos ADRC 1P30AG062429. A.N. was supported by the Alzheimer’s Association (AARF-18-531498) and the Altman Clinical & Translational Research Institute at UCSD (National Center for Advancing Translational Sciences, NIH KL2TR001444). I.R.H. was supported by the VENI research program, which is financed by the Netherlands Organization for Scientific Research. N.G.C. was funded by NIH K08 NS109200-01 and The Hartwell Foundation. C.Z.H. is supported by the Cancer Research Institute Irvington Postdoctoral Fellowship Program. C.O. was funded by NIHNCI CCSG: P30 014195 and S10-OD023689. Salk facilities are supported by the Salk Cancer Center (NCI grant: P30-CA014195). F.H.G. was supported by the JPB Foundation, The Engman Foundation, The AHA/ Allen Award, and the Dolby Foundation. J.B.B. and R.A.S. were supported by AG062429-01.
Source: http://www.roadmapepigenomics.org/
Publication: Integrative analysis of 111 reference human epigenomes
Citation: Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317-330. doi:10.1038/nature14248
Funding: This work was supported by the NIH Common Fund as part of the NIH Roadmap Epigenomics Program through U01ES017155 (BB/AM), U01ES017154 (JC/MM), U01ES017166 (BR), U01ES017156 (JS), U01DA025956 (AM/AB), and by NHGRI through RC1HG005334, R01HG004037 (MK), RO1NS078839 (L-HT). This work was also supported by NIH fellowship grants F32HL110473 and K99HL119617 (S.L.), and NSF CAREER award 1254200 (J.E.). We acknowledge program leadership by members of the NIH Epigenomics Workgroup, especially John S. Satterlee, Frederick L. Tyson, Joni Rutter, Kimberly A. McAllister, Astrid Haugen, Christine Colvis (NCATS), James Battey (NIDCD), Linda Birnbaum (NIEHS), and Nora Volkow (NIDA). We acknowledge feedback from our External Scientific Panel members Marisa Bartolomei, Stephen Baylin, Stephan Beck, Aravinda Chakravarti, Laurie Jackson-Grusby, Jason Lieb, Steve Peckman, John Quackenbush, and Steve Stice. Sample procurement was supported by grants 5R24HD000836 (IAG) for staged fetal tissues; P30AG10161, R01AG15819, R01AG17917 (DAB) and U01AG46152 (PLD, DAB) for adult brain samples.
Source: https://ihec-epigenomes.org/
Publication: The International Human Epigenome Consortium Data Portal
Citation: Bujold D, Morais DAL, Gauthier C, et al. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496-499.e2. doi:10.1016/j.cels.2016.10.019
Funding: The IHEC Data Portal is a service offered by the Canadian Center for Computational Genomics (C3G) and was developed by the McGill Epigenomics Data Coordination Centre (EDCC). It is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research (CIHR-EP2-120609) and by Genome Québec, with additional support from Genome Canada. The correlation matrix functionalities have been developed at the Université de Sherbrooke and funded by the Natural Sciences and Engineering Research Council of Canada (NSERC-435710–2013). The computing and networking infrastructure, and part of the software development, are provided by Calcul Québec, Compute Canada, and CANARIE
Source: https://ihec-epigenomes.org/
Publication: The International Human Epigenome Consortium Data Portal
Citation: Bujold D, Morais DAL, Gauthier C, et al. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496-499.e2. doi:10.1016/j.cels.2016.10.019
Funding: The IHEC Data Portal is a service offered by the Canadian Center for Computational Genomics (C3G) and was developed by the McGill Epigenomics Data Coordination Centre (EDCC). It is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research (CIHR-EP2-120609) and by Genome Québec, with additional support from Genome Canada. The correlation matrix functionalities have been developed at the Université de Sherbrooke and funded by the Natural Sciences and Engineering Research Council of Canada (NSERC-435710–2013). The computing and networking infrastructure, and part of the software development, are provided by Calcul Québec, Compute Canada, and CANARIE
Source: https://ihec-epigenomes.org/
Publication: The International Human Epigenome Consortium Data Portal
Citation: Bujold D, Morais DAL, Gauthier C, et al. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496-499.e2. doi:10.1016/j.cels.2016.10.019
Funding: The IHEC Data Portal is a service offered by the Canadian Center for Computational Genomics (C3G) and was developed by the McGill Epigenomics Data Coordination Centre (EDCC). It is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research (CIHR-EP2-120609) and by Genome Québec, with additional support from Genome Canada. The correlation matrix functionalities have been developed at the Université de Sherbrooke and funded by the Natural Sciences and Engineering Research Council of Canada (NSERC-435710–2013). The computing and networking infrastructure, and part of the software development, are provided by Calcul Québec, Compute Canada, and CANARIE
Source: https://ihec-epigenomes.org/
Publication: The International Human Epigenome Consortium Data Portal
Citation: Bujold D, Morais DAL, Gauthier C, et al. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496-499.e2. doi:10.1016/j.cels.2016.10.019
Funding: The IHEC Data Portal is a service offered by the Canadian Center for Computational Genomics (C3G) and was developed by the McGill Epigenomics Data Coordination Centre (EDCC). It is funded under the Canadian Epigenetics, Environment, and Health Research Consortium (CEEHRC) by the Canadian Institutes of Health Research (CIHR-EP2-120609) and by Genome Québec, with additional support from Genome Canada. The correlation matrix functionalities have been developed at the Université de Sherbrooke and funded by the Natural Sciences and Engineering Research Council of Canada (NSERC-435710–2013). The computing and networking infrastructure, and part of the software development, are provided by Calcul Québec, Compute Canada, and CANARIE