Enhancers

Enhancer annotations from EpiMap, ROADMAP, and FANTOM5, spanning tissues, primary cells, and cell lines across embryonic and adult samples. Coverage is broad across digestive, blood, brain, and lung tissues, with additional representation of skeletal muscle, kidney, and heart.

Methods

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.

Data Sources

Nott et al. 2019

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.

EpiMap Enhancers

Publication: Regulatory genomic circuitry of human disease loci by integrative epigenomics

Citation: Boix CA, James BT, Park YP, Meuleman W, Kellis M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature. 2021;590(7845):300-307. doi:10.1038/s41586-020-03145-z

Funding: We thank the ENCODE, Roadmap and GGR consortia for generating high-quality public datasets and rapidly disseminating their results to the broader community; D. Li and T. Wang, and I. Gabdank and J. S. Strattan for making our observed and imputed genome-wide tracks and chromatin-state annotations available through the WashU Epigenome Browser and the ENCODE portal, respectively; J. Ernst for advice, guidance and for developing the ChromImpute methodology and code base; P. Kheradpour for help with the motif enrichment analysis software; L. D. Ward for discussions on interactive visualizations of our predictions and HaploReg; C. Epstein, J. Schreiber, W. Noble, Z. Weng, M. Gerstein, ENCODE, Roadmap, GENCODE and GTEx consortia for feedback on early versions of this work; and I. Jungreis, X. Wang, L. Hou, L. Agudelo, S. Mohammadi, M. Wolf, A. Shi, K. Nguyen, M. Kousi, S. Kuosmanen, E. Schmauch and A. Amirabad for feedback on the work and the resource. This work was supported by the US National Institutes of Health grants HG008155, HG009446, HG009088, HG007234, HG007610, GM113708, MH109978, MH119509 and AG058002 (to M.K.) and the National Institutes of Health training grant GM087237 (to C.A.B.).

FANTOM5 Enhancers

Publication: On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Citation: Ienasescu H, Li K, Andersson R, et al. On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database (Oxford). 2016;2016:baw144. Published 2016 Dec 26. doi:10.1093/database/baw144

Funding: This work is part of the FANTOM5 project. Data, tools and co-published manuscripts are summarized at http://fantom.gsc.riken.jp/5/. FANTOM5 was made possible by a Research Grant for RIKEN OSC from MEXT to YH, Grant from MEXT for the RIKEN PMI to YH, Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to YH and Grant from MEXT to the RIKEN CLST. ELIXIR, the Novo Nordisk Foundation and the Lundbeck Foundation (to A.S.).

ROADMAP Enhancers

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.). Sample procurement was supported by grants 5R24HD000836 (IAG) for staged fetal tissues; P30AG10161, R01AG15819, R01AG17917 (DAB) and U01AG46152 (PLD, DAB) for adult brain samples.

VISTA Enhancer Browser

Publication: VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers

Citation: Kosicki M, Baltoumas FA, Kelman G, et al. VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers. Nucleic Acids Res. 2025;53(D1):D324-D330. doi:10.1093/nar/gkae940

Funding: National Institutes of Health [R01HG003988 to L.A.P.]; work conducted at the E.O. Lawrence Berkeley National Laboratory was performed under Department of Energy [DE-AC02-05CH11231], University of California; G.A.P. and F.A.B. were supported by: Fondation Santé; Onassis Foundation; Hellenic Foundation for Research and Innovation (H.F.R.I.) under the call ‘Greece 2.0 - Basic Research Financing Action, sub-action II [16718-PRPFOR]; Program 'Greece 2.0, National Recovery and Resilience Plan’, [TAEDR-0539180].