Kundaje, AnshulMeuleman, WouterErnst, JasonBilenky, MishaYen, AngelaKheradpour, PouyaZhang, ZhizhuoHeravi-Moussavi, AlirezaLiu, YapingAmin, VirenZiller, MichaelWhitaker, John WSchultz, Matthew DSandstrom, Richard SEaton, Matthew LWu, Yi-ChiehWang, JianrongWard, Lucas DSarkar, AbhishekQuon, GeraldPfenning, AndreasWang, XinchenClaussnitzer, MelinaCoarfa, CristianHarris, R AlanShoresh, NoamEpstein, Charles BGjoneska, ElizabetaLeung, DannyXie, WeiHawkins, R DavidLister, RyanHong, ChiboGascard, PhilippeMungall, Andrew JMoore, RichardChuah, EricTam, AngelaCanfield, Theresa KHansen, R ScottKaul, RajinderSabo, Peter JBansal, Mukul SCarles, AnnaickDixon, Jesse RFarh, Kai-HowFeizi, SoheilKarlic, RosaKim, Ah-RamKulkarni, AshwinikumarLi, DaofengLowdon, RebeccaMercer, Tim RNeph, Shane JOnuchic, VitorPolak, PazRajagopal, NishaRay, PradiptaSallari, Richard CSiebenthall, Kyle TSinnott-Armstrong, NicholasStevens, MichaelThurman, Robert EWu, JieZhang, BoZhou, XinBeaudet, Arthur EBoyer, Laurie ADe Jager, PhilipFarnham, Peggy JFisher, Susan JHaussler, DavidJones, StevenLi, WeiMarra, MarcoMcManus, Michael TSunyaev, ShamilThomson, James ATlsty, Thea DTsai, Li-HueiWang, WeiWaterland, Robert AZhang, MichaelChadwick, Lisa HBernstein, BradleyCostello, Joseph FEcker, Joseph RHirst, MartinMeissner, AlexanderMilosavljevic, AleksandarRen, BingStamatoyannopoulos, John AWang, TingKellis, Manolis2015-09-012015Kundaje, A., W. Meuleman, J. Ernst, M. Bilenky, A. Yen, P. Kheradpour, Z. Zhang, et al. 2015. “Integrative analysis of 111 reference human epigenomes.” Nature 518 (7539): 317-330. doi:10.1038/nature14248. http://dx.doi.org/10.1038/nature14248.0028-0836http://nrs.harvard.edu/urn-3:HUL.InstRepos:21458829The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection to-date of human epigenomes for primary cells and tissues. Here, we describe the integrative analysis of 111 reference human epigenomes generated as part of the program, profiled for histone modification patterns, DNA accessibility, DNA methylation, and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically-relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation, and human disease.en-USJournal Article2015-09-0110.1038/nature14248