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Nature Research, Nature, 7539(518), p. 317-330, 2015

DOI: 10.1038/nature14248

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Integrative analysis of 111 reference human epigenomes

Journal article published in 2015 by Roadmap Epigenomics Consortium, Philip L. de Jager, Anshul Kundaje, Wouter Meuleman, Zhizhuo Zhang, Jason Ernst, Xian Zhang, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Jianrong Wang, Pouya Kheradpour, Xiaolan Zhang, Xinchen Wang, Michael J. Ziller and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

The 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.