In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).
More information:
https://genome.ucsc.edu/ENCODE/pilot.html
Comments
You can access the collected papers by exploring the thematic ENCODE threads with topics such as DNA methylation, RNA or machine learning. http://www.nature.com/encode/#/threads
User can also find some useful ENCODE data at http://www.gencodegenes.org/releases/17.html
The annotation file is available at http://www.nimblegen.com/downloads/annotation/hg19/