annotations. For example, the Encyclopedia of DNA Elements (ENCODE) Consortium has recently generated extensive experimental data on gene expression (RNA-seq), DNA methylation status (RRBS-seq), chromatin modifications (ChIP-seq), chromatin accessibility (DNase-seq and FAIRE-seq), transcription factor (TF) binding sites (ChIP-seq), and long-range chromatin interactions (ChIA-PET, Hi-C, and 5C). As of September 2012, more than 1,600 data sets from 147 cell lines had been produced to annotate the human genome, including 2.89 million unique, non-overlapping DNase I hypersensitivity sites (DHSs) in 125 cell lines using DNase-seq and 630K binding regions of 119 DNA-binding proteins in 72 cell lines using ChIP-seq, among many [23]. The ENCODE Consortium [23] examined 4,492 risk-associated SNPs from the NHGRI GWAS catalog and found that 12% of them overlap with TF binding regions and 34% overlap with DHSs.
