A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
(A) A 1 Mb region including MYC and a gene desert upstream shows the linkage disequilibrium blocks and positions of SNPs associated with breast and prostate cancer, with both a custom track based on  and the resident track from the GWAS catalog. ENCODE tracks include GENCODE gene annotations, results of mapping RNAs to high-density Affymetrix tiling arrays (cytoplasmic and nuclear polyA+ RNA), mapping of histone modifications (H3K4me3 and H3K27Ac), DNaseI hypersensitive sites in liver and colon carcinoma cell lines (HepG2 and Caco-2), and occupancy by the transcription factor TCF7L2 in HCT116 cells. (B) Expanded view of a 9 kb region containing the cancer-associated SNP rs6983267 (shown on the top line). In addition to the histone modifications, DNaseI hypersensitive sites and factor occupancy described in (A), the ENCODE tracks also show occupancy by the coactivator p300 and the transcription factors RXRA, CEBPB, and HNF4A. Except as otherwise noted in brackets, the ENCODE data shown here are from the liver carcinoma cell line HepG2.