Table 1.

Summary of ENCODE experiments

Experiment	Description
DNA methylation	In 82 human cell lines and tissues: A549, Adrenal gland, AG04449, AG04450, AG09309, AG09319, AG10803, AoSMC, BE2 C, BJ, Brain, Breast, Caco-2, CMK, ECC-1, Fibrobl, GM06990, GM12878, GM12891, GM12892, GM19239, GM19240, H1-hESC, HAEpiC, HCF, HCM, HCPEpiC, HCT-116, HEEpiC, HEK293, HeLa-S3, Hepatocytes, HepG2, HIPEpiC, HL-60, HMEC, HNPCEpiC, HPAEpiC, HRCEpiC, HRE, HRPEpiC, HSMM, HTR8svn, IMR90, Jurkat, K562, Kidney, Left Ventricle, Leukocyte, Liver, LNCaP, Lung, MCF-7, Melano, Myometr, NB4, NH-A, NHBE, NHDF-neo, NT2-D1, Osteoblasts, Ovcar-3, PANC-1, Pancreas, PanIslets, Pericardium, PFSK-1, Placenta, PrEC, ProgFib, RPTEC, SAEC, Skeletal muscle, Skin, SkMC, SK-N-MC, SK-N-SH, Stomach, T-47D, Testis, U87, UCH-1 and Uterus
TF ChIP-seq	A total of 119 TFs: ATF3, BATF, BCLAF1, BCL3, BCL11A, BDP1, BHLHE40, BRCA1, BRF1, BRF2, CCNT2, CEBPB, CHD2, CTBP2, CTCF, CTCFL, EBF1, EGR1, ELF1, ELK4, EP300, ESRRA, ESR1, ETS1, E2F1, E2F4, E2F6, FOS, FOSL1, FOSL2, FOXA1, FOXA2, GABPA, GATA1, GATA2, GATA3, GTF2B, GTF2F1, GTF3C2, HDAC2, HDAC8, HMGN3, HNF4A, HNF4G, HSF1, IRF1, IRF3, IRF4, JUN, JUNB, JUND, MAFF, MAFK, MAX, MEF2A, MEF2C, MXI1, MYC, NANOG, NFE2, NFKB1, NFYA, NFYB, NRF1, NR2C2, NR3C1, PAX5, PBX3, POLR2A, POLR3A, POLR3G, POU2F2, POU5F1, PPARGC1A, PRDM1, RAD21, RDBP, REST, RFX5, RXRA, SETDB1, SIN3A, SIRT6, SIX5, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMC3, SPI1, SP1, SP2, SREBF1, SRF, STAT1, STAT2, STAT3, SUZ12, TAF1, TAF7, TAL1, TBP, TCF7L2, TCF12, TFAP2A, TFAP2C, THAP1, TRIM28, USF1, USF2, WRNIP1, YY1, ZBTB7A, ZBTB33, ZEB1, ZNF143, ZNF263, ZNF274 and ZZZ3
Histone ChIP-seq	A total of 12 types: H2A.Z, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me1, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3K79me2 and H4K20me1
DNase-seq	In 125 cell types or treatments: 8988T, A549, AG04449, AG04450, AG09309, AG09319, AG10803, AoAF, AoSMC/serum_free_media, BE2_C, BJ, Caco-2, CD20, CD34, Chorion, CLL, CMK, Fibrobl, FibroP, Gliobla, GM06990, GM12864, GM12865, GM12878, GM12891, GM12892, GM18507, GM19238, GM19239, GM19240, H7-hESC, H9ES, HAc, HAEpiC, HA-h, HA-sp, HBMEC, HCF, HCFaa, HCM, HConF, HCPEpiC, HCT-116, HEEpiC, HeLa-S3, HeLa-S3_IFNa4h, Hepatocytes, HepG2, HESC, HFF, HFF-Myc, HGF, HIPEpiC, HL-60, HMEC, HMF, HMVEC-dAd, HMVEC-dBl-Ad, HMVEC-dBl-Neo, HMVEC-dLy-Ad, HMVEC-dLy-Neo, HMVEC-dNeo, HMVEC-LBl, HMVEC-LLy, HNPCEpiC, HPAEC, HPAF, HPDE6-E6E7, HPdLF, HPF, HRCEpiC, HRE, HRGEC, HRPEpiC, HSMM, HSMMemb, HSMMtube, HTR8svn, Huh-7, Huh-7.5, HUVEC, HVMF, iPS, Ishikawa_Estr, Ishikawa_Tamox, Jurkat, K562, LNCaP, LNCaP_Andr, MCF-7, MCF-7_Hypox, Medullo, Melano, MonocytesCD14+, Myometr, NB4, NH-A, NHDF-Ad, NHDF-neo, NHEK, NHLF, NT2-D1, Osteobl, PANC-1, PanIsletD, PanIslets, pHTE, PrEC, ProgFib, PrEC, RPTEC, RWPE1, SAEC, SKMC, SK-N-MC, SK-N-SH_RA, Stellate, T-47D, Th0, Th1, Th2, Urothelia, Urothelia_UT189, WERI-Rb-1, WI-38 and WI-38_Tamox
DNase footprint	In 41 cell types: AG10803, AoAF, CD20+, CD34+ Mobilized, fBrain, fHeart, fLung, GM06990, GM12865, HAEpiC, HA-h, HCF, HCM, HCPEpiC, HEEpiC, HepG2, H7-hESC, HFF, HIPEpiC, HMF, HMVEC-dBl-Ad, HMVEC-dBl-Neo, HMVEC-dLy-Neo, HMVEC-LLy, HPAF, HPdLF, HPF, HRCEpiC, HSMM, Th1, HVMF, IMR90, K562, NB4, NH-A, NHDF-Ad, NHDF-neo, NHLF, SAEC, SkMC and SK-N-SH RA
MNase-seq	In GM12878 and K562
3C-carbon copy (5C)	In GM12878, K562, HeLa-S3 and H1-hESC
GWAS SNP targeting	296 noncoding GWAS SNPs were assigned a target promoter