Promoter-like regions based on DNase and H3K4me3 signals

DNase hypersensitivity and histone modification H3K4me3 are well-known indicators of promoter function. We have developed an unsupervised method that combines DNase and H3K4me3 signals in the same cell type to predict promoter-like regions. When used to predict ranked gene expression from RNA-seq data, our method shows higher accuracy than DNase and H3K4me3 individually. We have applied this method to 107 human cell types and 14 mouse cell types with both DNase and H3K4me3 data generated by the ENCODE and Roadmap Epigenomic consortia. For cell and tissues types with only H3K4me3 data, we centered predictions on H3K4me3 peaks and ranked them by H3K4me3 signals. You can query these promoter-like regions by genomic locations, nearby genes, or SNPs, and visualize them in the UCSC and WashU genome browsers. read more...

Search Promoter-like Regions (v3)


Examples: gene, SNP (ex. rs11742570), genomic region, or peak rank



  Download candidate enhancers computed using DNase and H3K4me3 signals for cell types below (genome wide)
Tissue of origin Cell Type Biosample
immortalized cell line Jurkat clone E61
blood immortalized cell line GM06990
blood immortalized cell line GM12864
blood immortalized cell line GM12865
blood immortalized cell line GM12878
blood immortalized cell line HL-60
blood immortalized cell line NB4
blood primary cell B cell (adult 43 year)
blood vessel primary cell fibroblast of pulmonary artery
brain immortalized cell line SK-N-MC
brain immortalized cell line SK-N-SH
brain primary cell astrocyte
brain primary cell astrocyte of the cerebellum
brain primary cell brain microvascular endothelial cell
brain primary cell choroid plexus epithelial cell
breast immortalized cell line MCF-7
bronchus primary cell bronchial epithelial cell
colon immortalized cell line Caco-2
connective tissue primary cell fibroblast of pedal digit skin (adult 21 year)
connective tissue primary cell fibroblast of the aortic adventitia
connective tissue primary cell fibroblast of upper leg skin (fetal 12 week)
embryonic structure stem cell H1-hESC
ESC immortalized cell line BE2C
ESC stem cell H7-hESC
esophagus primary cell epithelial cell of esophagus
extraembryonic component primary cell fibroblast of villous mesenchyme
eye immortalized cell line WERI-Rb-1
eye primary cell retinal pigment epithelial cell
foreskin primary cell HFF-Myc
heart primary cell cardiac fibroblast
heart primary cell cardiac muscle cell
intestine immortalized cell line HCT116
kidney primary cell epithelial cell of proximal tubule
kidney primary cell kidney epithelial cell
lung primary cell fibroblast of lung (fetal 12 week)
mammary primary cell fibroblast of mammary gland
muscle primary cell skeletal muscle cell
penis primary cell foreskin fibroblast
prostate immortalized cell line LNCaP clone FGC
skin primary cell fibroblast of dermis
skin primary cell fibroblast of skin of abdomen (adult 22 year)
spinal cord primary cell astrocyte of the spinal cord