Download the data

Genome-wide predicted CRMs and their transcription factor binding sites for human and mouse, as gzip-compressed BED files: CRMs with their binding sites, and the binding sites and CRMs on their own. Fruit fly, worm and thale cress are coming soon.

Human Homo sapiens

GRCh38 / hg38 · Version 2

CRMs: 1,426,947
TFBSs: 95,717,222
ChIP-seq datasets: 11,348
Genome covered by extended peaks* (how the predictions are made): 85.5%

Human_CRMs_TFBSs_v2_hg38.bed.gz CRMs and their binding sites · one CRM per line
1.5 GB · .bed.gz Download Human_CRMs_TFBSs_v2_hg38.bed.gz, 1.5 GB
Human_TFBSs_v2_hg38.bed.gz Binding sites · one site per line
1.3 GB · .bed.gz Download Human_TFBSs_v2_hg38.bed.gz, 1.3 GB
Human_CRMs_v2_hg38.bed.gz CRMs only · one CRM per line
28.5 MB · .bed.gz Download Human_CRMs_v2_hg38.bed.gz, 28.5 MB

Mouse Mus musculus

GRCm38 / mm10 · Version 2

CRMs: 912,197
TFBSs: 125,113,756
ChIP-seq datasets: 9,060
Genome covered by extended peaks* (how the predictions are made): 77.9%

Mouse_CRMs_TFBSs_v2_mm10.bed.gz CRMs and their binding sites · one CRM per line
2.0 GB · .bed.gz Download Mouse_CRMs_TFBSs_v2_mm10.bed.gz, 2.0 GB
Mouse_TFBSs_v2_mm10.bed.gz Binding sites · one site per line
1.7 GB · .bed.gz Download Mouse_TFBSs_v2_mm10.bed.gz, 1.7 GB
Mouse_CRMs_v2_mm10.bed.gz CRMs only · one CRM per line
18.7 MB · .bed.gz Download Mouse_CRMs_v2_mm10.bed.gz, 18.7 MB

Using the files

Each file is tab-separated text compressed with gzip. bedtools and most genome tools read it as it is; to look inside:

gzip -dc Human_TFBSs_v2_hg38.bed.gz | head

CRMs and their binding sites: One CRM per line: chromosome, start, end, its binding sites, CRM score and P-value. The binding sites are comma-separated, each written motif|start:end+binding score+motif score.
Binding sites: One binding site per line, in genomic order: chrom start end motif binding_score crm_id. motif is the motif number shown with its logo on CRM pages; crm_id is the CRM’s ID on this site.
CRMs only: One CRM per line, in genomic order: chrom start end crm_id score p_value.