A semi-curated list of enhancer and promoter databases. If you know of others, please put them in issues!
• RefSeq Functional Elements enhancer features, experimental validation
• VISTA enhancers, experimental validation for positives
• FANTOM5 enhancers, a subset are validated
• ENCODE predicted enhancers, a subset are validated
• Ensembl Regulatory Build enhancer features
• Roadmap Epigenomics (some overlap with ENCODE)
• GeneHancer
- ftp://ftp.ncbi.nih.gov/snp/.ASHG2018 has a curated list of SNPs in enhancers (ftp://ftp.ncbi.nih.gov/snp/.ASHG2018/rs_RefSeq_curated_enhancer_GRCh38.vcf.gz)
• RefSeq Functional Elements promoter features, experimental validation (alpha)
• ENCODE predicted promoters
• Ensembl Regulatory Build promoter features
• Roadmap Epigenomics (some overlap with ENCODE)
• EPDnew - SIB's promoter database, mostly CAGE-based mapping for 5' ends of annotated genes
• FANTOM5 - really a TSS db with promoter extrapolation based on those
Special thanks to Catherine Farrell from NCBI for seeding this list!