RegulomeDB Database

Overview

RegulomeDB integrates large-scale functional genomics data (ENCODE, Roadmap Epigenomics) to score genetic variants for regulatory potential. Each variant receives a score from 1a (highest regulatory confidence: eQTL + TF binding + DNase accessibility + motif + chromatin) to 7 (no known regulatory function). The v2 REST API supports single-variant queries, batch scoring, and region-based searches. Access is free and requires no authentication.

When to Use

• Prioritizing GWAS hits for regulatory follow-up — identify which SNPs land in active regulatory elements
• Annotating a VCF or variant list with regulatory scores to filter to functionally relevant variants
• Identifying which transcription factors bind near a variant of interest
• Checking whether a non-coding variant overlaps an eQTL and active chromatin simultaneously
• Retrieving all high-confidence regulatory variants in a genomic region for cis-regulatory analysis
• Use clinvar-database instead when you need clinical pathogenicity classifications (ClinSig); RegulomeDB is for regulatory function, not germline disease association
• Use gwas-database instead when you want published GWAS associations with traits; RegulomeDB scores regulatory evidence regardless of trait association

Prerequisites