RegulomeDB Database

Overview

RegulomeDB integrates large-scale functional genomics data (ENCODE, Roadmap Epigenomics) to score genetic variants for regulatory potential. Each variant receives a ranking from 1a (highest regulatory confidence: eQTL + TF + DNase + motif + chromatin) to 7 (no known regulatory function). The v2 API is exposed as GET https://regulomedb.org/regulome-search/; the legacy POST /regulome-search/, POST /regulome-summary/, and GET /regulome-datasets/ JSON endpoints are no longer functional (return regulome-notfound stubs or 500). 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 (via the @graph evidence rows)
• Checking whether a non-coding variant overlaps a QTL and active chromatin simultaneously (features.QTL)
• Retrieving all annotated rsIDs in a genomic region for cis-regulatory analysis (region query with nearby_snps)
• Use clinvar-database instead when you need clinical pathogenicity classifications; RegulomeDB scores regulatory function, not germline disease association
• Use gwas-database instead when you want published GWAS associations with traits

Prerequisites