Genomics · Database
RegulomeDB
A genomics resource providing regulatory evidence and prioritisation scores for non-coding variants.
What RegulomeDB is
RegulomeDB is a genomics database designed to assist researchers in interpreting non-protein-coding regions of the genome. It provides variant-level regulatory evidence along with prioritisation scores to help identify functional non-coding variants.
The platform supports genome-wide analysis across standard human reference builds, including GRCh38 and hg19. Researchers can explore regulatory annotations and experimental datasets, as well as incorporate linkage disequilibrium data across diverse ancestral populations.
How it is organised
Users submit non-coding variants either individually or in batches using identifiers such as dbSNP rsIDs, genomic coordinates, ranges, SPDI, or HGVS nomenclature. The system processes these against selected human assemblies (GRCh38 or hg19).
Queries evaluate regulatory annotations and experimental evidence to assign regulatory prioritisation scores. The platform also enables linkage disequilibrium calculations using an R-squared threshold across specified population ancestries, including AFR, EAS, EUR, SAS, and ALL.
Key facts
- Category
- Genomics
- Record type
- Variant-level regulatory scores
- Current release
- 3.0 Beta
- Supported assemblies
- GRCh38, hg19
- Accepted inputs
- rsID, coordinates, range, SPDI, HGVS, multiple dbSNPs
- Ancestry populations
- AFR, EAS, EUR, SAS, ALL
What you can use it for
- Non-coding variant prioritisation
- Evaluate variant-level regulatory evidence and obtain prioritisation scores to identify candidate functional variants in non-coding regions.
- Batch annotation of candidate variants
- Submit lists of genomic coordinates, ranges, or dbSNP identifiers simultaneously to retrieve functional annotations.
- Population-specific linkage disequilibrium analysis
- Inspect variant associations and LD patterns across AFR, EAS, EUR, SAS, or global (ALL) reference panels using custom R-squared thresholds.
Query it here
The research agent queries RegulomeDB directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Provides targeted prioritisation scores and regulatory evidence specifically for non-coding genomic variants.
- Accommodates standard human genome assemblies including both GRCh38 and hg19.
- Accepts a wide range of input representations, including rsIDs, coordinates, ranges, SPDI, and HGVS formats.
Watch out for
- Designed primarily for non-coding variants and regulatory evidence rather than coding variant pathogenicity.
- The platform interface is provided as a 3.0 Beta release.
Questions
Can I search RegulomeDB without writing code?
Yes. The research agent queries RegulomeDB directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from RegulomeDB?
ENCODE-derived annotations, unrestricted with citation. Terms: https://regulomedb.org/regulome-help/
Which genome assemblies are supported by RegulomeDB?
The platform supports both GRCh38 and hg19 human reference assemblies.
What input formats can be used to query variants?
Single queries can be submitted as dbSNP rsIDs, genomic coordinates, coordinate ranges, SPDI, or HGVS strings. Multiple entries can be queried via dbSNP lists, coordinates, or ranges.
What ancestral groups are available for linkage disequilibrium queries?
Linkage disequilibrium can be evaluated across African (AFR), East Asian (EAS), European (EUR), South Asian (SAS), or combined (ALL) populations.
Written from RegulomeDB's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.