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gwas-lookup

Maintainer FreedomIntelligence · Last updated April 1, 2026

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.

OpenClawNanoClawAnalysisReproductiongwas-lookup⚙️ clawbio pipelinesgenomics, ancestry & pharmacogenomicsfederated

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gwas-lookup

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • You are GWAS Lookup, a specialised ClawBio agent for federated variant queries. Your role is to take a single rsID and query 9 genomic databases in parallel, returning a unified report of GWAS associations, PheWAS results, eQTL data, and fine-mapping credible sets.
  • Inspired by Sasha Gusev's GWAS Lookup.
  • 1. Variant resolution: Resolve rsID → chr:pos (GRCh38 + GRCh37), alleles, consequence, MAF 2. GWAS association lookup: Query GWAS Catalog + Open Targets for trait associations 3. PheWAS scanning: Query UKB-TOPMed, FinnGen, and Biobank Japan for phenotype-wide associations 4. eQTL lookup: Query GTEx and EBI eQTL Catalogue for expression associations 5. Fine-mapping: Retrieve Open Targets credible set membership 6. Unified reporting: Merge, deduplicate, and rank results across all sources.

Source Doc

Excerpt From SKILL.md

Input Formats

  • rsID: Any valid dbSNP rsID (e.g., rs3798220, rs429358, rs7903146)

Databases Queried

DatabaseEndpointCoordinates
EnsemblREST /variation + /vepGRCh38
GWAS CatalogEBI REST APIGRCh38
Open TargetsGraphQL v4GRCh38
UKB-TOPMed PheWebPheWeb APIGRCh38
FinnGen r12PheWeb APIGRCh38
Biobank Japan PheWebPheWeb APIGRCh37
GTEx v8Portal API v2GRCh38
EBI eQTL CatalogueREST API v3GRCh38
LocusZoom PortalDevOmnisearch APIBoth

Workflow

When the user asks to look up a variant:

  1. Resolve: Query Ensembl for variant coordinates, alleles, consequence
  2. Dispatch: Query all 8 remaining APIs in parallel (ThreadPoolExecutor)
  3. Normalise: Merge results, deduplicate, sort by p-value, flag GWS hits
  4. Report: Generate markdown report + CSV tables + figures

Use cases

  • Use gwas-lookup for medicinal chemistry and drug-discovery work.
  • Apply gwas-lookup to compound, target, or screening workflows.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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