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gwas-lookup

Resolve rsIDs to genomic coordinates and aggregate variant evidence from public genomic APIs.

1.1k|238|Updated Feb 25, 2026
Search Tags:#genomics#gwas#rsid#variant-lookup#phewas#eqtl#open-targets
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill gwas-lookup
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-lookup
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup
Command: npx skills add https://github.com/ClawBio/ClawBio --skill gwas-lookup

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Quickly resolve an rsID to genomic coordinates and collate association, PheWAS, eQTL, and fine-mapping evidence from multiple public genomics APIs so researchers and clinicians can interpret variant-trait relationships without manual API scraping or error-prone aggregation.

Core Features & Use Cases

  • Variant resolution: Resolve rsID → chr:pos (GRCh38 + GRCh37), alleles, consequence, and population frequencies using Ensembl with a PortalDev fallback.
  • Federated querying: Parallel queries across GWAS Catalog, Open Targets (including credible sets), UKB-TOPMed PheWeb, FinnGen, Biobank Japan (GRCh37), GTEx, and the EBI eQTL Catalogue with rate-limiting and local caching.
  • Normalization & reporting: Merge, deduplicate, sort by p-value, flag genome-wide significant hits, and output a reproducible bundle containing a markdown report, CSV tables, figures, raw JSON, and commands for rerunning.
  • Use case: Rapidly generate an evidence pack for a candidate variant (e.g., rs3798220) that lists all associated traits, PheWAS hits across biobanks, tissue-specific eQTL effects, and credible set membership for downstream interpretation or manuscript reproducibility.

Quick Start

Use the gwas-lookup skill to look up rs3798220 and generate a full markdown report, CSV tables, figures, and a reproducibility bundle in a specified output directory.

Frequently Asked Questions about gwas-lookup

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I aggregate GWAS, PheWAS, and eQTL evidence for a single rsID across multiple genomic databases?▼

You can resolve an rsID to genomic coordinates and query GWAS Catalog, Open Targets, UKB-TOPMed, FinnGen, GTEx, and EBI eQTL Catalogue in parallel to aggregate association, expression, and fine-mapping evidence into a normalized report.

What is the best way to look up variant associations across biobanks like FinnGen and Biobank Japan simultaneously?▼

Federated variant lookup queries UKB-TOPMed PheWeb, FinnGen, and Biobank Japan in parallel, merging PheWAS hits and trait associations into a single deduplicated table sorted by normalized p-values.

Can I get genomic coordinates in both GRCh38 and GRCh37 when resolving an rsID for variant-centric research?▼

Yes, rsID resolution uses Ensembl with a PortalDev fallback to return chromosomal coordinates in both GRCh38 and GRCh37, alongside alleles, consequence, and population frequencies.

How do I generate a reproducibility bundle for variant-trait associations that includes CSV tables and figures?▼

The lookup process outputs a reproducible bundle containing markdown reports, CSV association tables, figures, raw JSON, and rerun commands, ensuring downstream interpretation and manuscript reproducibility.

Does querying multiple public genomic APIs concurrently cause rate-limiting issues during variant interpretation?▼

The federated querying process enforces per-API rate limits and uses local caching when pulling data from Ensembl, GWAS Catalog, Open Targets, and other genomic APIs to prevent request failures.

When do I need fine-mapping and credible set data for interpreting variant-trait relationships?▼

You need credible set membership and fine-mapping evidence when evaluating whether a specific variant is causally linked to a trait, which Open Targets integration provides alongside genome-wide significant hit flagging.

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