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gwas-database

Retrieve curated GWAS Catalog genetic associations by trait or variant.

4|1|Updated Jun 18, 2025
Search Tags:#api#associations#genetics#traits#variants#gwas#gwas-catalog
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill gwas-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/gwas-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill gwas-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The GWAS Catalog provides a centralized interface to access curated SNP-trait associations, studies, and variant data, enabling researchers to quickly retrieve meaningful results without manual data wrangling.

Core Features & Use Cases

  • Trait-centric association queries to fetch SNPs and p-values
  • Variant-level retrieval with study metadata and ancestry context
  • Cross-reference with external resources (Ensembl, dbSNP, gnomAD) for broader interpretation
  • Support for genome-wide significant signals and comprehensive summary statistics workflows
  • Workflow-ready API patterns for programmatic integration and reproducible analyses

Quick Start

Query the GWAS Catalog for trait EFO_0001360 to retrieve genome-wide significant associations.

Frequently Asked Questions about gwas-database

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

FAQPage Schema
How do I query the GWAS Catalog for SNP-trait associations using a REST API?▼

Query the GWAS Catalog via dedicated REST API endpoints to retrieve curated SNP-trait associations. Trait-centric searches fetch SNPs and p-values, returning structured, pagination-aware results for programmatic genetic epidemiology research.

Can I retrieve variant-level study metadata and ancestry context from the GWAS Catalog?▼

Yes, variant-level retrieval from the GWAS Catalog provides study metadata and ancestry context. The API cross-references external resources like Ensembl, dbSNP, and gnomAD to support broader genetic interpretation of genome-wide significant signals.

How does pagination work when fetching large sets of genetic associations from the GWAS Catalog?▼

The REST API exposure is pagination-aware, allowing you to systematically retrieve large sets of curated genetic associations. This ensures comprehensive summary statistics workflows and reproducible analyses without missing structured results across pages.

Do I need to manually wrangle GWAS data to cross-reference variants with Ensembl, dbSNP, or gnomAD?▼

No, the GWAS Catalog API is cross-reference-enabled, automatically linking variant lookups to external resources like Ensembl, dbSNP, and gnomAD. This eliminates manual data wrangling and directly supports broader genetic interpretation.

What is the best way to integrate GWAS Catalog summary statistics into a reproducible genetic epidemiology workflow?▼

Use the workflow-ready API patterns to query genome-wide significant signals and comprehensive summary statistics. The REST API returns structured results designed for programmatic integration, enabling automated and reproducible genetic epidemiology analyses.

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