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gwas-database

Query GWAS Catalog SNP-trait associations via REST API with pagination.

1|Updated Mar 11, 2026
Search Tags:#api#catalog#bioinformatics#gwas#variant#association
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill gwas-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/gwas-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill gwas-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Genetic researchers need a unified way to access SNP-trait associations from the NHGRI-EBI GWAS Catalog, retrieve key statistics, and compare studies without juggling multiple portals.

Core Features & Use Cases

  • REST API access to studies, variants, associations, and traits with built-in pagination and HAL links.
  • Query by variant (rsID), trait (EFO), or gene to fetch associations and metadata, plus access to summary statistics where available.
  • Cross-reference results with external resources (Ensembl, dbSNP, gnomAD) for genomic context and downstream analyses.

Quick Start

Query the GWAS Catalog for trait EFO_0001360 to retrieve all 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 GWAS Catalog SNP-trait associations programmatically?▼

Query GWAS Catalog SNP-trait associations via REST API to retrieve curated study metadata, using built-in pagination and HAL navigation to fetch variant lookups, trait searches, and summary statistics.

Can I search GWAS Catalog associations by EFO trait or rsID?▼

Search GWAS Catalog associations by querying specific variant rsID, EFO trait, or gene to fetch genome-wide significant associations and standardized response fields including pvalue and studyId for reproducible analyses.

Does the GWAS Catalog API support cross-referencing with Ensembl and gnomAD?▼

Cross-reference GWAS Catalog results with external resources like Ensembl, dbSNP, and gnomAD to add genomic context and support downstream bioinformatics variant analysis workflows.

What's the best way to retrieve summary statistics from the NHGRI-EBI GWAS Catalog?▼

Retrieve summary statistics by querying the GWAS Catalog REST API endpoints for studies and associations, utilizing HAL links for navigation and accessing available summary statistics where provided.

Are there limitations to querying large-scale GWAS variant data through REST APIs?▼

Large-scale GWAS variant queries require handling REST API pagination and HAL link navigation to manage response sizes and ensure complete retrieval of standardized association fields like rsId and efoTrait.

Do I need specific bioinformatics knowledge to use GWAS Catalog API endpoints?▼

Using GWAS Catalog API endpoints requires understanding of bioinformatics concepts like rsID variants, EFO traits, and HAL navigation to accurately query and interpret standardized SNP-trait association response fields.

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