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gwas-database

Query GWAS Catalog SNP-trait associations and retrieve p-values and summary statistics via REST API pagination.

1|Updated Jan 26, 2026
Search Tags:#REST API#summary-statistics#gwas#SNP#p-value#rsID#GWAS Catalog
One-click install
npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gwas-database-victory-hugo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/Victory-Hugo/S2-Agent-Skill/tree/main/skills/databases/gwas-database
Command: npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill gwas-database-victory-hugo

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides streamlined access to the NHGRI-EBI GWAS Catalog, enabling users to query SNP-trait associations and retrieve p-values and summary statistics for genetic variants, supporting epidemiological research and polygenic risk scoring.

Core Features & Use Cases

  • SNP lookups: Retrieve associations for a given rsID across multiple traits and studies.
  • Trait searches: Find variants linked to specific diseases or phenotypes via EFO terms.
  • Cross-study context: Merge results with variant metadata and study information for downstream analyses.

Quick Start

Use the GWAS Catalog REST API to fetch all associations for trait "EFO_0001360" (type 2 diabetes) with pagination. Then inspect top hits and follow variant links to variant details and summaries.

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 by rsID?▼

To query GWAS Catalog SNP-trait associations by rsID, use the REST API to fetch matching records. The service retrieves p-values and summary statistics for the variant across multiple traits and studies, returning paginated, HAL-based responses for programmatic access.

What is the best way to find genetic variants linked to a specific disease or phenotype?▼

Finding genetic variants linked to a specific disease or phenotype involves querying the GWAS Catalog using EFO terms. This retrieves all SNP-trait associations for the phenotype, providing p-values and summary statistics across available studies.

Can I retrieve p-values and summary statistics for genetic associations programmatically?▼

Yes, you can retrieve p-values and summary statistics programmatically. The Skill leverages the GWAS Catalog REST API and optionally the Summary Statistics API with pagination and HAL-based responses to enable automated data retrieval.

How do I get all associations for a trait like type 2 diabetes with pagination?▼

To get all associations for a trait like type 2 diabetes, query the GWAS Catalog REST API using the EFO term EFO_0001360 with pagination enabled. This fetches all matching SNP-trait records and allows you to follow variant links to details.

Does the GWAS Catalog API support searching for SNPs by nearby genes?▼

Yes, the GWAS Catalog API supports searching for SNPs by nearby genes. You can query associations using genomic context, which allows you to explore genetic associations and trait mapping across various studies.

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