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gwas-database

Retrieve GWAS Catalog SNP-trait associations by rs ID, EFO, gene, or genomic interval.

21|2|Updated Dec 8, 2025
Search Tags:#rest api#genetic epidemiology#summary statistics#gwas#variant lookup#trait associations
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gwas-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/gwas-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill gwas-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers need a reliable way to look up genome-wide association evidence—by variant, trait/disease, gene, study, or genomic region—then retrieve p-values and summary statistics for downstream genetic epidemiology and risk modeling.

Core Features & Use Cases

  • Variant and trait lookup: Find SNP-trait associations by rs ID, EFO trait/disease term, and related metadata.
  • Gene- and region-centric retrieval: Discover associations for variants in or near specific genes, or within chromosomal intervals.
  • Programmatic REST access: Use the GWAS Catalog REST API and Summary Statistics API to automate workflows with consistent JSON outputs.
  • Data integration guidance: Cross-reference API results with Ensembl, dbSNP, gnomAD, Open Targets, PGS Catalog, EFO, and other external resources for interpretation.

Quick Start

Ask the system to use the gwas-database skill to query the GWAS Catalog for associations for rs7903146 and return the most significant trait links with p-values.

Frequently Asked Questions about gwas-database

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

FAQPage Schema
How do I look up GWAS SNP-trait associations by rs ID or gene symbol?▼

Retrieve GWAS SNP-trait associations by querying the GWAS Catalog REST API with an rs ID, gene symbol, EFO trait, or genomic interval to return p-values, effect sizes, and summary statistics.

What is the GWAS Catalog REST API used for in genetic epidemiology?▼

The GWAS Catalog REST API retrieves curated genome-wide association study evidence, enabling genetic epidemiology analysis, pleiotropy exploration, and polygenic risk score variant discovery across published studies.

Can I fetch GWAS summary statistics for a specific chromosomal interval?▼

Yes, you can fetch GWAS summary statistics for a specific chromosomal interval by querying the GWAS Catalog REST API endpoints and parsing the returned HAL-style JSON with pagination support.

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

The GWAS Catalog API supports data integration guidance to cross-reference API results with Ensembl, dbSNP, gnomAD, Open Targets, PGS Catalog, and EFO for functional genomics interpretation.

How do I get p-values and effect sizes from GWAS Catalog associations?▼

Get p-values and effect sizes from GWAS Catalog associations by querying the Summary Statistics API by variant, trait, or publication to retrieve deterministic, query-driven JSON outputs with available summary statistics.

What are the limitations of using the GWAS Catalog REST API for variant lookup?▼

Limitations of using the GWAS Catalog REST API for variant lookup include requiring HAL-style JSON parsing and pagination handling to manage large result sets, which may constrain fully automated polygenic risk score workflows.

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