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alterlab-gwas

Query NHGRI-EBI GWAS Catalog data for SNP-trait associations and p-values.

58|9|Updated Mar 16, 2026
Search Tags:#bioinformatics#summary-statistics#gwas-catalog#genetic-epidemiology#rs-id#trait-search#snp-trait
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-gwas
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-gwas
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-gwas
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-gwas

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

The GWAS Catalog provides curated SNP-trait associations; this skill enables programmatic access to retrieve variant and trait data, p-values, and study metadata for analyses.

Core Features & Use Cases

  • Variant lookups: Query by rs ID to fetch all trait associations and p-values.
  • Trait and gene searches: Retrieve associations by trait (EFO) or nearby genes to explore pleiotropy.
  • Data access & integration: Access summary statistics for studies with deposited data and cross-reference with external resources.

Quick Start

Query associations for a given rs ID or trait and return top GWAS results.

Frequently Asked Questions about alterlab-gwas

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

FAQPage Schema
How do I query GWAS Catalog SNP-trait associations using an rs ID?▼

Query GWAS Catalog SNP-trait associations by inputting a variant rs ID to retrieve all associated traits, p-values, and study metadata. The skill queries the NHGRI-EBI GWAS Catalog REST API to return top results for that specific variant.

Can I search the GWAS Catalog for associations by EFO trait or nearby genes?▼

Yes, GWAS Catalog trait searches retrieve associations by EFO trait terms or nearby genes to explore pleiotropy. Querying by trait or gene-centered parameters returns matching SNP associations and study metadata from the NHGRI-EBI database.

What data fields are returned for SNP-trait associations from the GWAS Catalog?▼

SNP-trait association queries return data fields including rsId, pvalue, efoTrait, and studyId. Results also contain study metadata and support pagination to navigate through large sets of returned associations from the GWAS Catalog REST API.

Does the GWAS Catalog query skill support downloading summary statistics?▼

Yes, GWAS Catalog queries support optional download of summary statistics for studies with deposited data. Access summary statistics to support genetic epidemiology analyses and polygenic risk score calculations through the REST API or web interface.

Can I use GWAS Catalog summary statistics for polygenic risk score analyses?▼

GWAS Catalog summary statistics retrieved via rs ID and trait queries support polygenic risk score analyses. Variant lookups and trait searches provide p-values and study metadata necessary for genetic epidemiology applications and cross-referencing with external resources.

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