skills.rest
LeonChaoX
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gwas-database

Query NHGRI-EBI GWAS Catalog REST API for SNP-to-trait and gene-to-trait associations.

783|65|Updated Feb 27, 2026
Search Tags:#polygenic risk scores#summary statistics#gwas#variant lookup#trait associations#efo ontology
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gwas-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/gwas-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill gwas-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill helps you find and retrieve curated genome-wide association (GWAS) evidence linking SNPs to traits/diseases, including p-values, effect sizes, study metadata, and (when available) summary statistics.

Core Features & Use Cases

  • Variant (rsID) lookups: Retrieve all trait associations for a given rs ID.
  • Trait/disease searches (EFO): Discover associated variants for a phenotype using EFO ontology terms.
  • Gene-centric discovery: Find variants in/near a gene and then list their associated traits.
  • Summary statistics retrieval: Access harmonized study-level summary statistics via the GWAS Catalog summary statistics API/FTP patterns for downstream genetic epidemiology and polygenic risk score workflows.
  • Study and evidence context: Pull publication identifiers (e.g., PMID, GCST accessions), ancestry information, and cohort/sample size metadata to support interpretation and reproducibility.

Quick Start

Use the gwas-database skill to query NHGRI-EBI GWAS Catalog associations by a variant rs ID (e.g., rs7903146) and return its associated traits with p-values and effect directions.

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 SNP trait associations for a specific rsID?▼

To look up SNP trait associations, query the NHGRI-EBI GWAS Catalog REST API with a variant rsID to retrieve all curated trait associations, including p-values and effect directions for that specific variant.

How do I find GWAS variants associated with a disease using EFO ontology terms?▼

Finding GWAS variants by disease requires searching the GWAS Catalog REST API endpoints using EFO ontology terms to discover associated variants and retrieve study-level metadata for that phenotype.

Can I download GWAS summary statistics for polygenic risk score modeling?▼

You can download GWAS summary statistics for polygenic risk score modeling by accessing the GWAS Catalog summary statistics API or FTP patterns to retrieve full harmonized study-level data for downstream analysis.

How do I retrieve all trait associations for variants near a specific gene?▼

Retrieving trait associations for variants near a gene involves using gene-centric discovery via the GWAS Catalog REST API to find variants in or near the gene, then listing their associated traits and evidence context.

What metadata is included when querying GWAS study associations?▼

Querying GWAS study associations returns publication identifiers like PMID and GCST accessions, ancestry information, cohort sample size metadata, p-values, and effect sizes to support interpretation and reproducibility.

Does the GWAS Catalog REST API support pagination for large variant retrieval queries?▼

The GWAS Catalog REST API supports pagination for studies, associations, variants, and traits endpoints, allowing systematic retrieval of large result sets when querying extensive SNP-to-trait or gene-to-trait links.

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