gwas-database

Query the NHGRI-EBI GWAS Catalog for SNP-trait associations by rs ID, disease, or gene.

Updated Mar 15, 2026

Search Tags:#bioinformatics #genetics #epidemiology #gwas #snp #trait association

Ready to run

npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill gwas-database-sagunkayastha

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: gwas-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/gwas-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill gwas-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill simplifies the complex process of querying the NHGRI-EBI GWAS Catalog, enabling users to quickly find genetic variant-trait associations and related data without needing to navigate the complex web interface or understand intricate API structures.

Core Features & Use Cases

Variant-Trait Association Search: Find SNPs associated with specific diseases or traits.
Data Retrieval: Access p-values, effect sizes, and summary statistics for genetic associations.
Use Case: A researcher wants to investigate the genetic basis of type 2 diabetes. They can use this Skill to find all known SNPs associated with the disease, their associated p-values, and the risk alleles, which can then be used for further analysis or to build polygenic risk scores.

Quick Start

Use the gwas-database skill to find all SNP-trait associations for 'type 2 diabetes' with a p-value less than 1e-8.

Frequently Asked Questions about gwas-database

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

FAQPage Schema

How do I query the GWAS Catalog for SNP-trait associations?▼

Find SNP-trait associations by searching the NHGRI-EBI GWAS Catalog using rs ID, disease, trait, or gene. The skill retrieves p-values, effect sizes, and summary statistics directly via REST APIs.

What data do I need to retrieve p-values and effect sizes for genetic variants?▼

To retrieve p-values and effect sizes for genetic variants, provide an rs ID, trait, or gene query. The skill fetches summary statistics directly from the NHGRI-EBI GWAS Catalog.

Can I use Python pandas to filter GWAS summary statistics for polygenic risk score development?▼

Yes, you can use pandas to filter GWAS summary statistics for polygenic risk score development. The skill outputs queried association data into structured formats compatible with pandas dataframes.

How do I find all known SNPs associated with a specific disease like type 2 diabetes?▼

Find SNPs associated with a specific disease like type 2 diabetes by querying the trait name. The skill returns matching genetic variants, risk alleles, and p-values from the GWAS Catalog.

Are there limitations to programmatic data access using the NHGRI-EBI REST APIs?▼

Limitations of programmatic data access via NHGRI-EBI REST APIs include network availability and query rate limits. Retrieving extensive trait associations may require handling paginated responses.