gwas-database
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
npx skills add LeonChaoX/qinyan-academic-skills --skill gwas-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Seeks GWAS Catalog data to find SNP-trait associations, supports variant lookups by rs ID, searches by disease/trait or gene, and retrieves p-values and summary statistics for use in genetic epidemiology and polygenic risk scoring.
How it works
The skill organizes data concepts around Studies, Associations, Variants, and Traits. It provides REST API endpoints and code examples to:
- Retrieve studies by accession (e.g., GCST IDs) and follow _links to related resources like associations.
- Get variant details via singleNucleotidePolymorphisms/{rsID} and fetch variant associations via /associations with projection for SNP-based results.
- Query trait associations using efoTraits/{efoID}/associations and iterate to extract rsId, pvalue, strongestAllele.
- Access trait information through efoTraits/{efoID} and use summary statistics API at https://www.ebi.ac.uk/gwas/summary-statistics/api for genome-wide data.
- Download and process summary statistics via FTP or REST, filtering by p-values and aggregating across studies.
- Cross-reference results with external resources (Ensembl, gnomAD, etc.) by following _links in API responses.
When to use it
- When you need genetic variant associations for a disease/trait or gene
- When performing SNP lookups and extracting p-values or effect sizes
- When accessing GWAS Catalog summary statistics for large-scale analyses
- When conducting systematic reviews or meta-analyses of GWAS data
What it can touch
- API endpoints for Studies, Associations, Variants, Traits (REST API)
- Summary Statistics API at https://www.ebi.ac.uk/gwas/summary-statistics/api
- External resources linked in responses (e.g., Ensembl, gnomAD, HGNC, EFO)
- FTP site for downloads: ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
Caveats
- Data are curated from published associations and may include inconsistencies; effects are reported as published and may require harmonization
- Genome-wide significance threshold noted as p ≤ 5×10⁻⁸
- Rate limiting and ethical considerations apply to API usage; caching and delays recommended
- License field in this skill shows Unknown; usage should comply with GWAS Catalog terms and repository licenses
# GWAS Catalog Database ## Overview The GWAS Catalog is a comprehensive repository of published genome-wide association studies maintained by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EBI). The catalog contains curated SNP-trait associations from thousands of GWAS publications, including genetic variants, associated traits and diseases, p-values, effect sizes, and full summary statistics for many studies. ## When to Use This Skill This skill should be used when queries involve: - **Genetic variant associations**: Finding SNPs associated with diseases or traits - **SNP lookups**: Retrieving information about specific genetic variants (rs IDs) - **Trait/disease searches**: Discovering genetic associations for phenotypes - **Gene associations**: Finding variants in or near specific genes - **GWAS summary statistics**: Accessing complete genome-wide association data - **Study metadata**: Retrieving publication and cohort information - **Population genetics**: Exploring ancestry-specific associations - **Polygenic risk scores**: Identifying variants for risk prediction models - **Functional genomics**: Understanding variant effects a
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Understanding GWAS Catalog Data Structure
- 2. Web Interface Searches
- 3. REST API Access
- 4. Query Examples and Patterns
- 5. Working with Summary Statistics
- 6. Data Integration and Cross-referencing
- Query Workflows
- Workflow 1: Exploring Genetic Associations for a Disease
- Workflow 2: Investigating a Specific Genetic Variant
- Workflow 3: Gene-Centric Association Analysis
- Workflow 4: Systematic Review of Genetic Evidence
wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
What does the gwas-database skill do?
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill gwas-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.