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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.

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@K-Dense-AI

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GWAS Catalog Database Query Skill

Skill Overview

The GWAS Catalog database query skill provides convenient access to the NHGRI-EBI GWAS Catalog, helping researchers quickly find SNP–trait associations, variant data, and genome-wide association study results.

Applicable Scenarios

  • Genetic epidemiology research: Quickly query genetic associations for specific diseases or traits, identify relevant variant loci, and obtain key statistics such as P values, effect sizes, and confidence intervals.

  • Polygenic risk score construction: Filter independent variants associated with a trait, obtain effect sizes and risk allele information, and download complete summary statistics for use in risk model building.

  • Functional genomics analysis: Query all GWAS associations within a specific gene region, review functional annotations of variants, and explore gene–trait relationships (pleiotropy analysis).

    • Core Features

  • Multi-dimensional association queries: Support queries by rs ID, disease/trait, gene symbol, chromosomal region, and study publication info (PMID, authors), with data covering thousands of GWAS publications.

  • REST API data access: Provide programmatic access to the GWAS Catalog REST API and Summary Statistics API, supporting bulk data extraction, paginated queries, and custom filters, suitable for automated analysis workflows.

  • Complete study metadata: Retrieve GCST study accession numbers, sample sizes, ancestry groups, discovery/replication cohorts and other detailed study information, with cross-references to external resources such as Ensembl, gnomAD, and Open Targets.

    • Frequently Asked Questions

    What is the GWAS Catalog and how do I use it?

    The GWAS Catalog is a catalog of genome-wide association studies jointly maintained by the National Human Genome Research Institute (NHGRI) and the European Bioinformatics Institute (EBI). It contains manually curated SNP–trait association data. Users can query it via the official website (https://www.ebi.ac.uk/gwas/) or programmatically access the data through APIs using this skill.

    How do I query SNP–disease associations by rs ID?

    Provide an rs ID (e.g., rs7903146) to retrieve all trait associations for that variant, including P values, risk allele, effect size (odds ratio OR or beta coefficient), and source studies. Results will show the variant’s genomic coordinates, nearby genes, and association patterns across different populations.

    How do I call the GWAS Catalog API?

    The GWAS Catalog provides a REST API (https://www.ebi.ac.uk/gwas/rest/api) and a Summary Statistics API (https://www.ebi.ac.uk/gwas/summary-statistics/api). No API key is required and they are free to use. This skill wraps common query endpoints and supports searching studies, associations, variants, and traits, automatically handling pagination and rate limiting.

    How do I download GWAS study summary statistics?

    Some GWAS studies provide full summary statistics, which can be downloaded via FTP (ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/) or the Summary Statistics API. Summary statistics include all tested variants (not just genome-wide significant hits) and can be filtered by chromosome, position, and P value—suitable for fine-mapping and colocalization analyses.

    How do I query all variants related to a specific gene?

    Provide a gene symbol (e.g., APOE, TCF7L2) to query all GWAS-associated variants within that gene region (including promoter and regulatory regions). Results will display traits associated with that gene region and help identify gene pleiotropy.

    How often is GWAS Catalog data updated? Do I need to cite it?

    The GWAS Catalog is updated regularly to add newly published studies. When using the data, cite: Sollis E, et al. (2023) The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Research. PMID: 37953337, and note the access date. When discussing specific findings, also cite the original study.

    How do I query genetic variants by chromosomal region?

    Provide a chromosome number and start–end coordinates (e.g., "10:114000000-115000000") to query all GWAS-associated variants in that region—suitable for candidate region studies, fine-mapping, and validating specific loci.

    How does GWAS Catalog differ from other genetic databases?

    The GWAS Catalog focuses on published SNP–trait associations that have been manually curated and mapped to a unified EFO ontology. Unlike dbGaP (which requires access approval), the GWAS Catalog is fully open; unlike the UK Biobank (which provides raw cohort data), the GWAS Catalog provides aggregated study results.