GWAS Catalog Database

Overview

The GWAS Catalog is a curated repository of published genome-wide association studies maintained by NHGRI and EBI. It contains SNP-trait associations from thousands of GWAS publications — genetic variants, associated traits and diseases, p-values, effect sizes, and full summary statistics for many studies.

Scripts

scripts/query_gwas.py — query the GWAS Catalog REST API (stdlib only, JSON to stdout):

python scripts/query_gwas.py variant rs7903146                 # associations for a SNP (strongest first)
python scripts/query_gwas.py trait MONDO_0005148 --size 100    # associations for a trait
python scripts/query_gwas.py gene TCF7L2                       # associations mapped to a gene
python scripts/query_gwas.py find-trait "type 2 diabetes"      # free text -> efo_id
python scripts/query_gwas.py study GCST001795                  # study metadata (+ summary-stats FTP link)

When to Use This Skill