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GWAS Lookup

Query a variant by rsID across nine genomic databases in a single call: GWAS Catalog, ClinVar, gnomAD, GTEx, Open Targets, PheWAS, Biobank Japan, FinnGen, and UK Biobank. Returns unified trait associations, allele frequencies, eQTL data, and clinical significance.

Quick Demo

python3 skills/gwas-lookup/gwas_lookup.py \
  --demo \
  --output /tmp/gwas_lookup_demo

CLI Reference

# Look up a single variant
python3 skills/gwas-lookup/gwas_lookup.py \
  --rsid rs3798220 \
  --output <report_dir>

# Skip specific databases
python3 skills/gwas-lookup/gwas_lookup.py \
  --rsid rs3798220 \
  --skip gtex,bbj \
  --output <report_dir>

# Demo mode (pre-fetched rs3798220)
python3 skills/gwas-lookup/gwas_lookup.py \
  --demo \
  --output /tmp/gwas_lookup_demo
Argument Required Description
--rsid Yes* Variant rsID to query
--output Yes Output directory for report and tables
--skip No Comma-separated list of databases to skip
--demo No Run with pre-fetched demo data for rs3798220

*Not required when using --demo.

Output

  • report.md -- Unified variant report with cross-database findings
  • tables/ -- Per-database association tables (CSV)
  • commands.sh -- Reproducibility script
  • checksums.sha256 -- Output verification