gwas-lookup

To look up GWAS associations and eQTL data, you perform a federated variant query across nine genomic databases, including the GWAS Catalog, Open Targets, GTEx, and the EBI eQTL Catalogue. The tool merges and deduplicates parallel query results into unified reports.

Federated variant lookup is the process of querying multiple independent genomic databases in parallel to retrieve genetic associations. It resolves rsIDs to genomic coordinates and merges PheWAS, GWAS, and eQTL data into a single deduplicated dataset.

To find phenotype-wide associations for an rsID, you run a PheWAS scan against UKB-TOPMed, FinnGen, and Biobank Japan. This retrieves phenotype-wide associations and merges them with other genomic data for comprehensive variant annotation.

Yes, you can retrieve fine-mapping credible sets and variant consequences using the Open Targets API. The lookup process resolves rsIDs to alleles and consequences while simultaneously fetching credible set membership from Open Targets.

Yes, you need matplotlib and requests installed to query genomic databases through this tool. Requests handles parallel data retrieval from APIs like Ensembl and LocusZoom, while matplotlib generates figures for the unified reporting.

The best way to merge and deduplicate genetic variant data is to use a federated lookup tool that queries multiple APIs in parallel. This approach automatically consolidates GWAS, PheWAS, and eQTL results into unified markdown reports, CSV tables, and figures.