Use when validating GWAS findings, checking variant-gene-disease links, looking up known associations for SNPs or genes, annotating variants with functional consequences, or cross-referencing results against OpenTargets, GWAS Catalog, or Ensembl.
Validate statistical genetics findings against public databases. All APIs are open-access (no authentication required).
Query the OpenTargets Platform (GraphQL) for gene-disease evidence, target tractability, and genetic constraint.
API: query_target(), query_disease_associations(), query_variant(), search()
See reference/opentargets.md for query patterns and examples.
Query the EBI GWAS Catalog for known associations by variant, gene, or trait. Returns curated GWAS associations with p-values, effect sizes, and study metadata.
API: lookup_variant(), lookup_gene(), lookup_trait(), lookup_study()
See reference/gwas-catalog.md for endpoints and examples.
Annotate variants with functional consequences (missense, regulatory, splice), allele frequencies, and CADD/SIFT/PolyPhen scores via the Ensembl Variant Effect Predictor REST API.
API: annotate_variants(), annotate_by_rsid(), get_variant_info()
See reference/ensembl.md for endpoints and examples.
After SuSiE fine-mapping, validate credible set variants:
After FUSION TWAS, validate significant genes:
For any GWAS hit list:
"Validate my top 10 fine-mapping variants against GWAS Catalog and OpenTargets"
"Annotate these credible set SNPs with VEP consequences"
"Check if gene PCSK9 has known associations with LDL cholesterol in OpenTargets"
"Look up rs4420638 in GWAS Catalog"
"What are the functional consequences of variants in my credible set?"