Individual skill
tooluniverse-phewas
Cross-ancestry / cross-biobank phenome-wide association (PheWAS) and replication. Given ONE variant (rsID) or ONE gene, look up every phenotype it associates with across European/UK (UKB-TOPMed), Finnish (FinnGen), Japanese (BioBank Japan), and Taiwanese (TPMI) biobanks, plus exome-wide gene-burden PheWAS (Genebass), then judge whether an association replicates across ancestries or is population-specific. Use whenever the user asks "what else is this variant/gene associated with", "does this association replicate in other ancestries / biobanks", "is this effect East-Asian-specific", "pleiotropy of rsXXX", "phenome scan", or wants to compare effect sizes/allele frequencies of a variant across populations. NOT for the forward direction (trait → which SNPs: use the gwas-* skills), NOT for fine-mapping a locus (use tooluniverse-gwas-finemapping), and NOT for single-SNP mechanism tracing in one population (use tooluniverse-gwas-snp-interpretation).
skills/tooluniverse-phewas/SKILL.md
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# Cross-Biobank PheWAS & Replication
A **PheWAS is the inverse of a GWAS**: a GWAS fixes a phenotype and scans variants; a PheWAS fixes a variant (or gene) and scans the entire phenome. The scientific payoff of running it across *several* biobanks is **replication and ancestry resolution** — an association seen in one population that reappears in another (with the same effect direction) is far more credible, while one that appears only in East-Asian cohorts may reflect ancestry-specific LD, allele frequency, or biology.
This skill orchestrates one variant/gene across four ancestries plus a gene-burden layer. **Look up, don't guess** — never assert a variant's phenotype associations or effect sizes from memory; the whole point is the live cross-biobank numbers.
## The biobank panel
| Tool | Biobank | Ancestry | Build | Evidence type |
|---|---|---|---|---|
| `UKBTOPMed_phewas_by_variant` | UKB-TOPMed | European (UK) | GRCh38 | per-phenotype assoc (phecodes, ~1,400) |
| `FinnGen_get_variant_finemapping` | FinnGen | Finnish | GRCh38 | credible-set membership (fine-mapping) |
| `BioBankJapan_phewas_by_variant` | BioBank Japan | Japanese | **GRCh37** | per-phenotype assoc |
| `TPMI_phewas_by_variant` | TPMI | Taiwanese (Han) | GRCh38 | per-phenotype assoc (ICD-based) |