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tooluniverse-gwas-snp-interpretation

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Interpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gnomAD frequency. Use for 'what does this SNP do', SNP-to-mechanism tracing, and resolving lead-SNP-vs-causal-variant ambiguity. Always considers LD structure before claiming a SNP is mechanistically responsible.

skills/tooluniverse-gwas-snp-interpretation/SKILL.md

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# GWAS SNP Interpretation Skill

**SNP interpretation**: a GWAS hit is a REGION, not a single causal variant. The lead SNP may not be causal — it may be in LD with the causal variant. Always check LD structure and functional annotation before concluding a specific SNP is mechanistically responsible. Use `LDlink_get_proxies(variant="rs...", population="EUR")` to retrieve the high-R² LD proxies (needs a free LDLINK_TOKEN) — a proxy in a coding/regulatory region is a better mechanistic candidate than the lead SNP itself. Fine-mapping (SuSiE, FINEMAP credible sets) narrows the causal set but rarely identifies a single variant with certainty. L2G scores integrate eQTL, chromatin interaction, and distance data to predict the causal gene — a lead SNP mapping to gene A may actually regulate gene B 500 kb away via a distal enhancer.

**LOOK UP DON'T GUESS**: never assume a SNP's functional consequence, mapped gene, or population frequency — always call `gwas_get_snp_by_id` and `OpenTargets_get_variant_info` to retrieve current annotations.

## Overview

Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple sources to provide comprehensive clinical and biological context.

**Use Cases:**
- "Interpret rs7903146" (TCF7L2 diabetes variant)
- "What diseases is rs429358 associated with?" (APOE Alzheimer's variant)
- "Clinical significance of rs1801133" (MTHFR variant)