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tooluniverse-gwas-snp-interpretation

Interpret GWAS SNPs by aggregating associations, fine-mapping credible sets, and gene predictions.

1.7k|254|Updated Mar 3, 2025
Search Tags:#genomics#gwas#variant interpretation#snp#fine-mapping#credible sets#Open Targets
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-gwas-snp-interpretation
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-gwas-snp-interpretation
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-gwas-snp-interpretation
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-gwas-snp-interpretation

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires tooluniverse.

What problem does it solve?

A GWAS hit is a region, not a single causal variant, and manually tracing what a SNP does requires querying multiple databases for associations, LD structure, fine-mapping evidence, and gene predictions. This Skill automates that multi-source interpretation so you can answer "what does this SNP do" without guessing functional consequences or mapped genes.

Core Features & Use Cases

  • SNP Annotation Lookup: Retrieves genomic coordinates, alleles, functional consequence, mapped genes, and MAF from GWAS Catalog and Open Targets.
  • Association Discovery: Finds all trait and disease associations with p-values, effect sizes, and study metadata, filtered by genome-wide significance thresholds.
  • Fine-Mapping & Gene Prediction: Identifies credible set membership (SuSiE, FINEMAP) and L2G scores to prioritize likely causal genes, with a fast mode that skips fine-mapping for 2-5 second results.
  • Use Case: Interpret rs7903146 (TCF7L2) to find 100 trait associations including type 2 diabetes, plus 20 fine-mapped credible sets predicting TCF7L2 as the causal gene.

Quick Start

Ask the AI to interpret the SNP rs7903146 and summarize its disease associations, fine-mapping evidence, and predicted causal genes.

Frequently Asked Questions about tooluniverse-gwas-snp-interpretation

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I interpret a GWAS SNP like rs7903146?▼

Call interpret_snp with the rs identifier to retrieve SNP annotation, trait associations, and credible sets in one report. Use include_credible_sets=False for a fast 2-5 second associations-only result, or the default full mode taking 10-30 seconds.

What databases does GWAS SNP interpretation query?▼

It queries GWAS Catalog from EMBL-EBI for SNP annotations and trait associations, and Open Targets Genetics for fine-mapping credible sets and L2G gene predictions. Coverage includes UK Biobank, FinnGen, and over 670,000 associations.

How do I interpret L2G scores for causal gene prediction?▼

L2G scores above 0.5 indicate high confidence in a causal gene, 0.1-0.5 moderate confidence, and below 0.1 low confidence. Scores integrate eQTL, chromatin interaction, and distance data, so a lead SNP may regulate a distant gene via an enhancer.

Why does OpenTargets credible set lookup fail for my SNP?▼

OpenTargets requires the variant ID in chr_pos_ref_alt format, which needs exact allele lookup rather than just an rsID. If coordinates or alleles are missing, the skill skips fine-mapping gracefully and returns associations only.

What are the limitations of GWAS SNP interpretation?▼

Associations do not prove causation, effect sizes vary by study phenotype scale, and results may be ancestry-specific. Data reflects published GWAS only, so the latest studies may not yet be included.

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