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finngen-phewas-skill

Fetch FinnGen PheWAS association summaries for a single variant from rsID or genomic coordinates.

5.3k|765|Updated Mar 4, 2026
Search Tags:#genomics#Ensembl#rsID#variant lookup#grch38#PheWAS#finngen
One-click install
npx skills add https://github.com/openai/plugins --skill finngen-phewas-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: finngen-phewas-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/finngen-phewas-skill
Command: npx skills add https://github.com/openai/plugins --skill finngen-phewas-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Looking up phenome-wide association study (PheWAS) results for a genetic variant in FinnGen requires resolving identifiers across genome builds and querying the FinnGen API manually. This Skill accepts an rsID, GRCh37, or GRCh38 variant string, resolves it to the canonical GRCh38 query via Ensembl, and returns a compact summary of FinnGen associations.

Core Features & Use Cases

  • Flexible variant input: Accept exactly one of rsid, grch37, grch38, or a generic variant string, with automatic resolution to the canonical GRCh38 chr:pos-ref-alt query using Ensembl REST endpoints.
  • Compact PheWAS summaries: Return association counts, truncation status, regions, and a FinnGen variant URL, with max_results controlling output size and save_raw writing the full payload to disk.
  • Use Case: A researcher asks for FinnGen associations for rs7903146; the Skill resolves the rsID through Ensembl, queries the FinnGen R12 API, and returns the top 10 associations with a link to the variant page.

Quick Start

Ask the assistant to fetch FinnGen PheWAS associations for the variant rs7903146 and summarize the top results.

Frequently Asked Questions about finngen-phewas-skill

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

FAQPage Schema
How do I look up FinnGen PheWAS results for a variant?▼

Provide one variant identifier as JSON on stdin, such as {"rsid":"rs7903146"} or {"grch38":"10:112998590-C-T"}, and the script queries the FinnGen R12 API. It returns a JSON summary with association counts, top associations, and a variant URL.

What variant input formats does the FinnGen lookup accept?▼

It accepts exactly one of rsid, grch37, grch38, or a generic variant field. Coordinate strings use flexible separators like 10:112998590-C-T, and rsID or GRCh37 inputs are resolved to GRCh38 through Ensembl before querying FinnGen.

Can I convert GRCh37 coordinates to GRCh38 for FinnGen queries?▼

Yes, GRCh37 inputs are resolved by finding the overlapping rsID via the Ensembl GRCh37 server, then looking up the GRCh38 mapping. The canonical GRCh38 variant is used for the FinnGen query and reported in the output.

How do I get the full FinnGen association payload instead of a summary?▼

Set save_raw to true in the input JSON, optionally with raw_output_path. The complete API response is written to that file (or a default path in /tmp), and the output reports raw_output_path instead of pasting large arrays.

Why does the FinnGen lookup return zero associations for my variant?▼

A 404 from the FinnGen API means the variant is not present in the FinnGen PheWAS dataset, so the output returns ok=true with zero associations and a warning. It can also fail earlier if Ensembl cannot resolve the input to a known rsID.

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