skills.rest
openai
openaiOFFICIAL
Explore all skills by this author →
WebsiteGitHub

gtex-eqtl-skill

Fetch GTEx single-tissue eQTL associations for one variant as JSON.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Querying the GTEx v2 API requires a GRCh38 variant in a specific identifier format, but researchers often have an rsID or GRCh37 coordinates. This Skill resolves any of those inputs to the required GRCh38 query and returns eQTL associations as structured JSON.

Core Features & Use Cases

  • Flexible Variant Input: Accepts exactly one of rsid, grch37, grch38, or variant, with flexible separators like dashes, colons, underscores, or whitespace.
  • Coordinate Resolution: Uses Ensembl REST endpoints to map rsIDs and GRCh37 positions to GRCh38 coordinates before querying GTEx.
  • Structured JSON Output: Returns a single JSON object with eQTL rows, counts, truncation flags, paging info, and warnings.
  • Use Case: A geneticist with rsID rs7903146 wants its single-tissue eQTL associations; the Skill resolves the variant and returns the GTEx results limited by an optional max_results parameter.

Quick Start

Ask the assistant to fetch GTEx eQTL associations for the variant rs7903146 and return the results as JSON.

Frequently Asked Questions about gtex-eqtl-skill

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

FAQPage Schema
How do I query GTEx eQTL data for a variant?▼

Pass one variant as JSON on stdin to the gtex_eqtl.py script, using an rsid, grch37, or grch38 key. The script resolves the input to a GRCh38 variantId and returns single-tissue eQTL associations from the GTEx v2 API as JSON.

What variant input formats does the GTEx eQTL query accept?▼

It accepts exactly one of rsid, grch37, grch38, or variant, either as a JSON object or a plain string treated as GRCh38. Separators can be dashes, colons, underscores, slashes, or whitespace, such as 10:112998590:C:T.

Can I use GRCh37 coordinates with the GTEx v2 API?▼

Yes, GRCh37 coordinates are accepted and resolved to GRCh38 through Ensembl REST lookups before querying GTEx. The script finds the overlapping rsID and maps it across builds, adding warnings if resolution issues occur.

How do I limit the number of eQTL results returned?▼

Include a max_results field with a positive integer in the input JSON object. The output then truncates the eqtls array and sets the truncated flag and eqtl_count_total so you know rows were omitted.

Why does variant resolution fail for my position input?▼

Resolution fails when no rsID is found at the given chromosome and position via the Ensembl overlap endpoint, returning a not_found error. Network failures to Ensembl or GTEx also produce network_error responses in the JSON output.

Related Skills

Explore More Education & Research Skills→
ClawBioClawBio
1.1k

gwas-lookup

Resolve rsIDs to genomic coordinates and aggregate variant evidence from public genomic APIs.

Official
Advanced
felixboehmfelixboehm

gtex-database

Query GTEx REST API v2 for tissue-specific gene expression, eQTLs, and sQTLs.

Community
Intermediate
biomaps-infrabiomaps-infra

db-gtex

Query GTEx REST API v2 for tissue-specific gene expression, eQTLs, and sQTLs.

Official
Intermediate
NeuroAIHubNeuroAIHub
269

gtex-database

Retrieve RNA expression baselines and eQTL associations from the GTEx Portal API.

Official
Intermediate