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ukb-ppp-region-fetch

Fetch regional plasma pQTL summary statistics from UK Biobank Pharma Proteomics Project data.

1.1k|257|Updated Feb 25, 2026
Search Tags:#summary statistics#proteomics#SYNAPSE#pqtl#colocalisation#regenie#ukb-ppp
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill ukb-ppp-region-fetch
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: ukb-ppp-region-fetch
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/ukb-ppp-region-fetch
Command: npx skills add https://github.com/ClawBio/ClawBio --skill ukb-ppp-region-fetch

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires synapseclient, requests.

What problem does it solve?

Researchers running colocalisation, fine-mapping, or Mendelian randomisation against a protein exposure need per-variant pQTL summary statistics (beta, SE, p-value) for a specific genomic window, but UKB-PPP releases data as large per-protein tar archives on Synapse that require authentication, manual download, and format harmonisation before use.

Core Features & Use Cases

  • Regional pQTL slicing: Resolves a protein by HGNC symbol or UniProt accession, downloads the per-protein REGENIE archive, and extracts harmonised per-variant rows for any GRCh38 window across seven ancestry strata.
  • Offline bundled slices: Ships pre-computed gzipped JSON slices (e.g. SORT1 / EUR at the 1p13.3 LDL/CHD locus) that run with no Synapse account or network access.
  • Provenance-rich outputs: Writes a variants.tsv in Open Targets chr_pos_ref_alt ALT-effect convention, a manifest.yaml with release and cohort metadata, and a human-readable report.md.
  • Use Case: An agent building a multi-modality coloc render fetches the SORT1 plasma pQTL cis-window in European ancestry and joins it directly against eQTL Catalogue and GWAS Catalog feeds without extra harmonisation.

Quick Start

Ask the agent to fetch the SORT1 plasma pQTL summary statistics for chromosome 1 positions 108774968 to 109774968 in European ancestry from UKB-PPP using the bundled demo.

Frequently Asked Questions about ukb-ppp-region-fetch

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

FAQPage Schema
How do I fetch UKB-PPP pQTL summary statistics for a genomic region?▼

Provide a protein label (HGNC symbol or UniProt accession), ancestry code, chromosome, and start/end base pairs. The skill resolves the protein's Synapse tar archive, extracts the per-chromosome REGENIE file, and returns harmonised per-variant rows for the window.

Do I need a UK Biobank application to access UKB-PPP summary statistics?▼

No UK Biobank application is needed for the summary-statistics layer. Live fetches require only a free Synapse personal access token exported as SYNAPSE_AUTH_TOKEN, and the bundled demo slices need no authentication at all.

Which ancestries does UKB-PPP pQTL data support?▼

UKB-PPP provides EUR (N=46,673), AFR, CSA/SAS, EAS, MID, AMR, and a combined multi-ancestry meta-analysis (ALL, N=47,970). Cohort sizes vary widely, so effect-estimate precision differs substantially across strata.

Can I use this for eQTL or deCODE pQTL data?▼

No. This skill targets UKB-PPP plasma pQTL only. For eQTL or sQTL regional slices use the eqtl-catalogue-region-fetch skill, and the deCODE pQTL panel requires a different upstream source with separate access terms.

Why does the AWS Open Data bucket return AccessDenied for UKB-PPP?▼

The AWS Open Data Registry bucket is advertised as public but anonymous reads return AccessDenied as of 2026-05-15. Synapse with a free personal access token is the only functional access path the data owner currently offers.

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