Agent skill

Gwas Lookup

Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.

MITAuto-check passedResearch & Science

Install Gwas Lookup

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/gwas-lookup .claude/skills/gwas-lookup && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .claude/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/gwas-lookup .agents/skills/gwas-lookup && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .agents/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/gwas-lookup .cursor/skills/gwas-lookup && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .cursor/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/ClawBio/ClawBio.git --path skills/gwas-lookup

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/gwas-lookup .gemini/skills/gwas-lookup && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .gemini/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/gwas-lookup .github/skills/gwas-lookup && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .github/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add ClawBio/ClawBio --skill gwas-lookup -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install ClawBio/ClawBio gwas-lookup --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/gwas-lookup .opencode/skills/gwas-lookup && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "gwas-lookup" agent skill from https://github.com/ClawBio/ClawBio/tree/main/skills/gwas-lookup into .opencode/skills/gwas-lookup/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "gwas-lookup", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: gwas-lookup
GitHub stars: 1.2k
Used in: 2 other repos
Token cost: ~1.1k tokens
SKILL.md length: 408 words
Files: 31
Skills in repo: 104
Repo updated: Oct 9, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.

Works in 6 steps: Variant resolution: Resolve rsID →… → GWAS association lookup: Query GWAS… → PheWAS scanning: Query UKB-TOPMed,… → …
Tasks that involve Bioinformatics
SKILL.md covers Core Capabilities, Input Formats, Databases Queried and Workflow, plus 5 more sections
Runs Python scripts from its folder

What it does

Gwas Lookup is an agent skill from ClawBio/ClawBio. Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 33 other files (for example `INTENTS.json`, `data/demo_rs3798220.json` and `gwas_lookup.py`).

It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

Tasks that involve Bioinformatics

Example prompts

“/gwas-lookup”

Requirements

Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

Variant resolution: Resolve rsID → chr:pos (GRCh38 + GRCh37), alleles, consequence, MAF
GWAS association lookup: Query GWAS Catalog, plus trait associations from Open Targets credible sets
PheWAS scanning: Query UKB-TOPMed, FinnGen, and Biobank Japan for phenotype-wide associations
eQTL lookup: Query GTEx for expression associations. The EBI eQTL Catalogue REST API is retired (HTTP 410); for eQTL Catalogue data use…
Fine-mapping: Retrieve Open Targets credible set membership
Unified reporting: Merge, deduplicate, and rank results across all sources

What it can do on your machine

Read from SKILL.md and the folder at commit dece754. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python, from the files we listed), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- sashagusev.github.io
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Gwas Lookup loads about 1.1k tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 408 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~34
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from ClawBio/ClawBio at commit dece754, republished under its MIT licence (© ClawBio). 408 words, ~1,080 tokens.

Download SKILL.mdSave it as .claude/skills/gwas-lookup/SKILL.md (or your agent's skills folder). This skill also uses 30 other files; get the full folder from GitHub.

name: gwas-lookup
description: Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.
license: MIT
metadata.version: 0.1.0

🔍 GWAS Lookup

You are GWAS Lookup, a specialised ClawBio agent for federated variant queries. Your role is to take a single rsID and query 8 genomic databases in parallel, returning a unified report of GWAS associations, PheWAS results, eQTL data, and fine-mapping credible sets.

Inspired by Sasha Gusev's GWAS Lookup.

Core Capabilities

Variant resolution: Resolve rsID → chr:pos (GRCh38 + GRCh37), alleles, consequence, MAF
GWAS association lookup: Query GWAS Catalog, plus trait associations from Open Targets credible sets
PheWAS scanning: Query UKB-TOPMed, FinnGen, and Biobank Japan for phenotype-wide associations
eQTL lookup: Query GTEx for expression associations. The EBI eQTL Catalogue REST API is retired (HTTP 410); for eQTL Catalogue data use eqtl-catalogue-region-fetch
Fine-mapping: Retrieve Open Targets credible set membership
Unified reporting: Merge, deduplicate, and rank results across all sources

Input Formats

rsID: Any valid dbSNP rsID (e.g., rs3798220, rs429358, rs7903146)

Databases Queried

Database	Endpoint	Coordinates
Ensembl	REST /variation + /vep	GRCh38
GWAS Catalog	EBI REST API	GRCh38
Open Targets Platform	GraphQL v4 (GWAS credible sets)	GRCh38
UKB-TOPMed PheWeb	PheWeb API	GRCh38
FinnGen r12	PheWeb API	GRCh38
Biobank Japan PheWeb	PheWeb API	GRCh37
GTEx v8	Portal API v2	GRCh38
LocusZoom PortalDev	Omnisearch API	Both

Workflow

When the user asks to look up a variant:

Resolve: Query Ensembl for variant coordinates, alleles, consequence
Dispatch: Query all 8 remaining APIs in parallel (ThreadPoolExecutor)
Normalise: Merge results, deduplicate, sort by p-value, flag GWS hits
Report: Generate markdown report + CSV tables + figures

Show full SKILL.md (164 more words)Show less

Example Queries

"Look up rs3798220"
"What are the GWAS associations for rs429358?"
"Search all databases for variant rs7903146"
"GWAS lookup for the LPA missense variant"

Output Structure

output_directory/
├── report.md                    # Full markdown report
├── result.json                  # Standardised result envelope
├── raw_results.json             # Raw API responses (debug)
├── tables/
│   ├── gwas_associations.csv
│   ├── phewas_ukb.csv
│   ├── phewas_finngen.csv
│   ├── phewas_bbj.csv
│   ├── eqtl_associations.csv
│   └── credible_sets.csv
├── figures/
│   ├── gwas_traits_dotplot.png
│   └── allele_freq_populations.png
└── reproducibility/
    ├── commands.sh              # Command that reproduces this run
    ├── environment.yml
    ├── api_versions.json
    └── checksums.sha256         # cd <output_dir> && sha256sum -c reproducibility/checksums.sha256

Dependencies

Required:

requests >= 2.28 (HTTP client)
Python 3.10+

Optional:

matplotlib >= 3.5 (figures; skipped gracefully if absent)

Safety

All processing is local — genetic data never leaves this machine
API queries use only public rsIDs (no patient data transmitted)
24-hour local file cache to reduce API load
Graceful degradation: failed APIs produce warnings, not crashes
Rate limiting per API to respect server policies

Integration with Bio Orchestrator

This skill is invoked by the Bio Orchestrator when:

User mentions "GWAS lookup", "variant lookup", "rsID search"
User provides an rsID and asks about associations, PheWAS, or eQTLs
Query contains keywords: "gwas lookup", "variant search", "rs lookup"

It can be chained with:

clinpgx: Look up pharmacogenomic data for genes near the variant
gwas-prs: If the variant is part of a polygenic score, calculate PRS
lit-synthesizer: Find publications about the variant's associated traits

Files

SKILL.md and 30 other files in skills/gwas-lookup of ClawBio/ClawBio.

SKILL.md
INTENTS.json
data/demo_rs3798220.json
gwas_lookup.py
gwas_lookup_api/__init__.py
gwas_lookup_api/base_client.py
gwas_lookup_api/ensembl.py
gwas_lookup_api/finngen.py
gwas_lookup_api/gtex.py
gwas_lookup_api/gwas_catalog.py
gwas_lookup_api/open_targets.py
gwas_lookup_api/pheweb_bbj.py
gwas_lookup_api/pheweb_ukb.py
gwas_lookup_api/portaldev.py
gwas_lookup_core/__init__.py
gwas_lookup_core/normalise.py
gwas_lookup_core/report.py
gwas_lookup_core/resolve.py
… and 13 more

Open the folder on GitHubat commit dece754

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Gwas Lookup next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Gwas Lookup compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Gwas Lookup this skillClawBio/ClawBio	1.2k	2 repos	~1.1k	Automated safety check: Pass	MIT	yesterday
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	yesterday
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	6 days ago
Clinvar Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.9k	Automated safety check: Notes	Apache-2.0	yesterday
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago
Dbsnp Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.4k	Automated safety check: Notes	Apache-2.0	yesterday

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Questions about Gwas Lookup

What does Gwas Lookup do?

Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more. Gwas Lookup is an agent skill from ClawBio/ClawBio. Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.

When should I use Gwas Lookup?

Gwas Lookup fits situations like: tasks that involve Bioinformatics.

How do I install Gwas Lookup in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill gwas-lookup -a claude-code`. Or copy the skill folder (skills/gwas-lookup in ClawBio/ClawBio) into .claude/skills/gwas-lookup in your project. Claude Code loads it when a task matches its description.

How do I install Gwas Lookup in Codex?

Run `npx skills add ClawBio/ClawBio --skill gwas-lookup -a codex`. Or copy the skill folder (skills/gwas-lookup in ClawBio/ClawBio) into .agents/skills/gwas-lookup in your project. Codex loads it when a task matches its description.

Can I use Gwas Lookup in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add ClawBio/ClawBio --skill gwas-lookup -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/gwas-lookup, .gemini/skills/gwas-lookup, .github/skills/gwas-lookup and .opencode/skills/gwas-lookup in your project.

What does Gwas Lookup need to run?

Going by SKILL.md and its folder, Gwas Lookup needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Gwas Lookup access the network?

SKILL.md names 1 domain. As links in the text: sashagusev.github.io. This is read from the text; nothing was executed.

Is Gwas Lookup safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Gwas Lookup use?

Gwas Lookup is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Gwas Lookup use?

About 1.1k tokens (SKILL.md is roughly 4.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Gwas Lookup?

Skills that share tags, products or a category with Gwas Lookup: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Gwas Lookup?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,155 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 9, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Gwas Lookup

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

🔍 GWAS Lookup

Core Capabilities

Input Formats

Databases Queried

Workflow

Example Queries

Output Structure

Dependencies

Safety

Integration with Bio Orchestrator

Files

Used in 2 other repositories

Compare with similar skills

Similar skills

More from ClawBio/ClawBio

Related

Questions about Gwas Lookup