Skills gwas-database
🧬

gwas-database

Safe ⚙️ External commands🌐 Network access📁 Filesystem access

Query GWAS Catalog for SNP Trait Associations

Also available from: davila7

Access comprehensive genome-wide association study data from the NHGRI-EBI GWAS Catalog. Search variants by rs ID, trait, or gene to retrieve p-values, effect sizes, and summary statistics for genetic research.

Supports: Claude Codex Code(CC)
📊 69 Adequate
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Using "gwas-database". Show me variants associated with body mass index

Expected outcome:

  • Found 1,847 associations for body mass index (EFO_0004340)
  • Top variants with genome-wide significance (p < 5e-8):
  • rs1558902 (FTO gene) - p=1.3e-71, effect allele: A
  • rs1421085 (FTO gene) - p=4.4e-67, effect allele: T
  • Study sample size: 681,275 individuals across 88 studies

Security Audit

Safe
v4 • 1/17/2026

All 353 static findings are FALSE POSITIVES. This is a documentation-only skill containing no executable code. The static analyzer incorrectly flags Markdown code block backticks as shell commands, genetic research p-value notation (e.g., p=5e-8) as cryptographic algorithms, and the slug 'k-dense' as C2 keywords. The skill documents legitimate API queries to the public NHGRI-EBI GWAS Catalog maintained by EBI and NHGRI.

3
Files scanned
3,215
Lines analyzed
3
findings
4
Total audits

Risk Factors

⚙️ External commands (2)
SKILL.md:42-541 references/api_reference.md:23-785
🌐 Network access (2)
SKILL.md:49-604 references/api_reference.md:28-793
📁 Filesystem access (1)
references/api_reference.md:772
Audited by: claude View Audit History →

Quality Score

41
Architecture
100
Maintainability
83
Content
29
Community
100
Security
78
Spec Compliance

What You Can Build

Find disease-associated variants

Query the GWAS Catalog to identify genetic variants associated with specific diseases or traits for research studies.

Build polygenic risk scores

Retrieve significant SNP associations with p-values and effect sizes to develop polygenic risk prediction models.

Identify drug targets

Explore genetic associations between variants and traits to identify potential therapeutic targets and biomarkers.

Try These Prompts

Find variant associations 
Show me all trait associations for the genetic variant rs7903146 including p-values and risk alleles.
Search by disease trait 
Find all genetic variants associated with type 2 diabetes from the GWAS Catalog with genome-wide significance.
Gene-centric analysis 
What variants in or near the TCF7L2 gene are associated with any traits in the GWAS Catalog?
Summary statistics access 
Retrieve the summary statistics for GWAS study GCST001234 including all tested variants and their effect sizes.

Best Practices

  • Use EFO trait identifiers for precise queries instead of free-text trait names
  • Implement rate limiting (0.1-0.5 second delays) between API requests
  • Cite the GWAS Catalog publication when using data in research

Avoid

  • Making rapid consecutive requests without delays (causes rate limiting)
  • Assuming all associations have the same population applicability
  • Using p-value thresholds lower than 5e-8 for initial discovery

Frequently Asked Questions

What is the GWAS Catalog?
The NHGRI-EBI GWAS Catalog is a curated database of published genome-wide association studies containing SNP-trait associations.
Do I need an API key?
No. The GWAS Catalog APIs are open access and do not require authentication or API keys.
What is genome-wide significance?
Genome-wide significance is p < 5x10-8, the standard threshold for GWAS to account for multiple testing.
How do I find the EFO ID for a trait?
Search the EBI Ontology Lookup Service or use the GWAS Catalog web interface with the trait name.
Can I download full summary statistics?
Yes. Summary statistics are available via FTP download for studies that have deposited data.
What populations are represented in the data?
Ancestry information is provided in study metadata. Historically European-biased; newer studies include more diverse populations.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/gwas-database

Ref

main

File structure

📁 references/

📄 api_reference.md

📄 SKILL.md