Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Investigate API mapped gene kb range #1575

Open
earlEBI opened this issue Feb 24, 2025 · 0 comments
Open

Investigate API mapped gene kb range #1575

earlEBI opened this issue Feb 24, 2025 · 0 comments
Assignees

Comments

@earlEBI
Copy link

earlEBI commented Feb 24, 2025

User query:
Example API search:
https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs340630

rs340630 - mapped gene shows in UI as AFF1
https://www.ebi.ac.uk/gwas/variants/rs340630

According to our FAQ:
The annotation available on our online search interface includes any Ensembl genes in which a SNP maps, or the closest upstream and downstream gene within 50kb. More detailed mapping information is available through our REST API including all Ensembl and RefSeq genes mapping within 50kb upstream and downstream of each GWAS Catalog variant.

From this, I would expect genes to show in the API response up to 50kb distance away.
However, multiple genes are returned in the API response, with 'distance' up to 122,860 (KLHL8).

Please investigate what the returned range of mapped genes is for our API, in terms of distance.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants