Accessing Open Targets Genetics data following deprecation? (finding diseases associated with a SNP)

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1

I’m kind of new here. Is there a way to get access to the old open targets platform? For example, I want to select a SNP and look at all the different kinds of cancer associated with it, or look at all the different autoimmune diseases associated. Back in the spring of 2025 it was so easy to do that, but now that original site is down and I have no idea how to do that on the new platform, if it’s even possible. Thanks, Val.

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Hi @val5678, and welcome to the Open Targets Community! :tada:

We recently deprecated the Open Targets Genetics web interface (genetics.opentargets.org), following the merge of Open Targets Genetics with the Open Targets Platform. You can read more about this decision in this post.

This means that variant, credible set, and study information is now available to browse in the Open Targets Platform: platform.opentargets.org

(You can still access Open Targets Genetics data through the EMBL-EBI FTP, but I should stress that the data has been superseded by the merged Open Targets Platform, which contains much more up to date information.)

However, as one of my colleagues explained in this post:

We’re currently focusing on gene assignments for associations at the credible set level, so if you’re starting with a specific variant, you’ll need to scroll down to the bottom of the variant page and find an associated study or trait. From there, you can explore gene assignments via L2G scores, as well as individual molecular QTL colocalisations within the credible set.

We have a detailed documentation as well as a recorded intro webinar to the merged Platform. Let me know if you have any specific questions about the Platform that I can help with.

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Thank you so much for the info! I will definitely explore the new site as you stated. If I ever want to cross-check with the older EMBL-EBI FTP that you mentioned, where would I go for that?

Thanks again,

Val

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The files should be available at : http://ftp.ebi.ac.uk/pub/databases/opentargets/genetics/

We have instructions on accessing the FTP in the Platform documentation; you’ll need to modify them for the genetics data. Worth noting that other users have recently reported some issues with accessing FTP data.