Hi there, I have been using open target genetics to visualise the evidence for association of variants with different genes. I specifically used ot look at the Assigned Genes section which had the tabs, Summary, Distance by TSS, pQTL, sQTL, eQTL, enhancer TSS, PCHI-C (Javierre 2016) etc etc. This section was so useful for exploring variant/gene associations, is there a way to see these sections on the new platform merge please?
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Hi Rose!
Thanks for your message!
The V2G widget has now been deprecated. 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.
As for the enhancer–TSS links and PCHi-C (Javierre 2016) datasets, those older resources have been retired as they are outdated. However, we’re in the process of updating this datasource, and we hope to make them available again in the September release, directly within the credible set + variant pages.
Best wishes,
Xiangyu
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