As a user of the Open Targets Genetics, I would like to see associations for variants on the X chromosome.
We were investigating a variant (Open Targets Genetics) which is associated with SLE in a GWAS (GWAS Catalog) that doesn’t include sumstats.
The variant is present in OT genetics, but no lead or tag variants are shown.
The code for fine-mapping currently has a note saying that it fails for chrX/Y:
The same problem would be present for coloc, which relies on getting independent sumstats using GCTA-cojo in the same way as for fine-mapping.