How are tag variants identified in the Open Targets Genetics Portal?

In the Genetics Portal, two methods are used to expand lead disease-associated variants into a more complete set of possibly causal tag variants, depending on whether or not a study has summary statistics:

  • For studies in Europeans with summary statistics, we use credible set variants as the tag variants.

  • For studies without sumstats or which aren’t primarily European, we compute the linkage disequilibrium (LD) as a weighted average (based on the number of individuals) of LD correlations from the 1000 genomes super-populations most likely matching the reported study ancestries.

Check out the Genetics Portal documentation for more information.