In Open Targets Genetics, 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:
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For studies in Europeans with summary statistics, we use credible set variants as the tag variants.
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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 OT Genetics documentation for more information.