and simulated a set of 500 case and 500 control individuals using the remaining chromosomes. The susceptibility allele varied in frequency between 2.5 and 50%, with larger simulated effect sizes assigned to rarer alleles to ensure comparable power in a hypothetical fully genotyped sample. We also simulated 2,000 datasets where the disease allele had no effect to calibrate region-wide type I error rates for each approach.
