Let gp be a causal genotype in EA populations, and let gp′ be a tag SNP to gp that was detected in an association study, perhaps because gp was not genotyped at all. It is well known (Pritchard and Przeworski, 2001) that the size of trait association at gp′ is related to the LD of gp′ with gp, denoted by ρp, so that αp′=ρpαp. Given a large enough dataset, we expect that the lead variant (the variant with strongest association in the region) will be the one with ∣ρp∣ closest to the maximal value 1, among all available (genotyped or imputed) variants.
