Once most or even all variants within a locus have been genotyped (e.g., through sequencing), one can systematically test these variants for association. A common approach is to conduct stepwise forward selection conditional tests to exhaustively test all variants within a region conditional on all other associated variants. This can be done precisely when raw genotypes are available or approximated through tests that model the covariance among variant effects using LD as a proxy (Yang et al., 2012).
