In terms of trait-affecting variants, we consider a subset of M SNPs from the set of S SNPs. Each SNP in this subset tags variation in a segment that bears a causal influence on the phenotype. We refer to M as the associated number of SNPs. We assume that the M associated SNPs jointly capture the full SNP-based heritability for the trait of interest and, moreover, that each associated SNP has the same theoretical R2 with respect to the phenotype. In the simulation studies, we also assess the impact of violations of this ‘equal-R2’ assumption.
