The SNPs included in the genome-wide SNP chips used for identifying SNPs associated with complex traits are typically not the causal variants for a phenotype – more likely they may have an association with the trait because they are in linkage disequilibrium (LD) with one or more causal variants. Since the SNPs on SNP chips are chosen because both their alleles are common they cannot be in complete LD with a causal variant with one rare allele. If the variation generated by the causal variants is completely explained by the genotyped SNPs, then the SNPs potentially can explain all the genetic variation in the trait (i.e. hM2=h2, where hM2 is defined as the genetic variation captured by the SNPs, or markers). Sometimes (e.g.17) hM2 is referred to as "narrow-sense heritability", however in our opinion, the term "narrow-sense heritability" should be reserved as the definition of the total additive genetic variance, that is h2 (see refs9, 18).
