Sometimes called the SNP- or chip-heritability, an unbiased estimate of the variance explained by markers hM2 is achieved by correlating phenotypic similarity between pairs of individuals with their SNP-based genotypic similarity26, 59, 65. In human populations, the SNP-heritability is broadly between one-third and one-half of total heritability for traits studied to date28, 35, 68. A prediction of phenotype based upon the same set of SNPs would achieve an R2 = hM2 only if the individual SNP effects were estimated without error27. For example, when a multiple-SNP predictor that used the ‘profile scoring’ method was used for height61, it achieved an R2 of 10–15% in out-of-sample predictions. Yet Yang et al (2010)26 estimated that all the SNPs together would explain 40–50% of phenotypic variance if their effects were estimated without error. These results are not inconsistent when the error associated with the estimate of each SNP effect is appreciated.
