1800 from Scotland and 1491 from Northern England. The reason for excluding close relatives is that: (i) their phenotypic covariance will have a large impact on the estimate of variance explained; (ii) the phenotypic covariance of close relatives captures the effects of all causal variants in the genome and not just those in close LD with the genotyped SNPs; and (iii) phenotypic covariance of close relatives can include effects due to shared environment30. We fitted a linear mixed model y = μ + g + e, where y is phenotype, μ is the mean term, g is the aggregate additive genetic effect of all the SNPs, and e is the residual effect. We have previously demonstrated that this model is mathematically equivalent to the model of fitting all the SNPs28; i.e., y = μ + ∑xibi + e, where xi is the number of copies of the reference allele for a SNP i with its additive effect of bi. The covariance structure fitted in the data was the relationship estimated from all SNPs; i.e., cov(yj, yk)=Ajkσg2 + σe2, where Ajk is SNP-derived genetic relationship between individuals j and k, σg2 is the additive genetic variance and σe2 is the residual
