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 variance. We used restricted maximum likelihood (REML) to estimate additive genetic variance. To maintain consistency with the single SNP analyses, four principal components were fitted as covariates in the model. Genome-partitioning of genetic variation was done similarly, by fitting chromosomal relationships estimated from all SNPs on a particular chromosome. The cross-validation prediction analyses were done by including the genotypes of all individuals but setting the phenotype of individuals in the validation cohort to unknown, and then performing a regression of the phenotype on the best linear unbiased predictor28. For the Norwegian sample, SNP effects were estimated from the entire CAGES sample by exploiting the mathematical equivalence of a model based upon genome-wide genetic effects and individual SNP effects29.
