We first fitted a linear model including all autosomal SNPs to estimate the proportion of the variance explained by all the SNPs. The Study cohort status and the first 20 principal components from a principal-component analysis of the genome-wide genotypes were fitted as covariates in the model to control for the effects attributable to population structure. Analyses were repeated (i) without PC adjustment, (ii) adjusting for imprecise LD between genotyped SNPs and causal variants (See notes Supplementary Information Table S2 for details), (iii) separately for each study-cohort, (iv) for the total sample excluding one study-cohort at a time, (v) fitting only SNPs on the X chromosome, (vi) separately for men and women and (vii) including a genotype-by-sex interaction term.
