Cryptic population stratification has been proposed as a confounding factor in GWA studies7. A consequence of population stratification is that segments of ancestry specific chromosomes segregate together in the population. In this situation, variance attributed to causal variants on one chromosome can be predicted by SNPs from segments derived from the same ancestral population on other chromosomes. To investigate whether population stratification could contribute to our results (over and above the ancestry principal component scores included as covariates in the analyses), we performed two kinds of analyses: one in which the similarity matrix for each chromosome was fitted separately (22 analyses estimating one additive genetic variance component per analysis) and a joint analysis which fitted 22 similarity matrices simultaneously (estimating 22 additive genetic variance components in a single analysis) (Online Methods). A higher total variance explained by the 22 individually estimated variances compared to the 22 simultaneously estimated variances would provide evidence of stratification. The total variance explained was 26% for chromosomes fitted separately compared to a total of 23% when fitted together, demonstrating little evidence of population stratification (Figure
