To assess if functional annotation of SNPs is associated with the variance they explain we partitioned the variance explained by SNPs into three components by creating similarity matrices from SNPs in “CNS+” genes, other genes and no genes (Online Methods). The CNS+ genes were the four sets identified by Raychaudhuri et al.28 and comprised the genes in their brain-expressed (specifically, genes with differential CNS expression), neuronal activity, learning and synapse sets. We find that the variance attributable to the CNS+ genes is significantly greater than the proportion of the genome that they represent (31% s.e. 2% vs 20%, p = 7.6 × 10−8) (Figure 1b; Supplementary Table 4).
