The heritabilities explained by SNPs can be partitioned according to SNP annotation by the estimation of genetic similarity matrices from multiple, non-overlapping SNP sets. For the five disorders and the five disorder pairs showing significant SNP correlation, we partitioned the hSNP2 and SNP-based coheritabilities explained by functional annotation, allocating SNPs to one of three sets: (i) SNPs in genes preferentially expressed in the central nervous system (CNS+)34,35, (ii) SNPs in other genes and (iii) SNPs not in genes, with genes defined by 50-kb boundaries extending from their start and stop positions. The SNPs in the CNS+ gene set represented 0.20 of the total set, both in number and megabases of DNA. However, the proportion of the variance explained by SNPs attributable to this SNP set was significantly greater than 0.20 for schizophrenia (0.30; P = 7.6 × 10−8) and bipolar disorder (0.32; P = 5.4 × 10−6) and for schizophrenia and bipolar disorder coheritability (0.37; P = 8.5 × 10−8) (Fig. 2 and Supplementary Table 3). For other disorders or pairs of disorders, the estimates explained by CNS+ SNPs did
