It has been argued (e.g.6,7,18) that the low proportion of variance explained by previous GWA studies of schizophrenia implies that common variants are unimportant to the etiology of schizophrenia. To evaluate this hypothesis we undertook an analysis partitioning the variance tagged by SNPs into five components defined by minor allele frequency (MAF) (Online Methods). For close relatives (who are excluded from our analyses), estimated similarities based upon SNPs with different MAF will be similar. However, very distant relatives inherit chromosome segments from distant common ancestors. If a SNP is more recent than the common ancestor then the relationship between the individuals will not be reflected by the SNP; low MAF SNPs tend to be younger than high MAF SNPs. The variance explained by SNPs with MAF < 0.1 was 2% (s.e. 1%) from a joint analysis of all five MAF bins in the total PGC-SCZ data (Supplementary Table 5, Figure 1c). This low contribution to the total variance explained is likely to partly reflect under-representation of SNPs with low MAF in the analysis (minimum MAF 0.01) relative to those in
