Based upon a combination of HapMap and our in house polymorphism discovery the target region contains a total of 651 confirmed SNPs with MAF ≥0.01. Of these, 87% are tagged at r2=1 by the markers we had already genotyped, while 94% are tagged at r2=0.9. Of the 13% of markers (n=80) that were not tagged at r2=1, we were able to impute 74% (n=59) at the recommended ‘good practice’(16) value of INFO ≥0.8 using PLINK and 60% (n=48) with an R2 score of ≥0.9 using Beagle, in the fatSNP1 sample. None was associated with schizophrenia at a threshold P<1×10−4 and none was highly correlated with rs1344706 (supplemental table 10). Including these successfully imputed SNPs as if they were directly genotyped, we estimate that our coverage of all known SNPs in the region with MAF ≥0.01 is increased to 97% (r2=1) and to 99% for r2=0.9. Importantly, of the markers (21 out of a total of 651 confirmed markers) that we could not impute, none was even moderately highly correlated with rs1344706 (max r2 =0.13) making it very unlikely they could account for the strong association signal seen at that locus.
