The resulting λGC was 1.075 and λ1000 (references 19-21) was 1.013. Quantile-quantile and Manhattan plots are given in Supplemental Figures 5-6. For association with schizophrenia, 312 SNPs met a genome-wide significance threshold of 5×10−8 (reference 22). These SNPs were in two genomic regions (Supplemental Figure 7): 241 SNPs in the MHC region (chr6:28,502,794-32,536,501, minimum P=4.07×10−11 at rs115939516) and 71 SNPs from chr2:200,715,388-201,040,981 (minimum P=3.33×10−10 at rs35220450). We replicated the MHC association reported in prior studies. 14-17 The chr2 association with schizophrenia is novel, shows highly consistent effects in the Sw1-6 genotyping batches and encompasses C2orf69, C2orf47, C2orf60, and TYW5.
