(d) Alternative models, filters, and phenotypes. (i) For reoMDD, the minimum p-value over all GWAS SNPs was at the PCLO region SNP rs2715148 (8.4×10−8) which ranked second of all SNPs using the trend test (Table 2). (ii) rs2715148 also had the smallest p-value under a dominant model of SNP action (6.2×10−6). (iii) Given the female predominance in MDD, we analyzed data from females and males separately. For female cases and controls, rs2715148 had the smallest p-value (4.0×10−7) and multiple other PCLO SNPs had p-values in the 10−5 – 10−6 range. For males, most PCLO SNPs had p > 0.05 and the minimum was in the SLC9A9 SNP rs4839627 (9.1×10−7). (iv) Again, given sex differences in MDD prevalence, we investigated SNPs on chrX and chrY more closely. The minimum p-value in chrX pseudo-autosomal region 1 was 0.02. For the non-PAR regions of chrX in females, the SNPs with the smallest p-values were rs11094388 (p=0.0003, intergenic), rs5971108 (p=0.0003, PTCHD1), rs5930667 (p=0.0004, intergenic), rs4618863 (p=0.0005, intergenic), rs2207796 (p=0.0005, in the very large gene DMD), and rs5936428 (p=0.0009, FMR2). For males, the minimum p-value on chrX was at rs10521594 (p=5.4×10−5, intergenic) and 0.22 on chrY.
