For those loci for which we confirmed genome-wide significance (PITX2, ZFHX3, and HDAC9), we did conditional analyses. After conditioning on the lead SNP in the given region, no SNP showed significance at p<0·01 in PITX2 or ZFHX3, and no SNP showed significance at p<0·005 in HDAC9. Furthermore, all other SNPs in the regions that were associated at p<5×10−8 in the main analysis showed no significance (p>0·05) in any of the analyses after conditioning on the lead SNP. Figure 2 shows plots of –log10(p values) against genomic position in the selected regions for the unconditional and conditional analyses.
