We followed up on these results by examining the associations between these outcome variables and haplotypes formed from SNPs in this region using the HBAT function in the program FBAT. We chose haplotypes based on three criteria: 1) if there were consecutive SNPs that all showed a large number of significant results in Figure 6; 2) if there were consecutive SNPs with identical positions according to the Affymetrix map; and 3) if there were consecutive SNPs determined to be in the same haplotype block by HAPLOVIEW. Using the three criteria, we find the following haplotypes to be significantly associated with most of our phenotypes of interest: using the first we find haplotype tsc0548180|tsc0512074 at positions 209.412–210.28; using the second criteria, we find haplotypes tsc0052569|tsc0530060 at 225.8190 and tsc0977679|tsc0977680 at 226.7420; and finally using the third criteria, we find tsc1282391|tsc0539848 at 206.707–206.751, and tsc0675766|tsc0040071 at 228.372–228.455. Only the first of these (tsc0548180|tsc0512074) was significantly associated with the first EEG principal component. However, there is a 5-SNP haplotype (tsc0045051|tsc0620679|tsc0620681|tsc1612284|tsc0524593; based on the third criterion) at 234.047–235.395 that is significantly associated with this first EEG principal component.
