Investigating multi-SNP haplotype associations, we find that there are three SNP haplotypes showing consistent and significant associations at positions ~206, 210, and 228 cM on chromosome 2q. However, the principal component derived phenotypes were not found to show significant haplotype associations as those found with the latent variables. However there is a 5-SNP haplotype at 234.0–234.5 that shows significant association with the EEG principal component. We have analyzed multiple phenotypes and multiple SNP haplotypes for these association-based analyses, a total of 24 separate analyses, and have reported here the uncorrected p-values. Application of the conservative Bonferroni correction can be easily applied to these p-values, though this study is hypothesis generating rather than hypothesis testing, so we felt this unnecessary. Our results mirror the linkage signal previously found utilizing EEG phenotypes reported by Porjesz et al. [15].
