Overall tests that showed a significant association were followed by a more detailed analysis of individual haplotypes comprising SNPs involved in the overall test. P-values were computed by both the method of Shibata et al. and the CHM (with 500 000 permutations) to investigate the correspondence between P-values obtained by these two methods. Haplotype effects were computed by the method of Shibata et al. (54), as the mean phenotypic values among individuals carrying one or two copies of the haplotype of interest.
