214 trios with genotypes for rs3817198 that translates to a training set of 856 haplotypes. Adapting the statistical model employed by IMPUTE10, allele probabilities of rs3817198 were calculated for individuals with phased and parental origin determined haplotypes for this region (see Supplementary Information for details). With the imputation results for 1,803 cases and 34,909 controls (Table 1), the standard case-control test gave a non-significant OR of 1.04 (P = 0.36). However, when parental origin was taken into account, the paternally inherited allele showed a significant association (OR = 1.17, P = 0.0038). The direct test of parental-origin specific effects that used only the case data was even more significant (P = 6.2 × 10−4). This is because the estimated effect of the C allele when maternally inherited, while not significant (P = 0.11), is protective (OR = 0.91).
