I am examining the HWE on 6 HLA genes (A, B, C, DRB1, DQB1, DPB1) in a population which has 2 subpopulations (municipalities). I am using Arlequin v 126.96.36.199 for the HWE test using unphased genotypes. The p-values in one of the HLA genes (B) on the total population is 0.002, on subpopulation 1 is 0.037 and on subpopulation 2 is 0.098. We have set the p limit for a population NOT to be in HWE equal to 0.01. This means that although subpopulation 1 and 2 are in HWE, the total population is not.
Do you have any idea regarding the underlying genetic reasons why this might be happening? Would you consider any additional analysis that could shed some light on this? The rest of the HLA genes (A, C, DRB1, DQB1 and DPB1) are in HWE in all three populations (total + 2 subpopulations).