Sole variant and independent test carried out within the Class I and Class II loci of both protective and deleterious haplotype.

LRT EMPIRICAL p = empirical p-value of the likelihood ratio test obtained after permutation; *comparison of a model including both ‘everything else’ and the ‘particular variant’ with a model including the ‘particular variant’. If the p-value for the LRT is not statistically significant the particular variant is the ‘sole variant’. **Comparison of a model in which ‘everything else’ and the ‘particular variant’ are included with a model including ‘everything else’. If a p-value for the LRT is statistically significant, then this particular variant is associated independently on everything else.