between modalities is the sum of number of significant values for the two modalities for each age-SNP-scalp location combination. Permutation tests are applied to the null hypothesis that random permutation of SNP-phenotype association instances, preserving either the scalp locations for the intramodal correspondences and the modality for the intermodal correspondences, as well as the age relation, could be responsible for the observed pattern of correspondences. The tests permute the SNPs in each scalp location for the intramodal correspondences and in each modality for the intermodal correspondences while keeping all other relations constant. That is, it preserves the correlations which are the result of the regression method, as well as the phenotypes in the correspondences. A chi-squared test is used to compare the distribution of the correspondence measures between the observed data and the permuted data calculated for 1000 permutations of the SNPs.
