on significance, the maximum number of SNPs within each gene passing the nominal uncorrected significance threshold of p < .05 in a single permutation was used as the number of SNPs (NmaxSNPs) across which the SNP-level ΔR2 values were averaged to form gene-level statistics (Gene-Stats). For example, the gene MGLL contained 24 SNPs, but the maximum number of nominally significant SNPs obtained in any one of the 100,000 permutations was 14, so only the 14 highest ΔR2 values in the original analysis and each permutation were averaged to obtain the gene-level -statistic. In PLINK, in contrast, an arbitrary SNP cutoff across all genes would have been pre-specified.
