To test the significance of the gene ranking enrichment result for each weighting score matrix, we did 100 random permutations for the q-value enrichment. Since longer genes tend to have more SNPs in GWAS data, to reduce this gene length bias, we restricted the gene length of the random selections in each permutation within ± 50 kb of the average length of our ranked genes. We set the permutation p-value as the proportion of permutation times in which there are higher q-value proportions in randomly selected genes than in our ranked genes in the corresponding score region. For example, there were n genes with a score s under a specific weighting score matrix. Then, in each permutation, n genes were selected from all human genes whose length is ± 50 kb of the average length of the n ranked genes. The q-values for SNPs in the randomly selected genes were calculated based on the GWAS data. For simplicity of comparison, we compared the number of SNPs in each q-value range (e.g., < 0.9, < 0.8, etc.). The proportion of the
