According to our permutation results, the weighting score matrix 3 had the best performance, since it gave the lowest q-values among genes (Additional file 1). This matrix was then used to refine gene scores using 1000 permutations (Table 3). In general, the subset of SNP results restricted to the scored genes was enriched for significant effects as the gene rank score increased from 0.5 to 2.0 (see Table 4). Specifically, the minimum FDR based q-value was 0.605 for all SNPs passing QC. The minimum q-value decreased for SNPs in all scored genes, but then increased for genes with score ≥ 1 or ≥ 1.5. However, the minimum q-value became the smallest (0.357) when this analysis was applied to genes with score ≥ 2. There were 47 genes whose scores were ≥ 2, and a total of 2293 SNPs mapped to these genes. For this gene subset, we found many more SNPs having small q values, including 27 SNPs with q-value < 0.4 and 39 SNPs with q-value < 0.5, than those in other gene sets (e.g., gene subset with score
