Table 6. Minor allele frequencies for nonpleoitopic and pleiotropic SNPs found by the BEST method.
| Type of SNP | Multiple testing correction | P-value vs. GWAS | P-value vs. intergenic | Mean MAF | No. of SNPs |
|---|---|---|---|---|---|
| Nonpleiotropic | Holm | 1.676e-15 | 0.0088 | 0.1329 | 63 |
| FDR | 1.251e-17 | 4.975e-85 | 0.1227 | 359 | |
| Pleiotropic | Holm | 0.0028 | 7.692e-07 | 0.0898 | 14 |
| FDR | 1.005e-12 | 0.0125 | 0.1228 | 47 |
The BEST method refers to the best method of correction for each condition separately. The P-values are from one-sided Wilcoxon tests. By comparison, the mean MAF for intergenic SNPs was 0.1684, and the mean MAF for GWAS SNPs was 0.1839.