Table 6 Minor allele frequencies for nonpleoitopic and pleiotropic SNPs found by the BEST method
Type of SNPMultiple testing correctionP-value vs. GWASP-value vs. intergenicMean MAFNo. of SNPs
NonpleiotropicHolm1.676e-150.00880.132963
FDR1.251e-174.975e-850.1227359
PleiotropicHolm0.00287.692e-070.089814
FDR1.005e-120.01250.122847
  • 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.