p values, which appear as large values of −log10(p), was evident in the Q-Q plots, especially for P3 amplitude. These subthreshold p values may indicate that there are true associations hidden in the GWAS signal. We list the results for all SNPs with p values less than 10−4 in Tables S2 and S3 for P3 amplitude and the genetic factor score, respectively. Ninety-six SNP associations with P3 amplitude produced p values less than 10−4, whereas approximately 50 would be expected by chance (ignoring LD, which creates a correlation among SNPs). However, the degree of overlap between endophenotypes with respect to the specific SNPs producing small p values was limited (24 in all), especially considering the magnitude of the phenotypic correlation between the two.
