Q-Q plots show quantiles of one dataset against quantiles of a second dataset and are commonly used in GWAS to show a departure from an expected P-value distribution. We generated Q-Q plots for LD-pruned GWAS SNPs (PLINK with the settings “-- indep- pairwise 100 5 0.8”). We compared the sQTLs overlapping with LD-pruned GWAS SNPs and compared the distribution to a random set of SNPs with similar MAF.
