is not susceptible to biases due to SNP density or LD structure (for example, we are not more likely to identify eQTLs in regions of high SNP density—as typically is the case—because we always classify one eQTL SNP for each gene). In this case, if we only consider the GWAS P-values associated with the classified cis eQTL SNPs (namely, we do not consider all genotyped SNPs but exactly one SNP per gene), we expect that under the null the P-values would be drawn from the uniform distribution.
