trans-eQTL Methods Matrix eQTL: Pairwise SNP vs. gene. (genome-wide, or for a subset of SNPs e.g. protein-coding) CPMA: joint method (SNP vs. all genes, look at p-value distribution) x-QTL: joint method (SNP vs. all genes, look at mixture of p-values) Instructions of how to run each specific method are in their respective folders.