This study in human small intestinal tissue strongly corroborates the hypothesis of overarching gene expression changes associated with genotype. The vast majority of observed eQTL were detected in cis; however, the precise number was dependent on the choice of window size. Interestingly, enlarging the cis window to 1 mb from 50 kb did not result in substantial inflation of detected cis-eQTL. On the contrary, due to lower statistical power given the increased number of multiple comparisons combined with expansion of clusters in high LD, there was vast reduction in the number of independent eQTL that could be detected. Further substantiating the reduced diversity using larger window sizes was the comparative analysis of cis-eQTL with other tissues. At 1 mb, fewer expression traits overlap across different cell types.
