Comparative analysis with other eQTL studies showed that a substantial fraction of eQTL in the ileum were also eQTL in other tissues (Figure 5). A total of 30.2%, 36.9%, 30.4%, 29.3%, and 32.8% of the significant expression traits reported in monocytes, hepatic tissue, lymphoblastoid cell lines, T cells, and fibroblasts, respectively, were also significant in ileal tissue at an α level of 5% and using 50-kb windows (Supplementary Table 4). If instead an α level of 10% was applied to the data as suggested by Zeller et al,14 the overlap between these tissues and the intestine increased by 6.5% on average. Increasing the window size to 1 MB had a detrimental effect on the observed overlap between cell types.
