I want to find cis eQTL for a gene in GTEX for Colon tissue. When I tried to search directly in the QTL gene-centric window, no eQTLs were found for that gene in colon tissue. I then downloaded the all-pair association tables for colon tissue (sigmoid and transverse). Now I am having difficulty interpreting the data and deciding the threshold value to set for the p-val nominal. I just want to identify the strongest eQTL for that particular gene for now. Can anybody guide me related to this: 1) How to interpret the all-pair data sets with only p-val nominal? How is threshold set? 2) How to find the strongest eQTL for a gene in a specific tissue (colon in this case)?