As a novel application of the hapConstructor method, we explored multilocus associations in 16 tagging-SNPs across three genes that are functionally related, I-Kappa-B Kinase-Beta (IKBKB), Interleukin 6 (IL6), and Nuclear Factor Kappa-B, Subunit 1 (NFKB1) in two multicenter U.S. case-control studies of colon and rectal cancer. Here, IL6 is linked to rectal cancer.