To demonstrate its utility, we applied hapConstructor in a multilocus mining of 4 candidate intronic SNPs in IKBKB: rs2272733, rs3747811, rs5029748, and rs10958713; 5 SNPs in IL6: rs1800796, rs1800797, and rs2069827 (promoter); rs2069840 (intron), and rs2069860 (D162V); and 6 intronic SNPs in NFKB1: rs230510, rs3821958, rs4648090, rs4648110, rs4648127, rs11722146, and rs13117745 to comprehensively identify haplotype and composite genotype subsets of these 16 candidate inflammation-related loci associated with colon or rectal cancer. Here, IKBKB is linked to rectal cancer.