In addition to confirming the interaction between rs6983267 at the 8q24.21 locus and the MYC TSS18,29,30, chromatin looping interactions implicate several other genes with established roles in CRC biology, including LAMC1, TGFB1 and KLF5. Using Akita31, a convolutional neural network based model for predicting 3D chromatin structure, 20% (1,798 out of 8,880) of the tested variants were predicted to affect 3D genome folding; 244 variants mapped to a CTCF motif, and approximately half of these (n = 121) were predicted to severely affect the 3D chromatin structure. Here, KLF5 is linked to colorectal carcinoma.