The position weight matrix of the CTCF binding motif was obtained from JASPAR74. Genomic locations of CTCF binding motifs were identified using the FIMO75 function of the MEME tool suite76 with a P-value threshold of 0.01. Gastric-specific CBSs were defined as CBS motifs overlapping both a CTCF ChIP-seq peak in at least one ENCODE cell line and a DNaseI hypersensitivity site in gastric tissue from Roadmap epigenomics. We used the set of constitutive CTCF–CTCF loops shared across three cell lines (GM12878, Jurkat, and K562) obtained from the supplementary information of Hnisz et al.13 CBSs that overlap the boundaries of these constitutive CTCF loops were defined as boundary CBSs.