Chromatin Loops represent the finest structural layer of 3D genome organization, appearing as point-to-point interaction significantly enriched relative to local background in contact heatmaps. These loops are typically generated through the loop extrusion mechanism and facilitate long-range element–gene or element–element communication, stabilize TAD boundaries, or support key regulatory configurations. As critical mediators of long-range cis-regulation, chromatin loops play essential roles in transcriptional initiation, execution of gene expression programs, and maintenance of overall genome architecture. In this module, high-confidence loop interactions were identified using the HICCUPS algorithm from juicer toolkit.