This software archive contains R scripts used to identify and characterize MYOD1-related loop-chained enhancer modules in WT and SMCHD1-KO cells. The workflow includes: 1. Identification of directly MYOD1-bound super/stitched enhancers and loop-connected related super/stitched enhancers within TADs.2. Annotation of enhancer activity and stitched- or super-enhancer classification.3. Characterization of super/stitched enhancer–enhancer nexus connectivity and loop-hop structure.4. Identification of loop-supported super/stitched enhancer–promoter connections. The repository README provides requirements and usage instructions.