Chromatin in interphase nuclei has a hierarchical 3D structure consisting of compartments, topologically associated domains (TADs), and loops, all of which are essential for molecular processes. Numerous studies suggest that changes in chromatin organization can lead to cancer transformation. We address this phenomenon in chronic lymphocytic leukemia (CLL), the most common type of leukemia in adults. While some simple structural variations (SVs) are known to cause genetic mutations in CLL driver genes, complex SVs are far from being understood. We aim to investigate the functional consequences of complex SVs in CLL to shed light on the disease's development and progression.