Chromosomal rearrangement (CR) events have been implicated in many tumor and 
non-tumor human diseases. CR events lead to their associated diseases by 
disrupting gene and protein structures. Also, they can lead to diseases through 
changes in chromosomal 3D structure and gene expression. In this study, we 
search for CR-associated diseases potentially caused by chromosomal 3D structure 
alteration by integrating Hi-C and ChIP-seq data. Our algorithm rediscovers 
experimentally verified disease-associated CRs (polydactyly diseases) that alter 
gene expression by disrupting chromosome 3D structure. Interestingly, we find 
that intellectual disability may be a candidate disease caused by 3D chromosome 
structure alteration. We also develop a Web server (3Disease Browser, 
http://3dgb.cbi.pku.edu.cn/disease/) for integrating and visualizing 
disease-associated CR events and chromosomal 3D structure.