How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C data are used here to construct the 3D chromatin structure and then shown to be closely connected with a plethora of genetic and epigenetic features and functions. The chromatin structures are characterized by two spatially segregated compartments, which are further dissected into two types of domains with clearly different intra contact patterns and most importantly, the size of chromatin loops. The chromatin loops segregate in the space according to their sizes, reflecting the entropic effect in chromatin structure formation as well as chromosome positioning. Taken together, these results provide clues to the folding and principles of the spatial organization of chromatin fiber, and the resulted clustering of many genome features in the 3D space.