High-throughput chromosome conformation capture technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, the ability to obtain 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein report a computational method to precisely identify chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD_loop) that predicts chromatin-chromatin interaction (CCI) from low-resolution Hi-C data. The methods are built on a hypothesis that CCIs result in a characteristic nucleosome arrangement pattern flanking the interaction sites. Accordingly, we show that the predictions of CISD and CISD_loop overlap closely with chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) anchors and loops, respectively. Moreover, the methods trained in one cell type can be applied to other cell types with high accuracy. The validity of the methods was further supported by chromosome conformation capture (3C) experiments at 5kb resolution. Finally, we demonstrate that only modest amounts of MNase-seq and Hi-C data are sufficient to achieve ultrahigh resolution CCI map. The predictive power of CISD/CISD_loop supports the hypothesis that CCIs induce local nucleosome rearrangement and that the pattern may serve as probes for 3D dynamics of the genome. Thus, our method will facilitate precise and systematic investigations of the interactions between distal regulatory elements on a larger scale than hitherto have been possible.