Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is very limited. Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin regions by using only DNA sequences of the interacting open chromatin regions. CHINN is able to predict CTCF- and RNA polymerase II-associated chromatin interactions between open chromatin regions with good across-sample performances and captures various sequence features that are predictive of chromatin interactions. Overall design: 4C-seq experiments to validate predicted chromatin interactions at several gene locus.