We know that the the eukaryotic mRNA coding sequences reside on chromosomes inside a nucleus. Recent decades have brought us a wealth of information both on regulation of gene transcription as well as regulation of the chromatin state. However, usually these two issues are studied separately: either one is interested in particular chromatin effects or one studies transcription factor binding pertaining to a particular factor or a gene. Recently, due to the development of next-generation sequencing, we have seen a deluge of genomic data describing, transcription, protein binding, histone modification and (most recently) chromosomal contacts on a genome-wide scale for multiple cell types. In my talk I will discuss our recent efforts to computationally integrate these datasets and improve our understanding of regulatory processes.