Integrative analysis of a large amount of information accumulated in public databases can provide new biological insights, although the lack of robust methodologies has become a major bottleneck. Here, I present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes publicly available information to identify and characterize genome-wide cis-regulatory modules (CRMs). Using 61 genome-wide datasets, CCD successfully pinpointed more than 8,000 CRMs in the mouse genome. Further investigations identified 2,519 polycomb repressive complex 2 (PRC2) target sites as well as a signature of the imprinting control regions (ICRs) in mouse embryonic stem (ES) cells. Moreover, CCD discovered a new type of CRM named ‘multi-functional CRM’, which is presumed to be capable of switching functions by the binding of different combinations of transcription factors. Overall, these results demonstrate the remarkable capability of CCD in the field of integrative analysis.