Several technologies based on chromatin immunoprecipitation (ChIP) have been developed to study the binding of transcription factors (TF) to genomic DNA including microarray (ChIP-chip),ChIP-PET and ChIP-Seq [1].Such methods are unable to determine the target genes of the distal TF binding sites that present a challenge for bioinformatics research.Another challenge is to define whether such distal binding sites are functional,i.e.physically proximal to target gene promoters via chromosome loops attracting RNA polymerase Ⅱ complex for gene transcription [2,3].Therefore,identification of genome-wide distal chromatin interactions that lead the regulatory elements to their target genes may provide novel insights into the study of transcription regulation.Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) method fits these demands requiring development of specialized high-throughput software for data integration and statistical estimation of the data obtained.