Background: Growing evidence indicates that nucleosome positioning has roles not only in regulating gene transcription [1], but also in shaping distribution patterns of genomic variation.Around single nucleotide sites, nucleosome is positioned [2].On the other hand, DNA sequence can affect nucleosome positioning at some certain [3].Transcription factor binding sites (TFBSs) are generally conserved in evolution, and nucleosomes are often depleted around TFBSs [4].Thus, it is very interesting to investigate the patterns between SNP and nucleosome near TFBSs.