Studies of nucleosome positioning around the sites of nucleotide polymorphism are important for analysis of mechanism of genome variation. The distributions of sites single nucleotide polymorphism (SNP), simple insertion, insertion-deletion, and deletion are analyzed for human genome. Characteristics of nucleosomes in the vicinity of the polymorphism sites are also studied. The results indicated polymorphism sites downstream of transcription start sites (TSSs) occurs with an ～211 bp periodicities. For single nucleotide polymorphism, there is also a periodicity with 146 bp. The periodicity with ～211 bp is very close to the periodicity (204 bp) of nucleosome distribution downstream of TSS. The 146 bp periodicity is just the length of linker DNA sequence of a nucleosome. The results indicate that the distribution of polymorphism sites has an intimate relationship with nucleosome positioning. Further studies suggest that most of single nucleotide polymorphism sites are at two ends of core DNA, while sites of insertion, deletion, and insertion and deletion (in-del) tend to be in nucleosome-depleted region. The equally-spaced configuration of nucleosomes downstream of TSS causes the periodic distribution of polymorphism sites. The studies suggest genome variations occur in different regions relatively to nucleosomes, and nucleosome positioning has a role in forming nucleotide polymorphism.