Since there occurs an unavoidable rearrangement of the human DNA sequence during its transcription, such a rearrangement will influence the expression of the protein amino acid sequence, which becomes important information on genetic engineering. To approach the problem of chromosome variation derived from the sequence, we utilize bioinformatics procedures to search out chromosome sequence variations, deletion include 1761,inversion include 1963,translocation include 37735 sequences. It can provide the scholars and the researchers of related bioinformatics a more efficient and economic way to obtain desired information on chromosomal variation.