The pattern of genetic variation among 18 commonly used inbred mouse strains was analyzed and is available in the SNP database. Using this information, a high-resolution haplotypic map covering 75 Mb of the mouse genome was produced for 16 Mus Musculus strains. Two strains were excluded because we were unable to produce a stable haplotypic structure when the Cast/Ei and Spret/Ei strains were included. This haplotype map was used to develop a computational method for genetic analysis of phenotypic traits in mice as described in the following paper
G. Liao, J. Wang et al. In Silico Genetics: Identification of A Novel Functional Element Regulating H2-Ea Gene Expression, Science, Vol 306, Issue 5696, 690-695 , 22 October 2004 (full text).
For more detailed methods of constructing mouse haplotype map, please see
J. Wang, G. Liao et al., in Computational Genetics and Genomics: New Tools for Understanding Disease, G. Peltz, Ed. (Humana, Totowa, NJ, 2005).
Please click chromosome number to see the haplotype map