Studies of gene expression in the central nervous system (CNS) of mice have revealed major strain differences in the expression level of numerous genes located on distal Chr 1, e.g., Copa, Atp1a2, and Kcnj9 [26], [43]–[45]. These differentially expressed genes are strong candidates for the behavioral and neuropharmacological traits that map to this region. We have recently shown that sequence variants near each of these candidate genes are often responsible for the prominent differences in expression [26],[46],[47]. In other words, sequence differences near genes such as Kcnj9 cause expression to differ, and variation in transcript level maps back to the location of the source gene itself. Transcripts of this type are associated with cis-QTLs.
