A subset of 35 genes were initially selected as high priority candidates based on the number of known and inferred sequence differences between the B6 allele (B) and D2 allele (D) and based on expression levels in multiple CNS datasets (table 3). Eleven of these candidates contain missense SNPs segregating in B6×D2 crosses. We also scanned Qrr1 for variation in copy number [54],[55]. Graubert et al. [55] reported segmental duplication in Qrr1 with a copy number gain in D2 compared to B6 near the intelectin 1 (Itlna) gene at 173.352 Mb. We failed to detect any expression signatures of a copy number variation around Itlna in any of the GeneNetwork datasets. However, we did identify an apparent 150 kb deletion across the Ifi200 gene cluster (175.584–175.733 Mb). Affymetrix probe sets 1426906_at, 1452231_x_at, and 1452349_x_at detect Ifi204 and Mnda transcripts in B6 but not in D2. The expression difference is robust enough to generate cis-QTLs with very high LOD scores (>40). This gene cluster has low expression in the CNS (Affymetrix declares this probe sets to be “not present”), but high
