The trans-QTLs in Qrr1 are highly replicable. A large fraction of the transcripts, in some cases represented by multiple probes or probe sets, map to Qrr1 in multiple CNS datasets. For example, there are 747 unique trans-QTLs with LOD scores greater than 4 (genome-wide p-value≤0.01) in the BXD hippocampus dataset (assayed on Affymetrix M430v2 arrays). Out of these highly significant trans-QTLs, 155 are in Qrr1 and the remaining 592 are distributed across the rest of the genome (figure 1). We compared the trans-QTLs in the hippocampus dataset with a similar collection of trans-QTLs (LOD≥4) in the cerebellum dataset (assayed on Affymetrix M430 arrays). Only 101 trans-QTLs in the hippocampus are replicated in the cerebellum (for trans-QTLs that were declared as common, the average distance between peak QTL markers in the two datasets is 1.6 Mb). But it is remarkable that of the subset of common trans-QTLs, 64 are in Qrr1 (figure 1). The replication rate of trans-QTLs in Qrr1 is therefore about 6-fold higher relative to the rest of the genome. When we compared the BXD hippocampus dataset with the
