Hundreds of transcripts map to Qrr1 with LOD scores ≥3 in neural tissue datasets of BXD RI strains, B6D2F2 intercrosses, and B6C3HF2 intercrosses (table 2). The QTL counts in Qrr1 are far higher than the average of 15 to 35 expression QTLs in a typical 6 Mb interval. The fraction of QTLs in Qrr1 is as high as 14% of all trans-QTLs, and 5% of all cis-QTLs in the whole genome (table 2). The enrichment in trans-QTLs in Qrr1 is even more pronounced when the QTL selection stringency is increased to a LOD threshold of 4 (genome-wide p-value of approximately 0.01). For example, 27% of all highly significant trans-QTLs in the BXD cerebellum dataset are in Qrr1 (table 2). The BXD hippocampus dataset that was assayed on the Affymetrix Exon ST array is an exception—there are over a million probe sets in this array, and the percent enrichment of QTLs in Qrr1 appears to be relatively low. Nevertheless, about 1000 transcripts map to Qrr1 in this exon dataset.
