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Supporting Information

Additional Supporting Information may be found in the online version of this article:

Table S1: Primer sequences used for genotyping SNPs. The SNP ID, megabase (Mb) position, forward (F) and reverse (R) primer sequences and the amplicon size in base pairs (bp) are listed for the PCR reactions used for DNA sequencing and genotyping of the congenic lines at the indicated Mb position on chromosome 11.

Table S2: SNPs between B6 and A/J in the 84- to 96-Mb interval (Line 1). Using the Sanger Institute's mouse SNP query (http://www.sanger.ac.uk/cgi-bin/modelorgs/mousegenomes/snps.pl) and the indicated search coordinates for chromosome 11 (‘Location’), we identified 1590 SNPs that could potentially be targeted by probes. The types of SNPs included in the query are listed in the cell following ‘Consequence.’

Table S3: SNP ‘kill list' used in generation of RMA values. In considering the 1590 SNPs we identified within the 84- to 96-Mb congenic region (Line 1), a total of 145 probes on the array contained SNPs and thus, were removed from RMA analysis. We list the probe ID, the probe set as well as the ID indicated on the PGF file (Affymetrix Mouse Gene 1.0 ST array). We used the PGF file for implementing the kill list command in Affymetrix Powertools, and thus, the text file used for this analysis contained only the probe ID and the PGF ID.

Table S4: Nonsynonymous coding SNPs in the 84- to 96-Mb interval (Line 1). Using the Sanger Institute's mouse SNP query (http://www.sanger.ac.uk/cgi-bin/modelorgs/mousegenomes/snps.pl), we identified a total of 148 nonsynonymous coding SNPs in 65 genes between B6 and A/J.

Table S5: Expression QTLs from our data set (Table 2) that were also identified on WebQTL (GeneNetwork). Using the only available cDNA microarray data set available on WebQTL for B6 and A/J alleles, which were derived from AXB BXA recombinant inbred strains (Eye AXBXA Illumina V6.2 (Oct08) RankInv Beta), we first identified all the probe sets targeting any of the genes from our data set (Table 2). We then mapped the expression values of these probesets (27 total) in WebQTL and employed an arbitrary cutoff of LOD > 4 (bolded rows) for reporting whether or not there was a cis- or trans-eQTL (see also Table 2, last column).

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