Additional supporting information may be found in the online version of this article.

IBD_21479_sm_suppfig1.tif220KSupplemental Figure 1. LOD scores for the 129 N5 cohort, genotypes vs. proximal colon histopathology scores. The peak and the 95% confidence interval are shown as drop-down lines. The LOD plot is shown with distances in cM. These were converted back to Mbp using reference genetically mapped genes and microsatellite markers.
IBD_21479_sm_suppfig2.tif232KSupplemental Figure 2. LOD scores for the 129 N5 cohort, genotypes vs. distal colon histopathology scores.
IBD_21479_sm_suppfig3.tif208KSupplemental Figure 3. LOD scores for the 129 N5 cohort, genotypes vs. composite colon scores.
IBD_21479_sm_suppfig4.tif227KSupplemental Figure 4. LOD scores for the 129 N7 cohort, genotypes vs. colon length.
IBD_21479_sm_suppfig5.tif242KSupplemental Figure 5. LOD scores for the 129 N7 cohort, genotypes vs. E. coli colonies cultured from mouse cecal content.
IBD_21479_sm_suppfig6.tif220KSupplemental Figure 6. LOD scores for the 129 N7 cohort, genotypes vs. animal health based on disease activity index modified to account for growth arrest as well as weight loss.
IBD_21479_sm_supptable1.doc581KSupplemental Table 1. Genome-wide scan for B6 and 129 loci performed on ten 129 N5 mice using 142 single nucleotide polymorphism (SNP) markers. The first column shows the chromosome number, SNP marker, and the source of the original sequence (M- MIT, N- Novartis, C- Celera). The 2nd column shows the marker position at Mbp on each chromosome. The navy blue cells are sites homozygous for 129 DNA, the yellow cells are heterozygous sites, and the light-blue cells are homozygous B6 sites. The grey cells are sites failed to discriminate the two alleles.
IBD_21479_sm_supptable2.doc509KSupplemental Table 2. Genome-wide scan for 129 and B6 loci performed on ten 129 N7 mice (incross-generation 4 and 5) using 142 SNP markers. A similar panel of SNP markers was used as in Supplemental Table 1. The % at the 1st row indicates the % of 129 DNA in each mouse.
IBD_21479_sm_supptable3.doc119KSupplemental Table 3. List of genes in the candidate interval on chromosome 2 (Gdac1) with non-synonymous single nucleotide polymorphisms, B6 vs. 129 and C3Bir. Only those genes have different SNP between B6/129 and B6/C3Bir are included.

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