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Additional Supporting Information can be found in the online version of this article.

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ANA_22642_sm_SuppTabs.doc4792KSupplemental Table 1. Percentage of EAE susceptible mice in the phenotype-selected congenic backcrosses Supplemental Table 2. Retention of markers during phenotype selection of the B10.S-SJL-EAES congenics Supplemental Table 3. Retention of markers during phenotype selection of the SJL-B10.S-EAER lines Supplemental Table 4. Intervals chosen to represent known EAE BTL in B10.S/SJL strain combination. Supp. Table 5. GWAS and directly interacting genes + mouse homologs Supplemental Table 6. B10.S/SJL known BTL that are polymorphic and members of GWAS and directly interacting genes + mouse homologs Supplemental Table 7. Polymorphic genes that were retained significantly in phenotype selection phase and also are members of Table 5. Supplemental Table 8. Polymorphic genes that localize to EAE5 BTL and are in supplemental Table 5 Supplemental Table 9. Genes that were in first generation of EAE5 MAS congenic lines that are polymorphic and members of Supplemental Table 6 Supplemental Table 10. Canonical pathways with p<0.05, shared by human GWAS/interactors and mouse lists in the conserved evolutionary pathways discovered in this study Supplemental Table 11. Location of polymorphisms in B10.S vs. SJL EAE5 candidate genes. (B6 and SWR and FVB genotypes are included as they are closely related to B10.S and SJL respectively.)

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