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Supplementary Table 1: Overview and references of previously reported disease associations for the markers selected in the present study. Marker (alternative name) HLA-A HLA-B rs2239528 (BAT1 -348) rs9281523 (BAT1 NcoI RFLP) rs1129640 (BAT1 +348/+885) rs2071592 (IKBL -63/-62) rs3130062 (IKBL +738) rs909253 (LTA or TNFβ NcoI RFLP/+252/+249) rs1800629 (TNF -308) rs361525 (TNF -238) rs3093662 (TNF +851) rs2076523 Gene HLA-A HLA-B BAT1 BAT1 BAT1 NFKBIL1 NFKBIL1 LTA TNF TNF TNF BTNL2 Disease association JIA, MS, T1D AS, SLE, T1D RA T1D RA RA SLE, pSS, UC CD, GD AS, CD, UC GD JOA Sarcoidosis References 1-8 1; 9-14 15 16 17 18 19; 20 21; 22 22-25 26 27 28 Only markers with direct evidence for disease association are shown. Alternative name: previously used (common) marker names. AS: ankylosing spondylitis; CD: celiac disease; GD: Graves’ disease; JIA: juvenile idiopathic arthritis; JOA: juvenile oligoarthritis; MS: multiple sclerosis; RA: rheumatoid arthritis; SLE: systemic lupus erythematosus; pSS: primary Sjögren’s syndrome; T1D: type 1 diabetes; UC: ulcerative colitis. References: 1. Nejentsev S, Howson JM, Walker NM, Szeszko J, Field SF, Stevens HE et al. Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A. Nature 2007; 450(7171): 887-892. 2. Noble JA, Martin A, Valdes AM, Lane JA, Galgani A, Petrone A et al. Type 1 diabetes risk for human leukocyte antigen (HLA)-DR3 haplotypes depends on genotypic context: Association of DPB1 and HLA class I loci among DR3- and DR4-matched Italian patients and controls. Hum Immunol 2008; 69(4-5): 291300. 3. Noble JA, Valdes AM, Bugawan TL, Apple RJ, Thomson G & Erlich HA. The HLA class I A locus affects susceptibility to type 1 diabetes. Hum Immunol 2002; 63(8): 657-664. 4. Brynedal B, Duvefelt K, Jonasdottir G, Roos IM, Akesson E, Palmgren J et al. HLA-A confers an HLA-DRB1 independent influence on the risk of multiple sclerosis. PLoS ONE 2007; 2(7): e664. 5. Fogdell-Hahn A, Ligers A, Gronning M, Hillert J & Olerup O. Multiple sclerosis: a modifying influence of HLA class I genes in an HLA class II associated autoimmune disease. Tissue Antigens 2000; 55(2): 140-148. 6. Harbo HF, Lie BA, Sawcer S, Celius EG, Dai KZ, Oturai A et al. Genes in the HLA class I region may contribute to the HLA class II-associated genetic susceptibility to multiple sclerosis. Tissue Antigens 2004; 63(3): 237-247. 7. Zeggini E, Donn RP, Ollier WE & Thomson W. Evidence for linkage of HLA loci in juvenile idiopathic oligoarthritis: independent effects of HLA-A and HLADRB1. Arthritis Rheum 2002; 46(10): 2716-2720. 8. Hall PJ, Burman SJ, Laurent MR, Briggs DC, Venning HE, Leak AM et al. Genetic susceptibility to early onset pauciarticular juvenile chronic arthritis: a 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. study of HLA and complement markers in 158 British patients. Ann Rheum Dis 1986; 45(6): 464-474. Rahman P. Genetics of ankylosing spondylitis: an update. Current rheumatology reports 2007; 9(5): 383-389. Aly TA, Baschal EE, Jahromi MM, Fernando MS, Babu SR, Fingerlin TE et al. Analysis of SNPs Identifies Major Type 1A Diabetes Locus Telomeric of the MHC. Diabetes 2008; 57(3): 770-776. Nejentsev S, Reijonen H, Adojaan B, Kovalchuk L, Sochnevs A, Schwartz EI et al. The effect of HLA-B allele on the IDDM risk defined by DRB1*04 subtypes and DQB1*0302. Diabetes 1997; 46(11): 1888-1892. Valdes AM, Erlich HA & Noble JA. Human leukocyte antigen class I B and C loci contribute to Type 1 Diabetes (T1D) susceptibility and age at T1D onset. Hum Immunol 2005; 66(3): 301-313. Smerdel-Ramoya A, Finholt C, Lilleby V, Gilboe IM, Harbo HF, Maslinski S et al. Systemic lupus erythematosus and the extended major histocompatibility complex - evidence for several predisposing loci. Rheumatology (Oxford) 2005; 44(11): 1368-1373. Eike MC, Becker T, Humphreys K, Olsson M & Lie BA. Conditional analyses on the T1DGC MHC dataset: novel associations with type 1 diabetes around HLA-G and confirmation of HLA-B. Genes Immun; In press. Quinones-Lombrana A, Lopez-Soto A, Ballina-Garcia FJ, Alperi-Lopez M, Queiro-Silva R, Lopez-Vazquez A et al. BAT1 promoter polymorphism is associated with rheumatoid arthritis susceptibility. J Rheumatol 2008; 35(5): 741744. Cheong KY, Allcock RJ, Eerligh P, Witt CS, Christiansen FT, McCann V et al. Localization of central MHC genes influencing type I diabetes. Hum Immunol 2001; 62(12): 1363-1370. Kilding R, Iles MM, Timms JM, Worthington J & Wilson AG. Additional genetic susceptibility for rheumatoid arthritis telomeric of the DRB1 locus. Arthritis Rheum 2004; 50(3): 763-769. Okamoto K, Makino S, Yoshikawa Y, Takaki A, Nagatsuka Y, Ota M et al. Identification of I kappa BL as the second major histocompatibility complexlinked susceptibility locus for rheumatoid arthritis. Am J Hum Genet 2003; 72(2): 303-312. de la Concha EG, Fernandez-Arquero M, Lopez-Nava G, Martin E, Allcock RJ, Conejero L et al. Susceptibility to severe ulcerative colitis is associated with polymorphism in the central MHC gene IKBL. Gastroenterology 2000; 119(6): 1491-1495. Castiblanco J & Anaya JM. The IkappaBL gene polymorphism influences risk of acquiring systemic lupus erythematosus and Sjogren's syndrome. Hum Immunol 2008; 69(1): 45-51. Badenhoop K, Schwarz G, Schleusener H, Weetman AP, Recks S, Peters H et al. Tumor necrosis factor beta gene polymorphisms in Graves' disease. J Clin Endocrinol Metab 1992; 74(2): 287-291. Garrote JA, Arranz E, Telleria JJ, Castro J, Calvo C & Blanco-Quiros A. TNF alpha and LT alpha gene polymorphisms as additional markers of celiac disease 23. 24. 25. 26. 27. 28. susceptibility in a DQ2-positive population. Immunogenetics 2002; 54(8): 551555. Stone MA & Inman RD. The genetics of cytokines in ankylosing spondylitis. J Rheumatol 2001; 28(6): 1203-1206. de la Concha EG, Fernandez-Arquero M, Vigil P, Rubio A, Maluenda C, Polanco I et al. Celiac disease and TNF promoter polymorphisms. Hum Immunol 2000; 61(5): 513-517. Sashio H, Tamura K, Ito R, Yamamoto Y, Bamba H, Kosaka T et al. Polymorphisms of the TNF gene and the TNF receptor superfamily member 1B gene are associated with susceptibility to ulcerative colitis and Crohn's disease, respectively. Immunogenetics 2002; 53(12): 1020-1027. Simmonds MJ, Heward JM, Howson JM, Foxall H, Nithiyananthan R, Franklyn JA et al. A systematic approach to the assessment of known TNF-alpha polymorphisms in Graves' disease. Genes Immun 2004; 5(4): 267-273. Zeggini E, Thomson W, Kwiatkowski D, Richardson A, Ollier W & Donn R. Linkage and association studies of single-nucleotide polymorphism-tagged tumor necrosis factor haplotypes in juvenile oligoarthritis. Arthritis Rheum 2002; 46(12): 3304-3311. Valentonyte R, Hampe J, Huse K, Rosenstiel P, Albrecht M, Stenzel A et al. Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet 2005; 37(4): 357-364.