Table 1

Primary and secondary single marker association in the major histocompatibility complex region in UK, Spanish and Filipino systemic lupus erythematosus

SNP IDPositionF_UAssociated alleleOR (95% CI)pOther diseaseLocation (LD)*Gene expression
rs1269852321881690.11C2.68 (2.16 to 3.33)2.48×10−19TNXB-ATF6B (760 kb)
rs3906272313709030.04A2.84 (2.05 to 3.92)2.95×10−10HLA-C-HLA-B (22 kb)
rs3129868325123550.11T1.67 (1.29 to 2.14)8.65×10−5BTNL2 – DRA (1501 tag SNP) (375 kb)
rs4713419311012150.10C0.40 (0.25 to 0.63)7.55×10−5MUC21 – PSORS1C1 (9 kb)HLA-C
Spanish SLE
rs3130490318470990.04A2.96 (1.95 to 4.51)3.94×10−7C6orf27 (620 kb)
rs3129768327030610.13C1.91 (1.44 to 2.53)7.57×10−6MSBTNL2-DRA (1501 tag SNP) (182 kb)
rs3117213331725830.18A1.76 (1.37 to 2.25)7.18×10−6ACPA+ RA CBD, SSc, PBC, Hep BDPB1-DPB2 (29 kb)
rs409558318161260.20G0.57 (0.43 to 0.77)2.2×10−4MSH5 (20 kb)MSH5§
Filipino SLE
rs9271366326948320.34G2.46 (1.83 to 3.30)1.97×10−9MSDRB1-DQA1 (1502 tag SNP) (87 kb)
rs2571391300318170.16C0.36 (0.22 to 0.59)6.06×10−5MSHLA-G-HLA-H (300 kb)
rs2507987314510120.48A0.48 (0.35 to 0.66)6.80×10−6HLA-B-MICA (6 kb)
rs409558318161260.30G0.56 (0.37 to 0.86)7.47×10−3MSH5 (100 kb)MSH5§
rs2071351331519080.17A0.48 (0.28 to 0.83)8.44×10−3DPB1 (19 kb)HLA-DPB1
  • Stepwise logistic regression association results are shown in italics.

  • Meta-analysis of Spanish and Filipino data for the MSH5 SNP rs409558 revealed a locus-wide level of significance at p=1.92×10−5.

  • * LD surrounding each SNP calculated in control population of each cohort using r2 cut-off >0.8.

  • All HapMap populations, CEU, YRI, CHB and JPT.

  • CEU and YRI only.

  • § CEU only.

  • Data from GEO database (

  • ACPA+RA, anti-citrullinated protein antibody positive rheumatoid arthritis; CBD, chronic beryllium disease; F_U, frequency in unaffected controls; Hep B, hepatitis B; LD, linkage disequilibrium; MS, multiple sclerosis; p, corrected/conditional p value (see Methods); PBC, primary biliary cirrhosis; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism; SSc, systemic sclerosis; T1D, type 1 diabetes.