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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Ann Rheum Dis. 2012 Aug 17;72(3):437–444. doi: 10.1136/annrheumdis-2012-201851

Table 1.

Significant association of SNPs at Xq28 with SLE

Tested EA AS HA AA Meta-analysis
Type SNP Gene Annotation allele P OR Pc P OR Pc P OR Pc P OR Pc P OR
I rs2269368c ARHGAP4 intronic T 1.3E-10 1.38[1.25-1.52] 0.98 1.3E-05 1.32[1.17-1.49] 0.06 3.4E-05 1.32[1.16-1.50] 0.05 M M -- M M
G rs2071129 NAA10 intronic G 1.3E-10 1.38[1.25-1.52] 0.87 4.1E-05 1.29[1.14-1.46] 0.02 1.9E-05 1.32[1.16-1.50] 0.19 0.818 1.01[0.92-1.12] -- 4.7E-03 1.24
I rs2071130 NAA10 intronic C 2.0E-10 1.37[1.25-1.52] 0.99 2.7E-05 1.30[1.15-1.47] 0.03 1.9E-05 1.32[1.16-1.51] 0.11 0.773 1.02[0.92-1.12] -- 3.9E-03 1.24
G rs5945377 RENBP intronic C 8.4E-11 1.38[1.25-1.52] 0.86 1.7E-05 1.31[1.16-1.48] 0.02 3.2E-05 1.31[1.16-1.49] 0.22 0.465 0.96[0.87-1.07] -- 2.2E-02 1.23
I rs5945378 RENBP intronic G 3.6E-10 1.37[1.24-1.51] 0.79 2.0E-05 1.31[1.16-1.48] 0.03 2.9E-05 1.32[1.16-1.50] 0.19 M M -- M M
G rs4898374 TMEM187 intronic T 1.3E-07 1.28[1.17-1.40] 0.42 1.2E-09 1.53[1.34-1.76] 0.32 5.6E-09 1.48[1.30-1.69] 0.03 0.184 1.09[0.96-1.25] -- 6.2E-05 1.33
G rs13397 TMEM187 T245T A 1.9E-10 1.37[1.24-1.51] * 1.8E-07 1.39[1.23-1.58] * 3.0E-09 1.48[1.30-1.69] * 4.2E-03 1.41[1.12-1.79] * 8.4E-26 1.40F
G rs4898375 Intergenic A 3.9E-10 1.36[1.23-1.49] * 5.2E-09 1.52[1.32-1.75] * 1.2E-08 1.46[1.28-1.67] * 1.7E-03 1.44[1.15-1.82] * 1.5E-26 1.42F
G rs633 Intergenic C 1.5E-07 1.26[1.16-1.37] 0.94 2.6E-09 1.55[1.34-1.79] 0.34 1.3E-06 1.37[1.21-1.56] 0.53 0.950 1.00[0.91-1.11] -- 6.0E-03 1.27
I rs12400188 Intergenic G 1.2E-07 1.26[1.16-1.38] 0.82 1.7E-09 1.56[1.35-1.80] 0.30 2.3E-06 1.37[1.20-1.55] 0.42 0.998 1.00[0.99-1.11] -- 6.7E-03 1.27
G rs3027898 Intergenic C 3.4E-07 1.25[1.15-1.36] 0.77 2.3E-09 1.55[1.34-1.79] 0.28 5.5E-06 1.35[1.19-1.54] 0.43 0.948 1.00[0.99-1.19] -- 7.9E-03 1.26
I rs731642 IRAK1 intronic A 1.0E-07 1.27[1.16-1.39] 0.92 8.7E-10 1.58[1.36-1.82] ND 1.9E-06 1.37[1.21-1.57] 0.34 M M -- M M
G rs2239673a IRAK1 intronic C 1.3E-07 1.26[1.16-1.38] 0.96 1.3E-09 1.57[1.35-1.81] 0.35 7.3E-06 1.34[1.18-1.53] 0.46 0.976 1.00[0.90-1.19] -- 7.5E-03 1.27
I rs763737a IRAK1 intronic G 7.0E-08 1.27[1.16-1.39] 0.99 1.5E-09 1.56[1.35-1.81] 0.29 2.5E-06 1.36[1.20-1.55] 0.57 0.999 1.00[0.90-1.11] -- 6.7E-03 1.28
I rs1059703 IRAK1 L532S/intronic G 4.9E-10 1.35[1.23-1.48] ND 4.3E-09 1.53[1.33-1.77] ND 2.8E-07 1.41[1.24-1.60] 0.73 M M -- M M
I rs5945174a IRAK1 intronic G 6.9E-08 1.27[1.16-1.39] 0.98 1.1E-09 1.57[1.36-1.82] 0.29 3.4E-06 1.36[1.19-1.55] 0.53 0.945 1.00[0.91-1.11] -- 6.0E-03 1.28
G rs7061789a IRAK1 intronic G 1.3E-07 1.26[1.16-1.38] 0.96 1.0E-08 1.53[1.32-1.77] 0.22 6.8E-06 1.34[1.18-1.53] 0.28 0.650 0.98[0.88-1.08] -- 1.3E-02 1.26
G rs1059702 IRAK1 S196F A 1.2E-09 1.35[1.22-1.48] * 8.2E-10 1.56[1.35-1.79] * 1.5E-09 1.49[1.31-1.70] * 1.0E-03 1.48[1.17-1.87] * 1.3E-27 1.43F
G rs1059701 IRAK1 V562V G 3.9E-08 1.27[1.17-1.39] 0.75 2.5E-09 1.55[1.34-1.79] 0.24 9.0E-05 1.30[1.14-1.48] 0.09 0.879 0.99[0.89-1.11] -- 7.3E-03 1.26
G rs2734647 MECP2 3'UTR/intergenic T 7.8E-10 1.35[1.23-1.48] * 7.9E-09 1.51[1.32-1.74] * 1.7E-08 1.46[1.28-1.66] * 1.7E-03 1.42[1.14-1.78] * 7.1E-26 1.41F
G rs2075596b MECP2 intronic A 9.0E-09 1.33[1.21-1.46] * 3.0E-07 1.44[1.25-1.66] * 1.8E-09 1.50[1.31-1.71] * 9.8E-04 1.45[1.16-1.80] * 2.2E-24 1.40F
I rs4898467 MECP2 intronic G 1.4E-07 1.27[1.16-1.39] 0.93 8.0E-08 1.48[1.28-1.71] ND 9.0E-05 1.30[1.14-1.48] 0.03 M M -- M M
I rs1734790 MECP2 intronic C 1.4E-07 1.27[1.16-1.39] 0.93 1.5E-07 1.47[1.27-1.70] ND 9.0E-05 1.30[1.14-1.48] 0.02 M M -- M M
I rs909131 MECP2 intronic G 4.1E-07 1.25[1.15-1.37] 0.91 3.6E-08 1.50[1.30-1.73] ND 3.8E-05 1.32[1.16-1.50] 0.14 0.775 0.98[0.89-1.09] -- 1.0E-02 1.24
G rs17435b MECP2 intronic T 3.6E-08 1.28[1.17-1.39] 0.67 2.7E-09 1.53[1.33-1.76] ND 1.8E-04 1.28[1.13-1.46] 0.02 0.522 0.97[0.87-1.07] -- 1.8E-02 1.24
G rs1624766b MECP2 intronic C 5.0E-08 1.28[1.17-1.40] 0.77 1.5E-06 1.42[1.23-1.64] ND 9.9E-06 1.35[1.18-1.54] 0.34 M M -- M M
G rs1734787b MECP2 intronic C 6.4E-10 1.35[1.23-1.49] ND 1.6E-08 1.50[1.31-1.73] ND 4.0E-09 1.48[1.30-1.69] ND 0.021 1.22[1.03-1.45] 0.91 9.4E-25 1.39F
I rs1616369 MECP2 intronic A 4.2E-10 1.36[1.23-1.49] * 6.8E-08 1.48[1.28-1.71] * 2.9E-09 1.49[1.30-1.69] * 4.0E-04 1.50[1.20-1.88] * 1.2E-26 1.43F
I rs1734791b MECP2 intronic T 3.4E-10 1.36[1.23-1.49] ND 5.7E-08 1.49[1.29-1.71] ND 7.8E-08 1.43[1.26-1.63] 0.14 0.210 1.08[0.96-1.21] -- 9.1E-05 1.32
I rs1734789 MECP2 intronic G 6.9E-08 1.27[1.16-1.38] 0.91 3.3E-08 1.51[1.30-1.74] ND 7.6E-05 1.30[1.14-1.48] 0.08 0.492 0.96[0.87-1.07] -- 1.7E-02 1.24
I rs1734792b MECP2 intronic A 3.1E-10 1.36[1.24-1.49] ND 3.8E-08 1.50[1.30-1.73] ND 4.4E-08 1.44[1.26-1.64] 0.14 0.134 1.10[0.97-1.24] -- 1.4E-05 1.34
G rs2239464b MECP2 intronic A 8.4E-08 1.27[1.16-1.39] 0.79 5.3E-08 1.49[1.29-1.72] ND 1.2E-04 1.29[1.13-1.46] 0.03 0.517 0.97[0.87-1.07] -- 1.8E-02 1.23
I rs5945393 MECP2 intronic G 3.5E-08 1.28[1.17-1.40] 0.84 2.3E-08 1.51[1.31-1.74] ND 5.1E-05 1.31[1.15-1.49] 0.08 0.665 0.98[0.88-1.08] -- 1.3E-02 1.25
I rs2872736 Intergenic C 3.4E-08 1.28[1.17-1.39] 0.89 3.0E-08 1.51[1.31-1.75] ND 5.3E-05 1.31[1.15-1.48] 0.09 M M -- M M

Abbreviation: G, genotyped SNP; I, imputed SNP; OR, odds ratio; Pc, P value after conditioning on 6 SNPs shown as "*"; ND, non-distinguishable in conditional testing; F, fixed effect model in meta-analysis; M, missing data. Only SNPs that remained significant association with SLE after correction for multiple comparisons in EA, AS and HA are listed in this table. Position of each SNP is based on GRch37. SNPs that showed consistent association with SLE in all 4 ancestral groups are highlighted in bold. For SNPs that were not tested in conditional testing (P>0.05), the Pc value is denoted as “--”. Previously reported SLE-associated SNPs located in IRAK1,[7] MECP2 [6] and ARHGAP [17] were noted using "a", "b" and "c", respectively, all of which were confirmed to be significantly associated with SLE in EA, AS and HA.