Table 1.
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.