Table 3.
Reported SLE susceptibility loci and risk of LN among loci included in the LN meta-analysis
| Gene | dbSNP Identifier | Genetic Model of Inheritance | Location | Samples (n) | RA | OR (95% CI) | Genomic Control P Value | Directiona | References | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Set I | Set II | Set III | |||||||||
| IL12RB2 | rs1874791 | D | 1p31.2 | 1987 | A | 0.85 (0.68 to 1.06) | 5.88E-01 | − | + | − | 41 |
| PTPN22 | rs2476601 | A | 1p13.2 | 690 | A | 0.83 (0.22 to 3.1) | 9.84E-01 | ? | + | ? | 10, 41–43 |
| FCGR2A | rs1801274 | D | 1q23.3 | 1786 | A | 1.12 (0.89 to 1.41) | 5.42E-01 | + | + | ? | 10, 43, 44 |
| TNFSF4 | rs2205960 | R | 1q25.1 | 1770 | T | 2.41 (1.59 to 3.64) | 7.82E-05 | + | + | ? | 9, 41 |
| NMNAT2 | rs2022013 | D | 1q25.3 | 1969 | C | 1.07 (0.86 to 1.32) | 8.23E-01 | − | − | − | 9, 10, 41 |
| IL10 | rs3024505 | A | 1q32.1 | 690 | A | 0.89 (0.66 to 1.21) | 7.67E-01 | ? | − | ? | 9, 41 |
| LYST | rs9782955 | D | 1q42.3 | 832 | T | 0.86 (0.63 to 1.18) | 6.05E-01 | ? | − | − | 41 |
| IFIH1 | rs1990760 | R | 2q24.2 | 1779 | C | 0.80 (0.57 to 1.08) | 2.96E-01 | + | + | ? | 41 |
| STAT4 | rs7574865 | D | 2q32.2 | 1137 | T | 1.38 (1.06 to 1.81) | 2.84E-02 | − | ? | ? | 9, 10, 41, 43, 45 |
| PXK | rs6445975 | D | 3q14.3 | 1988 | G | 0.98 (0.8 to 1.21) | 1.00E+00 | + | + | − | 10, 43 |
| BANK1 | rs10516487 | A | 4q24 | 1834 | A | 0.84 (0.72 to 0.99) | 4.10E-02 | − | − | ? | 9–12, 41, 43 |
| PTTG1 | rs2431697 | D | 5q33.3 | 1781 | C | 0.86 (0.69 to 1.07) | 2.60E-01 | + | + | ? | 10, 41, 43 |
| HLA-DR2 | rs9271366 | D | 6p21.32 | 1798 | G | 1.37 (1.09 to 1.71) | 5.73E-02 | + | + | + | |
| HLA-DR3 | rs2187668 | D | 6p21.32 | 1955 | T | 1.55 (1.25 to 1.92) | 3.67E-05 | + | + | + | 11, 41, 43 |
| UHRF1BP1 | rs11755393 | D | 6p21.31 | 1844 | G | 1.08 (0.87 to 1.34) | 8.04E-01 | − | − | ? | 41 |
| ATG5 | rs6568431 | A | 6q21 | 1931 | A | 1.11 (0.96 to 1.29) | 1.68E-01 | + | + | − | 10, 41, 43 |
| TNFAIP3 | rs6920220 | D | 6q23.3 | 1965 | A | 0.92 (0.75 to 1.14) | 5.51E-01 | − | − | + | 41 |
| ICA1 | rs10156091 | A | 7p21.3 | 689 | T | 0.93 (0.66 to 1.32) | 1.00E+00 | ? | − | ? | 10, 41, 43 |
| JAZF1 | rs849142 | R | 7p15.1 | 1993 | C | 1.05 (0.83 to 1.35) | 1.00E+00 | − | − | + | 41 |
| IRF5 | rs12537284 | A | 7q32.1 | 1800 | A | 1.02 (0.84 to 1.23) | 1.00E+00 | − | + | ? | 10, 41 |
| BLK | rs2248932 | R | 8p23.1 | 1836 | A | 1.32 (0.97 to 1.78) | 9.30E-02 | + | + | ? | 9, 10 |
| LYN | rs7829816 | R | 8q12.1 | 1119 | G | 1.30 (0.72 to 2.36) | 6.65E-01 | − | ? | ? | 10 |
| PHRF1-IRF7 | rs4963128 | R | 11p15.5 | 680 | T | 0.62 (0.34 to 1.13) | 2.02E-01 | ? | − | ? | 10, 41, 43 |
| PDHX-CD44 | rs2732552 | A | 11p13 | 1966 | T | 0.82 (0.7 to 0.94) | 1.15E-02 | − | − | − | 46 |
| DDX6 | rs503425 | R | 11q23.3 | 1130 | C | 2.02 (1.15 to 3.53) | 2.30E-02 | − | ? | ? | 9, 41 |
| SLC15A4 | rs6486730 | R | 12q24.32 | 1073 | G | 1.11 (0.79 to 1.56) | 9.11E-01 | − | ? | ? | 41 |
| ITGAM | rs9888739 | A | 16p11.2 | 1841 | T | 1.42 (1.17 to 1.72) | 1.34E-03 | + | + | ? | 10, 41, 43 |
| IRF8 | rs12444486 | R | 16q24.1 | 1148 | T | 0.96 (0.72 to 1.29) | 1.00E+00 | − | ? | ? | 41 |
| CD226 | rs727088 | D | 18q22.2 | 1842 | A | 1.13 (0.88 to 1.44) | 5.95E-01 | + | + | ? | 47 |
| UBE2L3 | rs5754217 | D | 22q11.21 | 1974 | T | 0.98 (0.79 to 1.21) | 1.00E+00 | − | + | + | 10, 41, 43 |
| SCUBE1 | rs2071725 | D | 22q13.2 | 1794 | A | 0.89 (0.69 to 1.14) | 6.68E-01 | − | − | ? | 10 |
dbSNP, Single Nucleotide Polymorphism Database; RA, reference allele; D, dominant; A, additive; R, recessive.
a
Symbols represent the direction of the risk effect in sets I, II, and III, respectively: ?, not in meta-analysis; −, OR <1; +, OR >1.