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Table 2 Association evidence for 15 single nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS), replication and combined studies

From: Association analyses confirm five susceptibility loci for systemic lupus erythematosus in the Han Chinese population

Chr SNP Gene Stages* Allele MAF OR (95% CI) P -value a Meta-analysis P Q I 2
Cases Controls OR (95% CI) P -value b
1q25 rs1418190 TNFSF4 i G/A 0.3089 0.3579 0.80 (0.71, 0.91) 5.26 × 10−04 0.81 (0.75, 0.87) 1.08 × 10−08 0.92 0
ii G/A 0.3250 0.3738 0.81 (0.74, 0.88) 5.30 × 10−06
1q25 rs4916219 TNFSF4 i A/G 0.2722 0.3166 0.81 (0.71, 0.92) 1.15 × 10−03 0.80 (0.75, 0.86) 7.77 × 10−09 0.87 0
ii A/G 0.2903 0.3402 0.79 (0.73, 0.87) 1.74 × 10−06
2p16.3 rs2048979 NRXN1 i G/A 0.4173 0.4743 0.79 (0.71, 0.89) 1.26 × 10−04 0.87 (0.82, 0.91) 1.35 × 10−03 0.11 60.01
ii G/A 0.4238 0.4521 0.89 (0.82, 0.97) 7.72 × 10−03
iii G/A 0.4146 0.4517 0.86 (0.79, 0.94) 6.14 × 10−07
3q13.33 rs12494314 TMEM39A i G/A 0.2930 0.3318 0.83 (0.74, 0.95) 5.16 × 10−03 0.84 (0.80, 0.89) 1.01 × 10−09 0.87 0
ii G/A 0.2999 0.3455 0.81 (0.74, 0.89) 5.62 × 10−06
iii G/A 0.2997 0.3363 0.84 (0.78, 0.94) 6.01 × 10−08
3q13.33 rs6804441 CD80 i G/A 0.2949 0.3436 0.80 (0.70, 0.91) 4.90 × 10−04 0.86 (0.82, 0.91) 5.90 × 10−04 0.17 46.88
ii G/A 0.3038 0.3394 0.85 (0.78, 0.93) 3.71 × 10−04
iii G/A 0.3189 0.3359 0.93 (0.84, 1.02) 4.95 × 10−02
3q13.33 rs2222631 CD80 i G/A 0.4280 0.4743 0.83 (0.74, 0.93) 1.90 × 10−03 0.92 (0.88, 0.97) 9.08 × 10−02 0.05 74.41
ii G/A 0.4420 0.4666 0.91 (0.83, 0.99) 2.21 × 10−02
iii G/A 0.4600 0.4605 1.00 (0.92, 1.09) 3.30 × 10−01
3q29 rs9866504 FLJ25996 i A/G 0.1148 0.1568 0.70 (0.59, 0.83) 4.43 × 10−05 0.85 (0.79, 0.92) 6.44 × 10−02 0.01 83.81
ii A/G 0.1248 0.1471 0.83 (0.73, 0.94) 2.34 × 10−03
iii A/G 0.1225 0.1343 0.90 (0.73, 1.03) 7.60 × 10−02
4q34 rs997779 GPM6A i C/A 0.1324 0.1019 1.35 (1.12, 1.62) 1.50 × 10−03 1.17 (1.08, 1.26) 4.48 × 10−02 0.07 69.38
ii C/A 0.1216 0.1080 1.15 (1.00, 1.31) 4.54 × 10−02
iii C/A 0.1250 0.1113 1.17 (1.08, 1.26) 1.32 × 10−02
5q34 rs2431697 MIR146A i G/A 0.1391 0.1846 0.71 (0.61, 0.84) 3.76 × 10−05 0.69 (0.65, 0.75) 1.15 × 10−22 0.68 0
ii G/A 0.1410 0.1706 0.80 (0.71, 0.90) 1.49 × 10−04
iii G/A 0.1250 0.1722 0.69 (0.58, 0.82) 3.95 × 10−19
5q34 rs1862390 MIR146A i G/A 0.3552 0.3934 0.85 (0.75, 0.96) 8.30 × 10−03 0.87 (0.81, 0.94) 1.37 × 10−04 0.59 0
ii G/A 0.3497 0.3745 0.90 (0.82, 0.98) 1.59 × 10−02
iii G/A 0.4833 0.4363 1.20 (0.70, 2.07) 5.30 × 10−01
11p13 rs2732547 CD44 i A/G 0.2156 0.2560 0.80 (0.70, 0.92) 1.47 × 10−03 0.82 (0.77, 0.87) 1.55 × 10−11 0.82 0
ii A/G 0.2170 0.2479 0.84 (0.76, 0.93) 6.50 × 10−04
iii A/G 0.2075 0.2436 0.81 (0.67, 0.83) 2.56 × 10−09
11p13 rs1559759 CD44 i A/C 0.3518 0.3145 1.18 (1.05, 1.34) 8.04 × 10−03 1.08 (1.03, 1.14) 4.57 × 10−02 0.14 55.20
ii A/C 0.3515 0.3266 1.12 (1.02, 1.22) 1.42 × 10−02
iii A/C 0.3386 0.3350 1.02 (0.93, 1.11) 2.52 × 10−01
15q24.1 rs881536 ULK3 i A/C 0.4431 0.3925 1.23 (1.09, 1.39) 5.94 × 10−04 1.16 (1.07, 1.23) 5.78 × 10−03 0.15 51.34
ii A/C 0.4187 0.3942 1.11 (1.02, 1.20) 1.99 × 10−02
15q26.2 rs2535483 SPATA8 i A/G 0.3356 0.2871 1.25 (1.11, 1.42) 4.56 × 10−04 1.06 (0.96, 1.15) 7.36 × 10−01 0 94.28
ii A/G 0.2825 0.3047 0.90 (0.82, 0.98) 2.26 × 10−02
16q24.1 rs2934498 IRF8 i G/A 0.3789 0.3380 1.20 (1.06, 1.35) 4.29 × 10−03 1.25 (1.16, 1.34) 4.97 × 10−09 0.40 0
ii G/A 0.3915 0.3353 1.28 (1.17, 1.39) 3.31 × 10−07
  1. *Stage i: genotyping in 2,252 individuals by Illumina Human 610-Quad BeadChips; stage ii: genotyping in 4,410 individuals by the Sequenom MassArray system; stage iii: genotyping in 7,345 individuals by the Sequenom MassArray system. a P-values from the Cochran-Armitage trend test. b P-values from fix or random joint analysis (see Subjects and Methods).Chr, chromosome; MAF, minor allele frequency; OR, odds ratio.