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. 2016 Nov 2;6:35781. doi: 10.1038/srep35781

Table 1. Association between new SLE risk variants inNorthern Han Chinese with IgA nephropathy or lupus nephritis.

Chr SNP Genes/Loci dbSNP Annotation BP (hg19) Minor allele MAF control (%) IgAN
 LN
MAF case (%) P (Ppermutation) OR 95% CI of OR MAF case (%) P (Ppermutation) OR 95% CI of OR
1 rs12022418 9.7 kb 5′ of RGS1   192535106 C 31.67 36.48 6.27 × 10−4(1.27 × 10−2) 1.24 1.10–1.40 32.57 0.58 1.04 0.90–1.20
1 rs7556469 PTPRC intronic 198637581 G 14.5 15.33 0.43 1.07 0.91–1.26 13.28 0.31 0.90 0.74–1.10
3 rs10936599 MYNN synonymous 169492100 C 45.29 45.41 0.93 1.01 0.89–1.13 47.26 0.25 1.08 0.95–1.24
3 rs10936600 LRRC34 missense 169514584 A 45 45.15 0.92 1.01 0.87–1.13 46.67 0.33 1.07 0.93–1.22
5 rs2736100 TERT intronic 1286515 G 41 39.51 0.3 0.94 0.84–1.06 44.28 0.05 (0.067) 1.14 1.00–1.31
5 rs7726414 19 kb 5′ of TCF7   133431833 T 6.36 6.38 0.99 1.00 0.79–1.27 8.53 1.52 × 10−2(1.45 × 10−2) 1.37 1.06–1.76
5 rs2421184 LOC285627-IL12B intronic 158886938 A 44.26 44.22 0.98 1.00 0.89–1.12 47.19 0.08 1.13 0.98–1.29
7 rs11981999 GTF2I intronic 74002082 A 34.8 32.76 0.14 0.91 0.81–1.03 43.91 4.51 × 10−8 (1 × 10−6) 1.47 1.28–1.68
7 rs117026326 GTF2IRD1 intronic 74126033 T 15.88 14.13 0.1 0.87 0.74–1.03 31.65 5.58 × 10−29(1 × 10−6) 2.45 2.09–2.88
11 rs2009453 PCNXL3 intronic 65399527 T 42.97 40.09 0.05 0.89 0.79–1.00 41.11 0.27 0.93 0.81–1.06
11 rs931127 PCNXL3   65405299 A 43.61 40.83 0.06 0.89 0.79–1.00 41.41 0.19 0.91 0.80–1.05
11 rs11235604 ATG16L2 missense 72533535 T 10.31 8.68 0.06 0.83 0.68–1.01 9.64 0.52 0.93 0.74–1.16
11 rs11235667 FCHSD2   72863696 G 10.47 9.03 0.1 0.85 0.70–1.03 9.41 0.30 0.89 0.71–1.11
13 rs1885889 UBAC2-MIR548AN   100091299 T 37.88 35.38 0.08 0.90 0.80–1.01 38.22 0.84 1.02 0.88–1.16
15 rs7170151 RASGRP1 intronic 38846677 C 44.47 49.39 8.34 × 10−4(6.46 × 10−4) 1.22 1.09–1.37 41.04 4.27 × 10−2(0.05) 0.87 0.76–0.99
16 rs223881 6.1 kb 5′ of CCL22   57386565 T 49.35 48.73 0.67 0.98 0.87–1.10 51.11 0.30 1.07 0.94–1.23
18 rs1610555 CD226 intronic 67543146 T 30.48 31.86 0.31 1.07 0.94–1.21 33.85 3.42 × 10−2(4.05 × 10−2) 1.17 1.01–1.35
18 rs1788097 CD226 intronic 67543687 T 33.87 35.27 0.32 1.06 0.94–1.20 37.26 3.78 × 10−2(4.30 × 10−2) 1.16 1.01–1.33
19 rs2305772 SIGLEC6 missense 52033741 A 45.29 43.74 0.29 0.94 0.84–1.06 42.37 0.08 0.89 0.78–1.02
22 rs61616683 SYNGR1 intronic 39755772 C 21.44 22.37 0.45 1.06 0.92–1.21 18.37 2.58 × 10−2(2.93 × 10−2) 0.82 0.70–0.98

CI, confidence interval; Chr, chromosome; MAF, minor allele frequency; OR, odds ratio; IgAN, immunoglobulin-A nephropathy; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism.

OR values were calculated basing on minor alleles for comparison. *Reported OR values for SLE were derived from the meta-analysis data reported and the lead SNPs passing quality control were listed.

Only SNPs in RGS1 and RASGRP1 loci could retain statistically significant after multiple correction, which were marked in bold.

Ppermutation values based on 10000 permutations.