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

From: Novel identified associations of RGS1 and RASGRP1 variants in IgA Nephropathy

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

  1. CI, confidence interval; Chr, chromosome; MAF, minor allele frequency; OR, odds ratio; IgAN, immunoglobulin-A nephropathy; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism.
  2. 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.
  3. Only SNPs in RGS1 and RASGRP1 loci could retain statistically significant after multiple correction, which were marked in bold.
  4. Ppermutation values based on 10000 permutations.
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