Table 2 Three independent signals in the DEFA region. r2=0 between rs9314614 and rs12716641.

From: Identification of new susceptibility loci for IgA nephropathy in Han Chinese

SNP

Risk allele

Risk allele

  

Multivariate analysis *

Risk/non-risk allele

frequency cases (%)

frequency controls (%)

P value

OR (95% CI)

P value

OR (95% CI)

rs2738058

chr8:6821617

     

 T/C

      

 GWAS logistic

73.0

66.6

5.75E−10

1.310 (1.203–1.427)

2.06E−08

1.298 (1.185–1.422)

 GWAS gemma

  

1.51E−10

   

 Validation 1

72.4

69.0

6.10E−05

1.181 (1.089–1.281)

4.88E−03

1.131 (1.038–1.232)

 Validation 2 Southern

71.9

66.0

1.92E−06

1.327 (1.181–1.491)

6.46E−05

1.284 (1.136–1.451)

 Validation 2 Northern

72.3

67.6

7.08E−05

1.245 (1.117–1.386)

6.28E−04

1.219 (1.088–1.366)

 Validation 3 Southern

72.6

67.3

8.74E−05

1.303 (1.142–1.487)

8.58E−04

1.263 (1.101–1.450)

 Validation 3 Northern

73.4

67.0

1.64E−04

1.354 (1.156–1.585)

1.26E−03

1.310 (1.112–1.543)

 All validation

  

4.14E−19

1.253 (1.193–1.317)

1.67E−17

1.226 (1.170–1.285)

 Meta-analysis

I2=31%, Phet=0.400

2.31E−27

1.267 (1.214–1.323)

1.15E−19

1.232 (1.178–1.289)

rs9314614

chr8:6697731

     

 C/G

      

 GWAS logistic

39.7

36.0

3.54E−05

1.191 (1.097–1.295)

2.85E−04

1.161 (1.071–1.258)

 GWAS gemma

  

6.20E−05

   

 Validation 1

37.7

35.0

3.77E−03

1.121 (1.038–1.211)

2.03E−03

1.130 (1.046–1.222)

 Validation 2 Southern

38.6

35.6

2.10E−02

1.135 (1.019–1.264)

3.03E−02

1.127 (1.011–1.256)

 Validation 2 Northern

40.2

39.1

3.42E−01

1.051 (0.948–1.165)

3.72E−01

1.048 (0.945–1.163)

 Validation 3 Southern

38.4

36.0

1.03E−01

1.108 (0.980–1.253)

9.97E−02

1.109 (0.981–1.255)

 Validation 3 Northern

41.9

36.8

4.85E−03

1.234 (1.066–1.428)

6.73E−03

1.225 (1.058–1.419)

 All validation

  

2.66E−06

1.118 (1.067–1.171)

9.55E−08

1.121 (1.075–1.170)

 Meta-analysis

I2=0%, Phet=0.442

9.48E−10

1.135 (1.090–1.182)

4.25E−09

1.129 (1.084–1.176)

rs12716641

chr8:6898998

     

 T/C

      

 GWAS logistic

78.0

74.3

7.80E−07

1.260 (1.150–1.381)

4.40E−03

1.153 (1.045–1.272)

 GWAS gemma

  

1.79E−06

   

 Validation 1

78.2

73.6

1.22E−08

1.287 (1.180–1.404)

2.95E−06

1.244 (1.135–1.363)

 Validation 2 Southern

78.8

75.2

1.81E−03

1.219 (1.076–1.381)

8.47E−02

1.122 (0.984–1.278)

 Validation 2 Northern

80.4

78.4

5.44E−02

1.129 (0.998–1.278)

3.91E−01

1.058 (0.929–1.205)

 Validation 3 Southern

78.7

75.5

1.00E−02

1.204 (1.045–1.386)

1.01E−01

1.131 (0.976–1.311)

 Validation 3 Northern

80.5

77.4

3.85E−02

1.207 (1.010–1.442)

2.65E−01

1.112 (0.923–1.339)

 All validation

  

2.34E−13

1.224 (1.159–1.291)

1.66E−08

1.157 (1.100–1.218)

 Meta-analysis

I2=0%, Phet=0.432

1.13E−18

1.233 (1.177–1.292)

9.53E−09

1.154 (1.099–1.212)

  1. CI, confidence interval; GWAS, genome-wide association study; OR, odds ratio; SNP, single-nucleotide polymorphism.
  2. Only rs2738058 is in LD (r2=0.71) with the reported SNP rs2738048.For the GWAS samples, only the result from logistic regression analyses (GWAS logistic) was used in the fixed-effects meta-analysis with the validation samples.
  3. *Pairwise LD (r2) between rs2738058 and rs9314614=0.001, between rs12716641 and rs2738058=0.074. There is no LD between rs9314614 and rs12716641 (r2=0).
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