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Table 1 Significant SNPs identified in two independent stages of case-control studies

From: Further evidence for the existence of major susceptibility of nasopharyngeal carcinoma in the region near HLA-A locus in Southern Chinese

SNP

Position

Nearest

Allelesa

Stage Ie

  

Stage IIf

  

Combinedg

 
  

Gene

 

MAF(%)b

Pc

OR(95%CI)d

MAF(%)b

Pc

OR(95%CI)d

MAF(%)b

Pc

OR(95%CI)d

rs2517716

30025239

HLA-A

A/G

35.43

3 × 10-3

1.772(1.214-2.586)

39.6

4 × 10-3

1.420(1.120-1.800)

38.3

5.9 × 10-7

1.62(1.34-1.95)

rs9260734

30040645

HCG9

G/A

30.06

2 × 10-3

1.845(1.258-2.705)

32.8

4 × 10-4

1.535(1.209-1.95)

31.9

3.3 × 10-7

1.67(1.37-2.03)

rs9404952

29912144

HLA-G

A/G

34.86

1.7 × 10-2

1.528(1.080-2.163)

37.7

3 × 10-3

1.419(1.13-1.782)

36.7

6.6 × 10-5

1.45(1.21-1.75)

rs3869062-

30042870

HCG9

A/G

27.71

1.8 × 10-2

1.58(1.082-2.308)

      

rs9260475

30028105

HLA-A

T/C

37.57

1 × 10-4

2.034(1.426-2.902)

      
  1. a Major/minor alleles as determined by allele frequency among genotyped controls; b Minor allele frequency among genotyped controls; c, d OR, odds ratio for major allele, adjusted by logistic regression for gender and age; e Stage 1, n = 206 cases and 180 controls; f stage 2, n = 329 cases and 345 controls; g combined stage 1 and 2, n = 535 cases and 525 controls. In stage 2, variations with - call rate < 90% and HWE < 0.001 were omitted.