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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.