Skip to main content
. 2018 Sep 5;51(2):748–757. doi: 10.4143/crt.2018.162

Table 2.

SNPs associated with gastric cancer in both the genome-wide association stage and replication study

SNP Chr Gene Genotype frequency GWAS stage
 Replication
 Meta-analysis
Case Afreq Cont Afreq p-value OR (95% CI) Case Afreq Cont Afreq p-value OR (95% CI) p-value OR (95% CI)
Total population
rs2976394a) 8 PSCA Tb)Cc) 0.40 0.52 1.07E-08 0.62 (0.52-0.73) 0.43 0.50 5.09E-07 0.75 (0.67-0.84) 1.66E-13 0.70 (0.64-0.77)
TT 0.34 0.23 Ref 1 0.29 0.25 Ref 1 Ref 1
TC 0.51 0.50 0.00427 0.69 (0.53-0.89) 0.55 0.50 0.351 0.92 (0.77-1.10) 0.0155 0.84 (0.72-0.97)
CC 0.14 0.27 9.86E-09 0.37 (0.26-0.52) 0.16 0.25 1.61E-07 0.53 (0.42-0.67) < 0.0001 0.47 (0.39-0.57)
rs2294008d) 8 PSCA Tb)Cc) 0.40 0.52 1.38E-08 0.62 (0.53-0.73) 0.43 0.50 5.28E-07 0.75 (0.67-0.84) 1.94E-13 0.70 (0.64-0.77)
TT 0.35 0.23 Ref 1 0.29 0.25 Ref 1 Ref 1
TC 0.51 0.50 0.051 0.69 (0.54-0.90) 0.55 0.50 0.348 0.92 (0.76-1.10) 0.0164 0.85 (0.72-0.97)
CC 0.14 0.26 1.23E-08 0.37 (0.26-0.52) 0.16 0.25 1.67E-07 0.53 (0.41-0.67) < 0.0001 0.47 (0.39-0.57)
rs12025565e) 1 - Gb)Ac) 0.32 0.24 4.47E-05 1.45 (1.21-1.73) 0.28 0.27 0.3841 1.06 (0.93-1.20) 0.0023 1.17 (1.06-1.30)
GG 0.44 0.57 Ref 1 0.51 0.54 Ref 1 Ref 1
GA 0.45 0.36 9.39E-06 1.72 (1.35-2.19) 0.42 0.39 0.087 1.15 (0.97-1.36) < 0.001 1.31 (1.15-1.50)
AA 0.09 0.07 0.0261 1.64 (1.06-2.55) 0.07 0.07 0.808 0.96 (0.70-1.32) 0.2115 1.18 (0.91-1.61)
Male
rs6936644f) 6 ZSCAN31 Cb)Tc) 0.54 0.42 9.60E-06 1.57 (1.29-1.92) 0.49 0.47 0.3367 1.07 (0.93-1.24) 0.0008 1.22 (1.09-1.37)
CC 0.22 0.35 Ref 1 0.24 0.26 Ref 1 Ref 1
CT 0.48 0.46 0.002785 1.71 (1.20-2.44) 0.53 0.52 0.328 1.13 (0.89-1.43) 0.0155 1.27 (1.05-1.55)
TT 0.30 0.19 1.42E-05 2.45 (1.63-3.67) 0.22 0.22 0.357 1.14 (0.86-1.52) 0.0011 1.47 (1.17-1.86)
rs7215433g) 17 - Tb)Cc) 0.20 0.29 2.80E-05 0.59 (0.46-0.75) 0.23 0.24 0.6649 0.96 (0.82-1.14) 0.0081 0.83 (0.73-0.95)
TT 0.64 0.49 Ref 1 0.60 0.58 Ref 1 Ref 1
TC 0.33 0.43 0.000343 0.57 (0.42-0.78) 0.34 0.36 0.436 0.92 (0.75-1.14) 0.0069 0.79 (0.66-0.94)
CC 0.04 0.07 0.007788 0.39 (0.19-0.78) 0.06 0.06 0.908 1.02 (0.68-1.55) 0.1962 0.79 (0.55-1.13)
rs74396937 11 OR4C46 Ab)Gc) 0.08 0.14 3.65E-05 0.49 (0.35-0.69) 0.25 0.26 0.3150 0.92 (0.79-1.08) 0.0079 0.82 (0.71-0.95)
AA 0.86 0.74 Ref 1 0.58 0.54 Ref 1 Ref 1
AG 0.12 0.24 5.72E-06 0.39 (0.26-0.58) 0.35 0.39 0.159 0.86 (0.70-1.06) 0.0016 0.74 (0.62-0.89)
GG 0.02 0.03 0.235 0.55 (0.21-1.47) 0.07 0.07 0.831 0.96 (0.65-1.42) 0.6295 0.92 (0.64-1.31)
Female
rs2976394a) 8 PSCA Tb)Cc) 0.38 0.53 3.36E-06 0.53 (0.40-0.69) 0.43 0.50 0.0043 0.77 (0.64-0.92) 6.71E-07 0.68 (0.58-0.79)
TT 0.35 0.22 Ref 1 0.29 0.25 Ref 1 Ref 1
TC 0.54 0.50 0.036255 0.65 (0.43-0.97) 0.55 0.50 0.799 0.96 (0.72-1.29) 0.1761 0.85 (0.67-1.08)
CC 0.11 0.28 5.55E-06 0.25 (0.14-0.46) 0.16 0.25 0.002 0.54 (0.37-0.81) < 0.0001 0.42 (0.31-0.59)
rs2294008d) 8 PSCA Tb)Cc) 0.38 0.53 5.10E-06 0.53 (0.41-0.70) 0.43 0.50 0.0043 0.76 (0.64-0.92) 8.00E-07 0.68 (0.59-0.79)
TT 0.35 0.22 Ref 1 0.29 0.25 Ref 1 Ref 1
TC 0.43 0.50 0.05599 0.67 (0.45-1.01) 0.55 0.50 0.838 0.97 (0.72-1.30) 0.2281 0.86 (0.68-1.10)
CC 0.11 0.28 7.39E-06 0.26 (0.14-0.46) 0.15 0.25 0.002 0.54 (0.36-0.80) < 0.0001 0.42 (0.30-0.59)
rs12233126f) 2 EIF5B Tb)Ac) 0.38 0.27 4.97E-05 1.77 (1.34-2.33) 0.28 0.28 0.9352 1.01 (0.82-1.24) 0.0135 1.23 (1.04-1.45)
TT 0.38 0.54 Ref 1 0.52 0.51 Ref 1 Ref 1
TA 0.48 0.39 0.003291 1.80 (1.21-2.66) 0.40 0.42 0.851 0.97 (0.75-1.27) 0.1753 1.16 (0.93-1.45)
AA 0.14 0.07 0.000249 3.11 (1.69-5.69) 0.08 0.07 0.769 1.08 (0.66-1.76) 0.0185 1.57 (1.07-2.30)

GWAS, genome-wide association study; SNP, single-nucleotide polymorphism; Chr, chromosome; CaseAfreq, case allele frequency; ContAfreq, control allele frequency; OR, odds ratio; CI, confidence interval; LD, linkage disequilibrium.

a)

49 SNPs were included in the same LD block,

b)

Major allele,

c)

Minor allele,

d)

Moststudied SNP and included in the same LD block with rs2976394,

e)

2 SNPs were included in the same LD block,

f)

3 SNPs were included in the same LD block,

g)

17 SNPs were included in the same LD block.