1Department of Medicine, Hanyang University College of Medicine, Seoul, Korea
2Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
3Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, Goyang, Korea
4Department of Public Health, Graduate School of Public Health, Seoul National University, Seoul, Korea
5Center for Gastric Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Korea
Copyright © 2019 by the Korean Cancer Association
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
SNP | Chr | Gene | Maj | Min |
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 | |||||||||||||||
rs371061408a) | 1 | - | T | C | 0.32 | 0.24 | 3.72E-05 | 1.46 (1.22-1.75) | 0.28 | 0.27 | 0.3395 | 1.06 (0.94-1.21) | 0.0017 | 1.18 (1.06-1.31) | |
Male | |||||||||||||||
rs6936644b) | 6 | ZSCAN31 | C | T | 0.49 | 0.48 | 1.81E-05 | 1.56 (1.27-1.90) | 0.44 | 0.48 | 0.3231 | 1.07 (0.93-1.24) | 0.0010 | 1.22 (1.08-1.37) | |
rs7669841b) | 4 | TET2 | G | C | 0.30 | 0.30 | 3.64E-05 | 1.58 (1.27-1.97) | 0.31 | 0.30 | 0.2850 | 0.92 (0.79-1.07) | 0.1405 | 1.10 (0.97-1.24) | |
rs7215433c) | 17 | - | T | C | 0.26 | 0.28 | 3.80E-05 | 0.59 (0.46-0.76) | 0.25 | 0.26 | 0.5488 | 0.95 (0.81-1.12) | 0.0060 | 0.83 (0.72-0.95) | |
Female | |||||||||||||||
rs12233126d) | 2 | EIF5B | T | A | 0.38 | 0.27 | 6.27E-05 | 1.77 (1.34-2.35) | 0.28 | 0.28 | 0.8231 | 1.02 (0.83-1.26) | 0.0109 | 1.24 (1.05-1.46) | |
rs111673703b) | 11 | APLP2 | C | T | 0.11 | 0.05 | 7.08E-05 | 2.49 (1.59-3.91) | 0.07 | 0.06 | 0.6472 | 1.09 (0.75-1.59) | 0.0037 | 1.53 (1.15-2.05) | |
rs10463885 | 5 | CDC42SE2 | A | G | 0.06 | 0.02 | 9.73E-05 | 4.17 (2.03-8.55) | 0.02 | 0.03 | 0.6665 | 0.88 (0.48-1.6) | 0.0289 | 1.68 (1.05-2.66) |
SNP, single-nucleotide polymorphism; GWAS, genome-wide association study; Chr, chromosome; Maj, major allele; Min, minor allele; CaseAfreq, case allele frequency; ContAfreq, control allele frequency; OR, odds ratio; CI, confidence interval; LD, linkage disequilibrium.
a) 8 SNPs were included in the same LD block,
b) 2 SNPs were included in the same LD block,
c) 16 SNPs were included in the same LD block,
d) 5 SNPs were included in the same LD block.
SNP | Chr | Gene |
GWAS in previous report |
GWAS stage in this study |
|||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ethnicity | Effect | Cont Afreq | p-value | OR (95% CI) | Maj | Min | Case Afreq | Cont Afreq | p-value | OR (95% CI) | |||
rs140081212 [11] | 1 | - | European (Icelanders) | A | 0.65 | 7.90E-10 | 0.79 (0.73-0.86) | G | A | 0.09 | 0.12 | 0.0366 | 0.73 (0.55-0.96) |
rs760077 [11] | 1 | MTX1 | European (Icelanders) | A | 0.65 | 1.10E-08 | 0.79 (0.73-0.85) | T | A | 0.09 | 0.11 | 0.0152 | 0.71 (0.54-0.94) |
rs6676150 [11] | 1 | - | European (Icelanders) | C | 0.67 | 1.50E-08 | 0.80 (0.74-0.86) | G | C | 0.06 | 0.10 | 0.0018 | 0.61 (0.44-0.83) |
rs2274223[7] | 10 | PLCE | Asian (Chinese) | G | 0.21 | 8.40E-09 | 1.31 (1.19-1.43) | C | T | 0.26 | 0.26 | 0.4074 | 1.08 (0.90-1.30) |
rs3765524[7] | 10 | PLCE | Asian (Chinese) | T | 0.21 | 5.32E-09 | 1.31 (1.20-1.44) | C | T | 0.26 | 0.26 | 0.5340 | 1.08 (0.90-1.30) |
rs9841504[8] | 3 | Asian (Han Chinese) | G | 0.15 | 1.70E-09 | 0.76 (0.69-0.83) | - | - | - | - | - | - | |
rs13361707 [8] | 5 | Asian (Han Chinese) | C | 0.48 | 7.60E-29 | 1.41 (1.32-1.49) | - | - | - | - | - | - | |
rs10074991 [10] | 5 | PRKAA1 | Asian (China, Korea) | A | 0.48 | 4.83E-26 | 0.80 (0.77-0.83) | - | - | - | - | - | - |
rs2294693 [10] | 6 | UNC5CL, TSPO2 | Asian (China, Korea) | C | 0.24 | 7.22E-08 | 1.14 (1.09-1.20) | - | - | - | - | - | - |
rs4072037 [10] | 1 | MUC1 | Asian (China, Korea) | G | NR | 7.00E-08 | 1.32 (1.19-1.45) | T | C | 0.12 | 0.14 | 0.2070 | 0.82 (0.64-1.05) |
rs2494938[9] | 6 | LRFN2 | Asian (Han Chinese) | A | 0.26 | 4.91E-09 | 1.18 (1.12-1.25) | - | - | - | - | - | - |
rs2285947[9] | 7 | DNAH11 | Asian (Han Chinese) | A | 0.27 | 1.36E-06 | 1.14 (1.08-1.21) | G | A | 0.32 | 0.32 | 0.7298 | 0.99 (0.84-1.17) |
NCC |
KoGES |
|||
---|---|---|---|---|
Gastric cancer cases | Controls | Gastric cancer cases | Controls | |
Total | 450 | 1,134 | 803 | 3,693 |
Sex | ||||
Male | 297 (66.0) | 539 (47.5) | 533 (66.4) | 1,648 (44.6) |
Female | 153 (34.0) | 595 (52.5) | 270 (33.6) | 2,045 (55.4) |
Age (yr) | ||||
Mean±SD | 55.4±10.7 | 52.1±8.5 | 56.1±11.6 | 53.1±8.6 |
Gastric cancer type | ||||
Diffuse | 191 (42.4) | - | 394 (49.1) | - |
Intestinal | 167 (37.1) | - | 409 (50.9) | - |
Mixed, indeterminate | 92 (20.4) | - | 0 | - |
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 | ||||||||||||||
rs2976394 |
8 | PSCA | T |
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) | ||||
rs2294008 |
8 | PSCA | T |
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) | ||||
rs12025565 |
1 | - | G |
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 | ||||||||||||||
rs6936644 |
6 | ZSCAN31 | C |
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) | ||||
rs7215433 |
17 | - | T |
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 | A |
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 | ||||||||||||||
rs2976394 |
8 | PSCA | T |
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) | ||||
rs2294008 |
8 | PSCA | T |
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) | ||||
rs12233126 |
2 | EIF5B | T |
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) |
SNP | Chr | Gene | Maj | Min | 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 | |||||||||||||||
rs371061408 |
1 | - | T | C | 0.32 | 0.24 | 3.72E-05 | 1.46 (1.22-1.75) | 0.28 | 0.27 | 0.3395 | 1.06 (0.94-1.21) | 0.0017 | 1.18 (1.06-1.31) | |
Male | |||||||||||||||
rs6936644 |
6 | ZSCAN31 | C | T | 0.49 | 0.48 | 1.81E-05 | 1.56 (1.27-1.90) | 0.44 | 0.48 | 0.3231 | 1.07 (0.93-1.24) | 0.0010 | 1.22 (1.08-1.37) | |
rs7669841 |
4 | TET2 | G | C | 0.30 | 0.30 | 3.64E-05 | 1.58 (1.27-1.97) | 0.31 | 0.30 | 0.2850 | 0.92 (0.79-1.07) | 0.1405 | 1.10 (0.97-1.24) | |
rs7215433 |
17 | - | T | C | 0.26 | 0.28 | 3.80E-05 | 0.59 (0.46-0.76) | 0.25 | 0.26 | 0.5488 | 0.95 (0.81-1.12) | 0.0060 | 0.83 (0.72-0.95) | |
Female | |||||||||||||||
rs12233126 |
2 | EIF5B | T | A | 0.38 | 0.27 | 6.27E-05 | 1.77 (1.34-2.35) | 0.28 | 0.28 | 0.8231 | 1.02 (0.83-1.26) | 0.0109 | 1.24 (1.05-1.46) | |
rs111673703 |
11 | APLP2 | C | T | 0.11 | 0.05 | 7.08E-05 | 2.49 (1.59-3.91) | 0.07 | 0.06 | 0.6472 | 1.09 (0.75-1.59) | 0.0037 | 1.53 (1.15-2.05) | |
rs10463885 | 5 | CDC42SE2 | A | G | 0.06 | 0.02 | 9.73E-05 | 4.17 (2.03-8.55) | 0.02 | 0.03 | 0.6665 | 0.88 (0.48-1.6) | 0.0289 | 1.68 (1.05-2.66) |
SNP | Chr | Gene | GWAS in previous report |
GWAS stage in this study |
|||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Ethnicity | Effect | Cont Afreq | p-value | OR (95% CI) | Maj | Min | Case Afreq | Cont Afreq | p-value | OR (95% CI) | |||
rs140081212 [11] | 1 | - | European (Icelanders) | A | 0.65 | 7.90E-10 | 0.79 (0.73-0.86) | G | A | 0.09 | 0.12 | 0.0366 | 0.73 (0.55-0.96) |
rs760077 [11] | 1 | MTX1 | European (Icelanders) | A | 0.65 | 1.10E-08 | 0.79 (0.73-0.85) | T | A | 0.09 | 0.11 | 0.0152 | 0.71 (0.54-0.94) |
rs6676150 [11] | 1 | - | European (Icelanders) | C | 0.67 | 1.50E-08 | 0.80 (0.74-0.86) | G | C | 0.06 | 0.10 | 0.0018 | 0.61 (0.44-0.83) |
rs2274223[7] | 10 | PLCE | Asian (Chinese) | G | 0.21 | 8.40E-09 | 1.31 (1.19-1.43) | C | T | 0.26 | 0.26 | 0.4074 | 1.08 (0.90-1.30) |
rs3765524[7] | 10 | PLCE | Asian (Chinese) | T | 0.21 | 5.32E-09 | 1.31 (1.20-1.44) | C | T | 0.26 | 0.26 | 0.5340 | 1.08 (0.90-1.30) |
rs9841504[8] | 3 | Asian (Han Chinese) | G | 0.15 | 1.70E-09 | 0.76 (0.69-0.83) | - | - | - | - | - | - | |
rs13361707 [8] | 5 | Asian (Han Chinese) | C | 0.48 | 7.60E-29 | 1.41 (1.32-1.49) | - | - | - | - | - | - | |
rs10074991 [10] | 5 | PRKAA1 | Asian (China, Korea) | A | 0.48 | 4.83E-26 | 0.80 (0.77-0.83) | - | - | - | - | - | - |
rs2294693 [10] | 6 | UNC5CL, TSPO2 | Asian (China, Korea) | C | 0.24 | 7.22E-08 | 1.14 (1.09-1.20) | - | - | - | - | - | - |
rs4072037 [10] | 1 | MUC1 | Asian (China, Korea) | G | NR | 7.00E-08 | 1.32 (1.19-1.45) | T | C | 0.12 | 0.14 | 0.2070 | 0.82 (0.64-1.05) |
rs2494938[9] | 6 | LRFN2 | Asian (Han Chinese) | A | 0.26 | 4.91E-09 | 1.18 (1.12-1.25) | - | - | - | - | - | - |
rs2285947[9] | 7 | DNAH11 | Asian (Han Chinese) | A | 0.27 | 1.36E-06 | 1.14 (1.08-1.21) | G | A | 0.32 | 0.32 | 0.7298 | 0.99 (0.84-1.17) |
Values are presented as number (%). NCC, National Cancer Center; KoGES, Korean Genome Epidemiology Study; SD, standard deviation.
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. 49 SNPs were included in the same LD block, Major allele, Minor allele, Moststudied SNP and included in the same LD block with rs2976394, 2 SNPs were included in the same LD block, 3 SNPs were included in the same LD block, 17 SNPs were included in the same LD block.
SNP, single-nucleotide polymorphism; GWAS, genome-wide association study; Chr, chromosome; Maj, major allele; Min, minor allele; CaseAfreq, case allele frequency; ContAfreq, control allele frequency; OR, odds ratio; CI, confidence interval; LD, linkage disequilibrium. 8 SNPs were included in the same LD block, 2 SNPs were included in the same LD block, 16 SNPs were included in the same LD block, 5 SNPs were included in the same LD block.
SNP, single-nucleotide polymorphism; GWAS, genome-wide association study; Chr, chromosome; ContAfreq, control allele frequency; OR, odds ratio; CI, confidence interval; Maj, major allele; Min, minor allele.