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. 2015 Apr 27;44(4):1341–1352. doi: 10.1093/ije/dyv050

Table 2.

Top-ranked SNPs in genes (P-valueGENE < 0.05) associated with risk of UGI cancers

Oesophageal squamous cell carcinoma (ESCC)
Gene (n = 11) Gene function Genomic location P-valueGENE Top-ranked SNP Major/minor MAF Cases MAF Controls OR (95% CI) P-valueSNP
SETD1B Chromatin remodelling 12q24.31 0.006 rs2242259 C/T 0.39 0.35 1.14 (1.04–1.24) 0.006
CBX4 Chromatin remodelling 17q25.3 0.020 rs4889898 C/A 0.33 0.30 1.15 (1.05–1.27) 0.003
KAT5 Chromatin remodelling 11q13 0.021 rs1151500 C/T 0.13 0.11 1.21 (1.06–1.39) 0.006
ZGPAT Chromatin remodelling 20q13.3 0.022 rs8957 C/A 0.34 0.36 0.93 (0.84–1.02) 0.104
BTD Chromatin remodelling 3p25 0.025 rs2455823 G/A 0.50 0.47 1.14 (1.04–1.24) 0.005
EED Chromatin remodelling 11q14.2-q22.3 0.026 rs10898459 C/T 0.47 0.50 0.88 (0.81–0.96) 0.005
SMARCD1 Chromatin remodelling 12q13-q14 0.027 rs836178 G/T 0.14 0.16 0.86 (0.76–0.97) 0.013
POLE3 Chromatin remodelling 9q33 0.030 rs8177812 C/T 0.22 0.20 1.17 (1.05–1.30) 0.005
AGO2 microRNA biosynthesis 8q24.3 0.031 rs6983924 A/G 0.50 0.47 1.16 (1.06–1.27) 0.001
RING1 Chromatin remodelling 6p21.3 0.046 rs213194 G/A 0.08 0.07 1.18 (1.00–1.40) 0.051
MBD3L1 DNA methylation 19p13.2 0.047 rs10412487 T/C 0.32 0.34 0.88 (0.80–0.97) 0.008
Gastric cancer (GC)
Gene (n = 11) Gene function Genomic location P-valueGENE Top-ranked SNP Major/minor MAF Cases MAF Controls OR (95% CI) P-valueSNP
SUV420H1 Chromatin remodelling 11q13.2 0.006 rs10896300 G/A 0.11 0.13 0.86 (0.75–0.99) 0.036
ASH1L Chromatin remodelling 1q22 0.010 rs12724079 T/C 0.17 0.20 0.84 (0.75–0.94) 0.003
KAT5 Chromatin remodelling 11q13 0.011 rs1151500 C/T 0.13 0.11 1.23 (1.07–1.42) 0.004
JARID2 Chromatin remodelling 6p24-p23 0.023 rs7769291 C/T 0.26 0.24 1.14 (1.02–1.26) 0.016
PRMT1 Chromatin remodelling 19q13 0.029 rs3745469 C/T 0.06 0.08 0.79 (0.66–0.95) 0.011
MBD3L1 DNA methylation 19p13.2 0.029 rs10412487 T/C 0.31 0.34 0.87 (0.79–0.96) 0.005
SRRT microRNA biosynthesis 7q21 0.030 rs13245899 A/G 0.42 0.39 1.14 (1.04–1.25) 0.006
SIRT3 Chromatin remodelling 11p15.5 0.033 rs1045454 C/T 0.18 0.16 1.17 (1.03–1.32) 0.013
KDM5A Chromatin remodelling 12p13.33 0.033 rs527118 T/C 0.31 0.34 0.87 (0.79–0.96) 0.004
DROSHA microRNA biosynthesis 5q11.2 0.035 rs7735863 G/A 0.41 0.43 0.89 (0.81–0.97) 0.011
KAT6A Chromatin remodelling 8p11 0.040 rs7008906 G/A 0.42 0.39 1.14 (1.04–1.24) 0.006
Gastric cardia adenocarcinoma (GCA)
Gene (n = 14) Gene function Genomic location P-valueGENE Top-ranked SNP Major/minor MAF Cases MAF Controls OR (95% CI) P-valueSNP
GSG2 Chromatin remodelling 17p13 0.003 rs7220026 G/A 0.28 0.25 1.19 (1.05–1.33) 0.005
MBD3L1 DNA methylation 19p13.2 0.004 rs10412487 T/C 0.30 0.34 0.82 (0.74–0.92) 0.001
SIRT6 Chromatin remodelling 19p13.3 0.009 rs352493 T/C 0.27 0.24 1.21 (1.08–1.37) 0.002
KDM4A Chromatin remodelling 1p34.1 0.013 rs304303 C/A 0.18 0.22 0.81 (0.71–0.93) 0.002
PRMT7 Chromatin remodelling 16q22.1 0.016 rs2863973 T/G 0.07 0.09 0.73 (0.60–0.89) 0.002
SUV420H1 Chromatin remodelling 11q13.2 0.016 rs10896300 G/A 0.11 0.13 0.87 (0.74–1.03) 0.105
ASH1L Chromatin remodelling 1q22 0.018 rs8179271 A/G 0.23 0.26 0.85 (0.75–0.96) 0.007
SRRT microRNA biosynthesis 7q21 0.021 rs13245899 A/G 0.42 0.39 1.16 (1.05–1.29) 0.005
SMARCD1 Chromatin remodelling 12q13-q14 0.026 rs836178 G/T 0.14 0.16 0.83 (0.71–0.96) 0.011
DROSHA microRNA biosynthesis 5q11.2 0.034 rs7735863 G/A 0.40 0.43 0.86 (0.77–0.95) 0.004
EZH1 Chromatin remodelling 17q21.1-q21.3 0.034 rs4792953 T/C 0.41 0.44 0.87 (0.78–0.97) 0.011
KAT2A Chromatin remodelling 17q12-q21 0.034 rs1122326 A/C 0.08 0.10 0.80 (0.66–0.96) 0.015
DICER1 microRNA biosynthesis 14q32.13 0.036 rs7157322 A/C 0.42 0.38 1.17 (1.05–1.30) 0.004
CARM1 Chromatin remodelling 19p13.2 0.048 rs1541596 G/A 0.20 0.23 0.86 (0.75–0.97) 0.019
Gastric non-cardia adenocarcinoma (GNCA)
Gene (n = 12) Gene function Genomic location P-valueGENE Top-ranked SNP Major/minor MAF Cases MAF Controls OR (95% CI) P-valueSNP
SMARCC1 Chromatin remodelling 3p21.31 0.012 rs13094264 G/A 0.32 0.28 1.18 (1.02–1.35) 0.022
PPP1CA Chromatin remodelling 11q13 0.016 rs1790733 T/C 0.32 0.29 1.16 (1.01–1.33) 0.038
RPS6KA5 Chromatin remodelling 14q31-q32.1 0.017 rs3783834 C/T 0.42 0.37 1.25 (1.10–1.43) 0.001
GEMIN4 microRNA biosynthesis 17p13.3 0.018 rs910924 C/T 0.10 0.13 0.73 (0.59–0.89) 0.002
KAT8 Chromatin remodelling 16p11.1 0.018 rs2855475 C/T 0.10 0.07 1.34 (1.07–1.68) 0.010
ASH1L Chromatin remodelling 1q22 0.019 rs12724079 T/C 0.16 0.20 0.79 (0.67–0.94) 0.007
KAT5 Chromatin remodelling 11q13 0.029 rs1151500 C/T 0.14 0.11 1.29 (1.07–1.56) 0.009
PRMT1 Chromatin remodelling 19q13 0.033 rs3745469 C/T 0.06 0.08 0.74 (0.57–0.96) 0.023
KDM8 Chromatin remodelling 16p12.1 0.037 rs12051243 T/G 0.17 0.20 0.80 (0.68–0.95) 0.011
SETD7 Chromatin remodelling 4q31.1 0.042 rs720257 G/A 0.36 0.32 1.22 (1.07–1.40) 0.003
SETD1A Chromatin remodelling 16p11.2 0.046 rs897986 G/A 0.08 0.06 1.33 (1.04–1.70) 0.021
SMAD3 microRNA biosynthesis 15q21-q22 0.047 rs1465842 G/A 0.21 0.17 1.27 (1.08–1.50) 0.003

Abbreviations: CI, confidence intervals; MAF, minor allele frequency; OR, odds ratio; UGI, upper gastrointestinal.

Note: Per-allele ORs and P-valueSNP were estimated for minor allele among controls in combined population adjusted for age, sex, study, and eigenvectors. The table was sorted by P-valueGENE.