Table 1.
Association results for all replicated SNPs in 1065 EAC cases and 1019 controls of German descent
| MAF in %3 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr: Pos1 | Allele2 | Group | Cases | Controls | OR (95% CI)4 | P 2-d.f. 5 | P 1-d.f. 5 | Nearby genes6 | ||||
| rs17030152 | 1: 7083719 | C/T | All | 25.5 | 28.2 | 0.87 (0.75–1.01) | 0.068 | 0.034 | THAP3, DNAJC11, CAMTA1 | ||||
| M | 25.6 | 27.6 | 0.89 (0.75–1.06) | 0.190 | 0.095 | ||||||||
| F | 24.4 | 28.8 | 0.80 (0.59–1.10) | 0.167 | 0.083 | ||||||||
| rs2687201 | 3: 70928930 | A/C | All | 36.0 | 30.6 | 1.26 (1.09–1.46) | 0.0014 | 0.0007 | MITF, FOXP1, EIF4E3 | ||||
| M | 36.4 | 30.2 | 1.33 (1.13–1.57) | 0.0007 | 0.0004 | ||||||||
| F | 32.8 | 31.0 | 1.08 (0.81–1.43) | 0.620 | 0.310 | ||||||||
| rs9837992 | 3: 70959438 | A/G | All | 35.5 | 31.4 | 1.23 (1.07–1.42) | 0.005 | 0.002 | MITF, FOXP1, EIF4E3 | ||||
| M | 35.7 | 30.1 | 1.30 (1.10–1.54) | 0.002 | 0.001 | ||||||||
| F | 33.9 | 32.6 | 1.04 (0.78–1.39) | 0.779 | 0.389 | ||||||||
| rs11771429 | 7: 153271877 | T/C | All | 15.3 | 16.9 | 0.85 (0.71–1.02) | 0.083 | 0.042 | XRCC2, ACTR3B, DPP6 | ||||
| M | 15.4 | 17.2 | 0.86 (0.70–1.06) | 0.157 | 0.079 | ||||||||
| F | 14.2 | 16.6 | 0.81 (0.55–1.21) | 0.308 | 0.154 | ||||||||
| rs4523255 | 8: 8713038 | T/C | All | 39.5 | 37.3 | 1.14 (0.99–1.31) | 0.061 | 0.031 | CLDN23, MFHAS1, ERI1 | ||||
| M | 38.7 | 37.1 | 1.07 (0.91–1.25) | 0.420 | 0.210 | ||||||||
| F | 45.7 | 37.6 | 1.40 (1.06–1.85) | 0.018 | 0.009 | ||||||||
| rs11789015 | 9: 96716028 | G/A | All | 25.1 | 28.1 | 0.87 (0.75–1.02) | 0.088 | 0.044 | BARX1, PTPDC1, MIRLET7DHG | ||||
| M | 25.5 | 26.8 | 0.94 (0.79–1.13) | 0.533 | 0.267 | ||||||||
| F | 22.0 | 29.3 | 0.67 (0.48–0.94) | 0.020 | 0.010 | ||||||||
| rs2669333 | 13: 63574196 | A/G | All | 35.3 | 33.6 | 1.15 (1.00–1.33) | 0.050 | 0.025 | DIAPH3, TRDR3, PCDH20 | ||||
| M | 35.1 | 31.4 | 1.19 (1.01–1.41) | 0.036 | 0.018 | ||||||||
| F | 36.8 | 35.6 | 1.04 (0.78–1.39) | 0.776 | 0.388 | ||||||||
| rs10144632 | 14: 55242336 | G/A | All | 23.2 | 25.9 | 0.87 (0.75–1.02) | 0.088 | 0.044 | SAMD4A, GCH1, WDHD1 | ||||
| M | 23.2 | 25.8 | 0.88 (0.73–1.05) | 0.156 | 0.078 | ||||||||
| F | 23.2 | 26.1 | 0.86 (0.63–1.18) | 0.342 | 0.171 | ||||||||
| rs2895917 | 14: 102052775 | T/C | All | 32.7 | 35.6 | 0.88 (0.76–1.02) | 0.086 | 0.043 | DIO3, PPP2R5C, DYNC1H1 | ||||
| M | 33.0 | 35.1 | 0.91 (0.77–1.08) | 0.278 | 0.139 | ||||||||
| F | 30.7 | 36.1 | 0.79 (0.59–1.06) | 0.120 | 0.060 | ||||||||
| rs9936833 | 16: 86403118 | C/T | All | 39.4 | 36.9 | 1.13 (0.98–1.29) | 0.090 | 0.045 | FENDRR, FOXF1, MTHFSD | ||||
| M | 39.3 | 36.8 | 1.11 (0.95–1.30) | 0.178 | 0.089 | ||||||||
| F | 40.6 | 37.0 | 1.16 (0.88–1.51) | 0.289 | 0.144 | ||||||||
| rs4800353 | 18: 19654137 | G/A | All | 12.8 | 14.7 | 0.83 (0.69–1.01) | 0.067 | 0.034 | MIB1, GATA6, CTAGE1 | ||||
| M | 12.9 | 14.9 | 0.84 (0.67–1.04) | 0.115 | 0.058 | ||||||||
| F | 12.2 | 14.5 | 0.82 (0.54–1.25) | 0.351 | 0.175 | ||||||||
In total, 11 SNPs show EAC association when one-side tested (P1-d.f. < 0.05) with the same risk allele as observed in the previously published GWAS on EAC/Barrett’s esophagus 1,6. The results are given for the whole sample set (All) as well as for males (M) and females (F) separately (column “Group”).
Chromosome (Chr) and position (Pos) according to hg19.
First allele represents the minor allele.
Minor allele frequency (MAF) is given for cases and controls.
Odds ratio (OR) with 95% confidence interval (CI) indicating the genetic effect size is given for the minor allele.
P-values using n − 2 degrees of freedom (column “P2-d.f.”) and n − 1 degree of freedom (column “P1-d.f.”) are shown, whereby P-values below 0.05 are highlighted in bold.
Nearby genes are shown with the closest gene to the associated SNP given in bold.