Table 2. Allele frequency distribution between the ESCC and control populations.
SNP name | Gene locus | Location | Function | Major/major allele | Major/minor allele | Minor/minor allele | No. of Major/major alleles in cases | No. of Major/minor alleles in cases | No. of Minor/minor alleles in cases | No. of Major/major alleles in controls | No. of Major/minor alleles in controls | No. of Minor/minor alleles in controls | X2 test (Hardy-Weinberg test for controls) | P value ((Hardy-Weinberg test for controls)) | P (Fisher’s test) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rs3805322 | ADH4 | 100056998 | Intron region | AA | AG | GG | 236 | 256 | 123 | 125 | 246 | 141 | 0.744 | 0.689 | 0.000 |
rs4822983 | CHEK2 | 28719078 | Intron region | CC | CT | TT | 358 | 226 | 32 | 324 | 166 | 23 | 0.087 | 0.957 | 0.225 |
rs10082466 | MBL2 | 52766862 | 3'-UTR | AA | AG | GG | 437 | 161 | 15 | 369 | 147 | 13 | 0.621 | 0.733 | 0.844 |
rs1152620 | MALAT1 | 65489858 | N/A | AA | AG | GG | 188 | 120 | 303 | 149 | 112 | 267 | 161.733 | <0.001 | 0.6 |
rs11548103 | S100A14 | 52766862 | 3'-UTR | GG | AG | AA | 49 | 286 | 278 | 58 | 231 | 239 | 0.038 | 0.981 | 0.198 |
rs11716316 | ABI3BP | 100764451 | Intron region | AA | AC | CC | 188 | 138 | 286 | 150 | 117 | 262 | 152.489 | <0.001 | 0.6 |
rs9327870 | ABI3BP | 102667853 | N/A | TT | TC | CC | 186 | 258 | 85 | 218 | 281 | 115 | 2.079 | 0.353 | 0.426 |
rs12904 | EFNA1 | 155134221 | Near Gene-5 | AA | AG | GG | 451 | 152 | 11 | 393 | 125 | 11 | 0.082 | 0.959 | 0.862 |
rs1321311 | CDKN1A | 36655123 | N/A | GG | GT | TT | 425 | 166 | 16 | 364 | 146 | 16 | 0.085 | 0.958 | 0.901 |
rs17618244 | KLB | 39446909 | Missense | GG | AG | AA | 415 | 175 | 23 | 372 | 139 | 18 | 1.234 | 0.54 | 0.634 |
rs2073498 | RASSF1A | 50332115 | Missense | CC | CA | AA | 530 | 81 | 4 | 461 | 64 | 5 | 2.614 | 0.271 | 0.74 |
rs2114358 | miR-1206 | 128008933 | Intron region | TT | TC | CC | 314 | 181 | 32 | 339 | 238 | 37 | 0.315 | 0.854 | 0.194 |
rs2285947 | DNAH11 | 21544470 | Intron region | GG | GA | AA | 263 | 284 | 66 | 232 | 235 | 58 | 0.017 | 0.991 | 0.869 |
rs351855* | FGFR | 177093242 | Missense | TT | CT | CC | 402 | 5 | 191 | 334 | 14 | 146 | 430.686 | <0.001 | 0.035 |
rs4072037 | MUC1 | 155192276 | Cds-synonymous | AA | AG | GG | 383 | 127 | 15 | 441 | 150 | 17 | 0.945 | 0.623 | 0.982 |
rs550894 | miR-612 | 65444469 | ncRNA | GG | GT | TT | 342 | 238 | 31 | 282 | 208 | 35 | 0.163 | 0.922 | 0.466 |
rs699517 | TYMS | 673016 | 3'-UTR | TT | CT | CC | 259 | 287 | 67 | 236 | 240 | 53 | 0.499 | 0.779 | 0.698 |
rs8191664 | NEIL2 | 11786044 | Missense | GG | GT | TT | 400 | 191 | 22 | 355 | 148 | 25 | 3.382 | 0.184 | 0.431 |
Abbreviations: ESCC, esophageal squamous cell carcinoma; SNP, single nucleotide polymorphism; OR, odds ratio; CI, confidence interval.
* Because the number of heterozygous alleles was too small, the P values for comparisons of major/major allele vs. major/minor allele vs. minor/minor allele were not sufficiently persuasive. The comparisons of TT+CT versus CC or TT versus CT+CC were not significant. Thus, we did not further evaluate this SNP.