Table 2.
Top signals from African-Chinese meta-analysis for esophageal squamous cell carcinoma
| Chr | Position (hg19) | rsID | Allelea | EAF affected individuals (CHN) | EAF affected individuals (AFR) | INFO score (CHN) | INFO score (AFR) | p value (CHN) | p value (AFR)b | p value meta-analysis | OR | 95% CI | Heterogeneity p valuec |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 230941048 | rs34115901d | A/G | 0.228 | 0.029 | 0.905 | 0.883 | 1.48 × 10−3 | 2.06 × 10−5 | 1.39 × 10−7 | 1.86 | 1.72–2.01 | 0.4764 |
| 2 | 230937668 | rs34590391 | A/G | 0.249 | 0.028 | 0.962 | 0.906 | 4.27 × 10−3 | 5.90 × 10−6 | 1.65 × 10−7 | 1.81 | 1.67–1.96 | 0.2580 |
| 2 | 230940750 | rs35396967 | A/G | 0.246 | 0.030 | 0.937 | 0.883 | 1.94 × 10−3 | 2.17 × 10−5 | 1.97 × 10−7 | 1.81 | 1.68–1.96 | 0.4472 |
| 9 | 96182487 | rs12379660d | A/G | 0.406 | 0.251 | 1.000 | 1.000 | 1.09 × 10−3 | 7.89 × 10−8 | 9.36 × 10−10 | 1.51 | 1.42–1.60 | 0.1533 |
| 9 | 96181075 | rs10992729 | T/C | 0.388 | 0.254 | 0.967 | 0.995 | 1.51 × 10−3 | 2.01 × 10−7 | 2.97 × 10−9 | 1.50 | 1.41–1.60 | 0.1694 |
| 9 | 96179785 | rs1351117 | A/G | 0.408 | 0.254 | 0.974 | 0.994 | 2.20 × 10−3 | 2.75 × 10−7 | 6.12 × 10−9 | 1.48 | 1.39–1.58 | 0.1579 |
| 10 | 96065694 | rs7099485d | C/T | 0.231 | 0.456 | 0.999 | 0.998 | 2.26 × 10−9 | 3.74 × 10−2 | 1.42 × 10−8 | 1.94 | 1.86–2.03 | 0.0049 |
| 10 | 96074157 | rs7903902 | C/T | 0.231 | 0.456 | 0.995 | 0.998 | 3.38 × 10−9 | 4.70 × 10−2 | 2.74 × 10−8 | 1.93 | 1.85–2.01 | 0.0046 |
| 10 | 96063279 | rs3781265 | A/T | 0.231 | 0.459 | 0.998 | 0.996 | 2.26 × 10−9 | 5.48 × 10−2 | 2.76 × 10−8 | 1.94 | 1.86–2.02 | 0.0035 |
| 10 | 96058298 | rs3765524 | T/C | 0.230 | 0.465 | 1.000 | 1.000 | 1.88 × 10−9 | 6.62 × 10−2 | 3.42 × 10−8 | 1.94 | 1.86–2.03 | 0.0027 |
| 10 | 96070375 | rs3781264 | G/A | 0.170 | 0.234 | 1.000 | 1.000 | 6.50 × 10−9 | 4.55 × 10−2 | 4.00 × 10−8 | 2.05 | 1.96–2.14 | 0.0061 |
| 22 | 29130300 | rs1033667d | T/C | 0.279 | 0.442 | 0.993 | 1.000 | 1.28 × 10−8 | 3.82 × 10−3 | 1.47 × 10−9 | 1.84 | 1.76–1.92 | 0.0417 |
| 22 | 29140823 | rs5752783 | C/A | 0.731 | 0.506 | 0.992 | 0.984 | 8.80 × 10−7 | 5.97 × 10−4 | 3.78 × 10−9 | 0.58 | 0.41–0.82 | 0.2682 |
| 22 | 29135121 | rs9613668 | C/G | 0.275 | 0.506 | 0.967 | 0.981 | 1.23 × 10−6 | 6.78 × 10−4 | 5.79 × 10−9 | 1.73 | 1.65–1.81 | 0.2781 |
| 22 | 29105415 | rs5752773 | C/G | 0.779 | 0.419 | 0.998 | 0.993 | 1.62 × 10−7 | 4.42 × 10−3 | 1.20 × 10−8 | 0.55 | 0.34–0.87 | 0.0807 |
Chr2/SLC16A, Chr9/FAM120A, Chr10/PLCE1, Chr22/CHEK2. EAF, effect allele frequency; OR, odds ratio; 95% CI, confidence interval.
a
Effect allele/non-effect allele.
b
p value (AFR) differs from the main LMM as the AFR GWAS was remodeled to match the conditions of the CHN GWAS.
c
Heterogeneity p value threshold is p < 0.05.
d
Lead SNP at each locus, with their supporting SNPs.