Table 1.
Top SNPs associated with African esophageal squamous cell carcinoma from chromosome 9 and chromosome 2
| rsID | Chr | Position (hg19) | Gene | Alleles (effect/non-effect) | EAF affected individuals | EAF control individuals | OR (95% CI) | pLMMvalue | ppermvaluea | Impute2 score |
|---|---|---|---|---|---|---|---|---|---|---|
| rs12379660b | 9 | 96182487 | FAM120A | A/G | 0.251 | 0.207 | 1.28 (1.22–1.34) | 4.58 × 10−8 | 3.71 × 10−8 | –c |
| rs10992729 | 9 | 96181075 | FAM120A | T/C | 0.254 | 0.212 | 1.26 (1.21–1.32) | 1.64 × 10−7 | 9.71 × 10−8 | 0.995 |
| rs142741123b | 2 | 192207115 | MYO1B | C/T | 0.017 | 0.007 | 2.66 (2.43–2.89) | 5.49 × 10−8 | 3.86 × 10−8 | 0.935 |
| rs141499985 | 2 | 192212930 | MYO1B | T/G | 0.017 | 0.007 | 2.64 (2.41–2.87) | 6.33 × 10−8 | 5.57 × 10−8 | 0.929 |
OR, odds ratio; 95% CI, confidence interval; pLMM, p value from linear mixed model.
a
p value from 700 million adaptive permutations, see material and methods.
b
Lead SNP at each locus, with their strongest supporting SNP.
c
Genotyped SNP.