Table 2.
The based information of selected SNPs in C10orf90 and the association with the risk of colorectal cancer in the allele model.
| SNP | Chromosome | Alleles A / B |
dbSNP func annot | MAF | p HWE | OR (95% CI) | p * | RegulomeDB | HaploReg v4.2 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | |||||||||
| rs12412320 | 10:126461527 | T/G | Missense D (Asp) > E (Glu) |
0.205 | 0.249 | 0.758 | 0.78 ( 0.65 - 0.93 ) | 0.006* | TF binding or DNase peak | Enhancer histone marks, Motifs changed |
| rs11245007 | 10:126504416 | T/C | Missense D (Asp) > N (Asn) |
0.480 | 0.452 | 0.436 | 1.12 ( 0.96 - 1.31 ) | 0.134 | TF binding + any motif + DNase peak | Promoter histone marks, Enhancer histone marks, DNAse, Proteins bound, Motifs changed |
| rs11245008 | 10:126504799 | T/C | Missense R (Arg) > L (Leu) |
0.137 | 0.121 | 0.145 | 1.16 ( 0.92 - 1.45 ) | 0.209 | TF binding + any motif + DNase peak | Enhancer histone marks, DNAse, Motifs changed |
SNP, Single nucleotide polymorphism; MAF, Minor allele frequency; HWE, Hardy-Weinberg equilibrium; OR, Odds ratio; 95% CI, 95% confidence interval.
p values of Hardy-Weinberg equilibrium were calculated using Chi-square test.
p values were calculated by two sided Chi-square test, and * p < 0.05 was considered statistical significance.
Bold p means that the data is statistically significant after Bonferroni correction (p < 0.05/3).
dbSNP (https://www.ncbi.nlm.nih.gov/snp/), RegulomeDB (https://regulome.stanford.edu/regulome-search/) and HaploReg v4.2 (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php).