Table 2.
The basic information and HWE about the candidate SNPs of CYP4A22.
| SNP ID | Function | Chr: Position | Alleles (A/B) |
MAF | AF | HWE (P Value) |
dbSNP func annot | HaploReg v4.1 | RegulomeDB | Polyphen | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cases | Controls | CHB | AFR | EUR | |||||||||
| rs76011927 | missense variant | 1: 47,137,516 | T/C | 0.063 | 0.064 | 0.058 | - | 0.006 | 0.436 | R (Arg) > C (Cys) | Promoter histone marks, Enhancer histone marks, Motifs changed | TF binding + chromatin accessibility peak | BENIGN |
| rs12564525 | missense variant | 1: 47,141,609 | C/T | 0.398 | 0.444 | 0.602 | 0.225 | 0.206 | 0.519 | R (Arg) > W (Trp) | Motifs changed, Selected eQTL hits | eQTL/caQTL + TF binding / chromatin accessibility peak | BENIGN |
| rs2056900 | missense variant | 1: 47,142,113 | A/G | 0.527 | 0.478 | 0.539 | 0.207 | 0.193 | 0.315 | G (Gly) > S (Ser) | Motifs changed, Selected eQTL hits | eQTL/caQTL + TF binding / chromatin accessibility peak | BENIGN |
| rs4926581 | missense variant | 1: 47,143,311 | T/G | 0.520 | 0.480 | 0.539 | 0.206 | 0.193 | 0.171 | V (Val) > I (Ile) | - | eQTL/caQTL + TF binding / chromatin accessibility peak | BENIGN |
A: minor allele; B: wild-type allele; SNP: Single nucleotide polymorphisms; MAF: minor allele frequency; AF: allele frequency; CHB: Han Chinese in Beijing, China; EUR: European; AFR: African; HWE: Hardy–Weinberg equilibrium; TF: transcription factor
HWE P value > 0.05 indicates that the genotypes were in Hard-weinberg Equilibrium
‘-’: data missing
dbSNP (https://www.ncbi.nlm.nih.gov/snp/), Haploreg (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php); RegulomeDB (https://regulome.stanford.edu/regulome-search/); Polyphen (http://genetics.bwh.harvard.edu/pph2/)