Table 1. Association of variants in small GTPase genes with epithelial ovarian cancer risk (p-value<10−4) and functional annotation.
| Genetic Association | Functional Annotation | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene | SNP | Chr:Position | Alleles |
MAF | Histology | OR (95% CI) | P-value | Conserved site | eQTL | Tissues with enhancer histone mark | Tissues with DNAse site | In super-enhancer |
| ARHGEF10L | rs2256787 | 1:17,765,403 | A/C | 0.07 | Endometrioid | 1.33 (1.18–1.50) | 4.5 x 10−6 | No | No | ESC, ESDR, IPSC, FAT, STRM, BRST, BRN, SKIN, VAS, LIV, GI, HRT, MUS, LNG, OVRY, PANC | None | Yes |
| rs10788679 | 1:17,789,549 | A/G | 0.42 | Serous | 1.07 (1.03–1.11) | 2.6 x 10−4 | No | No | None | None | Yes | |
| AKAP6 | rs1955513 | 14:32,245,693 | C/A | 0.07 | All invasive | 0.90 (0.85–0.95) | 3.3 x 10−4 | Yes | No | FAT, SKIN, VAS, BRN, MUS, GI, BLD | SKIN,MUS,MUS,THYM,BLD | No |
| rs927062 | 14:32,164,800 | G/A | 0.21 | All invasive | 0.94 (0.90–0.97) | 5.9 x 10−4 | No | Yes, ARHGAP5 | None | GI | No | |
SNP, single nucleotide polymorphism; alleles show minor/major; MAF, minor allele frequency; OR, odds ratio; CI, confidence interval; eQTL, expression quantitative locus with p<0.05 in EOC tumors; histone marks and DNAse I hypersensitive sites from HaploReg v 4.1 indicating tissue types as defined therein; super enhancer information based on the human super-enhancer database available at http://bioinfo.au.tsinghua.edu.cn/dbsuper/index.php; none of these SNPs had previous GWAS associations with any phenotype based on the EBI GWAS catalog or resided within promoter histone marks; all SNPs are intronic to the gene indicated.