Association of PTGER4 and PRKAA1 genetic polymorphisms with gastric cancer

BMC Medical Genomics

Table 2 Details of candidate SNPs and allele model for association between these polymorphisms and GC risk

Genes	SNP-ID	Chr: position	Alleles A/B	MAF		HWE-p	OR (95%CI)	p	RegulomeDB
Genes	SNP-ID	Chr: position	Alleles A/B	Case	Control	HWE-p	OR (95%CI)	p	RegulomeDB
PTGER4	rs4613763	5: 40,392,626	C/T	0.193	0.002	0.999	3.00 (0.60–1.90)	0.158	Other
PTGER4	rs6880778	5: 40,398,994	G/A	0.193	0.183	0.140	1.06 (0.85–1.33)	0.599	Other
PTGER4	rs11742570	5: 40,410,482	C/T	0.188	0.184	0.182	1.06 (0.85–1.32)	0.625	eQTL/caQTL + TF binding / chromatin accessibility peak
PTGER4	rs9292777	5: 40,437,846	T/C	0.268	0.180	0.097	1.05 (0.84–1.32)	0.651	eQTL/caQTL + TF binding / chromatin accessibility peak
PTGER4	rs7725052	5: 40,487,168	T/C	0.194	0.261	0.208	1.03 (0.85–1.26)	0.745	eQTL/caQTL + TF binding + any motif + Footprint + chromatin accessibility peak
PTGER4	rs12186979	5: 40,524,758	G/A	0.443	0.202	0.494	0.95 (0.76–1.18)	0.631	eQTL/caQTL + TF binding / chromatin accessibility peak
PTGER4	rs10036575	5: 40,685,693	C/T	0.443	0.491	0.214	0.82 (0.69–0.98)	0.029	eQTL/caQTL + TF binding + any motif + Footprint + chromatin accessibility peak
PRKAA1	rs10074991	5: 40,790,449	A/G	0.444	0.493	0.287	0.82 (0.69–0.97)	0.024	eQTL/caQTL + TF binding / chromatin accessibility peak
PRKAA1	rs13361707	5: 40,791,782	T/C	0.193	0.492	0.329	0.82 (0.69–0.98)	0.030	eQTL/caQTL + TF binding / chromatin accessibility peak

GC: gastric cancer; SNP: single nucleotide polymorphism; Chr: chromosome; A: minor alleles; B: major alleles; MAF: minor allele frequency; HWE: Hardy-Weinberg equilibrium; OR: Odds ratio; 95%CI: 95% confidence interval; eQTL: expression quantitative trait locus; caQTL: chromatin accessibility quantitative trait loci; TF: transcription factor
p values were calculated from Person’s chi-square test (two-sided)
Bold font and p < 0.05 indicates statistical significance

ISSN: 1755-8794