. 2018 Sep 5;51(2):748–757. doi: 10.4143/crt.2018.162

Table 3.

SNPs associated with gastric cancer in both the genome-wide association stage and replication study after conditioning on the PSCA gene (rs2294008)

SNP		Chr	Gene	Maj	Min	GWAS stage				Replication				Meta-analysis
SNP		Chr	Gene	Maj	Min	Case Afreq	Cont Afreq	p-value	OR (95% CI)	Case Afreq	Cont Afreq	p-value	OR (95% CI)	p-value	OR (95% CI)
Total population
	rs371061408^a)	1	-	T	C	0.32	0.24	3.72E-05	1.46 (1.22-1.75)	0.28	0.27	0.3395	1.06 (0.94-1.21)	0.0017	1.18 (1.06-1.31)
Male
	rs6936644^b)	6	ZSCAN31	C	T	0.49	0.48	1.81E-05	1.56 (1.27-1.90)	0.44	0.48	0.3231	1.07 (0.93-1.24)	0.0010	1.22 (1.08-1.37)
	rs7669841^b)	4	TET2	G	C	0.30	0.30	3.64E-05	1.58 (1.27-1.97)	0.31	0.30	0.2850	0.92 (0.79-1.07)	0.1405	1.10 (0.97-1.24)
	rs7215433^c)	17	-	T	C	0.26	0.28	3.80E-05	0.59 (0.46-0.76)	0.25	0.26	0.5488	0.95 (0.81-1.12)	0.0060	0.83 (0.72-0.95)
Female
	rs12233126^d)	2	EIF5B	T	A	0.38	0.27	6.27E-05	1.77 (1.34-2.35)	0.28	0.28	0.8231	1.02 (0.83-1.26)	0.0109	1.24 (1.05-1.46)
	rs111673703^b)	11	APLP2	C	T	0.11	0.05	7.08E-05	2.49 (1.59-3.91)	0.07	0.06	0.6472	1.09 (0.75-1.59)	0.0037	1.53 (1.15-2.05)
	rs10463885	5	CDC42SE2	A	G	0.06	0.02	9.73E-05	4.17 (2.03-8.55)	0.02	0.03	0.6665	0.88 (0.48-1.6)	0.0289	1.68 (1.05-2.66)

SNP, single-nucleotide polymorphism; GWAS, genome-wide association study; Chr, chromosome; Maj, major allele; Min, minor allele; CaseAfreq, case allele frequency; ContAfreq, control allele frequency; OR, odds ratio; CI, confidence interval; LD, linkage disequilibrium.

^a)

8 SNPs were included in the same LD block,

^b)

2 SNPs were included in the same LD block,

^c)

16 SNPs were included in the same LD block,

^d)

5 SNPs were included in the same LD block.