Gastric precancerous lesions are associated with gene variants in Helicobacter pylori-susceptible ethnic Malays

Table 1 Single nucleotide polymorphisms associated with atrophic gastritis among Malays with Helicobacter pylori

rs ID	Chromosome	Gene	Minor allele	Allele frequency		χ2	HWE
				Cases	Control	P-value1	P-value
rs2614074	8 p21.1	PNOC	B	0.409	0.062	0.008	0.983
rs10504944	8 q22.1	GDF6	A	0.5	0	0.034	0.516
rs9315542	13 q13.3	UFM1	B	0.409	0.064	0.007	0.994
rs4943552	13 q13.3	UFM1	A	0.318	0.075	0.040	0.815
rs489977	18 q12.3	KC6	A	0.181	0	0.064	0.752

rs ID: The unique ID for the identified single nucleotide polymorphisms; HWE: Hardy-Weinberg Equilibrium.

¹All markers were run using the FAMHAP (Haplotype Association Analysis) program. The P value represents the simulated overall significance for the particular marker corrected for multiple testing and P < 0.05 was considered statistically significant.

Table 2 Single nucleotide polymorphisms associated with intestinal metaplasia among Malays with Helicobacter pylori

rs ID	Chromosome	Gene	Minor allele	Allele frequency		χ2	HWE
				Cases	Control	P-value	P-value
rs1166704	1p31.1	NEXN	B	0.375	0.031	0.0694	0.654
rs2191508	2q32.3	SLC39A10	A	0.081	0.375	0.297	0.591
rs1992736	3p24.3	TBC1D5	A	0.750	0.193	0.192	0.78
rs10511297	3q13.13	CD96	A	0.375	0.030	0.171	0.659
rs2615485	4q22.1	DSPP	A	0.750	0.136	0.190	0.625
rs2434316	5q14.1	THBS4	A	0.750	0.257	0.118	0.743
rs6878264	5q14.1	THBS4	B	0.625	0.010	0.010	1.000
rs7800141	7p15.3	DNAH11	B	0.666	0.096	0.154	0.717
rs4746259	10q22.2	PPIAL4G	B	0.750	0.015	0.062	0.794
rs9300471	13q32.2	FARP1	A	0.375	0.030	0.145	0.659
rs1881344	16p13.2	C16orf68	A	0.375	0.030	0.078	0.659
rs2253429	20p13	SIRPB1	B	0.375	0.030	0.0119	0.659
rs2834681	21q22.12	RUNX1	B	0.250	0	0.0623	0.859

rs ID: The unique ID for the identified single nucleotide polymorphisms; HWE: Hardy-Weinberg Equilibrium.

Table 3 Single nucleotide polymorphisms associated with intestinal metaplasia and dysplasia among Malays with Helicobacter pylori

rs ID	Chromosome	Gene	Minor allele	Allele frequency		χ2	HWE
				Cases	Control	P-value	P-value
rs10493872	1p21.3	ABCD3	A	0.375	0.062	0.00601	0.518
rs10510792	3p14.3	DNAH12	A	0.25	0.030	0.341	0.728
rs2889259	4p14	KIAA1239	A	0.375	0.015	0.0623	0.724
rs6837437	4p14	KIAA1239	A	0.375	0.015	0.0623	0.728
rs10498879	6q13	RIMS1	A	0.75	0.196	0.160	0.629
rs4073894	7q22.1	LHFPL3	A	0.375	0.015	0.0623	0.728
rs10487929	7q35	CNTNAP2	B	0.25	0.031	0.260	0.724
rs10503727	8p21.2	SLC25A37	B	0.75	0.183	0.151	0.908
rs2251417	10q21.3	ANXA2P1	A	0.375	0.045	0.579	0.591
rs1042194	10q23.33	CYP2C19	B	0.625	0.011	0.00536	0.972
rs10506855	12q21.31	CCDC59	B	0.375	0.046	0.0269	0.585
rs10492652	13q22.1	KLF12	B	0.25	0.015	0.0623	0.797
rs1565946	14q23.1	SLC35F4	A	0.625	0.156	0.0151	0.658
rs10483683	14q23.1	SLC35F4	B	0.625	0.181	0.314	0.964
rs10483837	14q24.2	RGS6	B	0.5	0.031	0.171	0.585
rs245615	16q21	CDH8	A	0.5	0.140	0.183	0.844
rs2058879	19q13.32	IGFL2	A	0.375	0.015	0.0623	0.728

rs ID: The unique ID for the identified single nucleotide polymorphisms; HWE: Hardy-Weinberg Equilibrium.

Table 4 Single nucleotide polymorphisms associated with dysplasia among Malays with Helicobacter pylori

rs ID	Chromosome	Gene	Minor allele	Allele frequency		χ2	HWE
				Cases	Control	P-value	P-value
rs10505799	12p12.3	MGST1	B	0.5	0.016	0.006	0.855
rs10498391	14q21.2	FSCB	B	0.5	0	0.069	0.928

rs ID: The unique ID for the identified single nucleotide polymorphisms; HWE: Hardy-Weinberg Equilibrium.