Replication analysis of genetic association of the NCAN-CILP2 region with plasma lipid levels and non-alcoholic fatty liver disease in Asian and Pacific ethnic groups

Boonvisut, Supichaya; Nakayama, Kazuhiro; Makishima, Saho; Watanabe, Kazuhisa; Miyashita, Hiroshi; Lkhagvasuren, Munkhtulga; Kagawa, Yasuo; Iwamoto, Sadahiko

doi:10.1186/s12944-016-0181-z

Lipids in Health and Disease

Table 1 Association study of SNPs in NCAN-CILP2 region with serum lipid levels in East Asian ethnic groups

From: Replication analysis of genetic association of the NCAN-CILP2 region with plasma lipid levels and non-alcoholic fatty liver disease in Asian and Pacific ethnic groups

dbSNP ID position Nearest gene Allele		Japanese (n = 3014)		Chinese (n = 401)		Mongol (n = 947)		Thai (n = 212)			Palau (n = 119)		Combined (n = 4693)
rs58542926 chr19:19268740	MAF (P-HWE)	0.080 (0.858)		0.0682 (0.787)		0.078 (0.707)		0.114 (0.227)			0.237 (0.663)
rs58542926 chr19:19268740	MAF (P-HWE)	β	P value	β	P value	β	P value		β	P value	β	P value	β	P value
TM6SF2	total cholesterol	−0.035	0.048	−0.089	0.0835	−0.116	0.0003*		−0.095	0.157	0.012	0.907	−0.051	0.0005*
E167K	LDL	−0.027	0.130	−0.041	0.4276	−0.091	0.005		−0.077	0.258	0.077	0.454	−0.030	0.039
C/t	HDL	0.005	0.747	0.0265	0.5837	−0.018	0.551		0.107	0.109	−0.128	0.195	−0.007	0.600
	Log TG	−0.054	0.0009*	−0.109	0.0224	−0.030	0.334		−0.222	0.0008*	−0.023	0.813	−0.056	3.15×10^-5*
rs735273	MAf (P-HWE)	0.291 (0.719)		0.277 (0.613)		0.351 (0.788)			0.342 (0.151)		0.572 (0.966)
chr19:19274602		β	P value	β	P value	β	P value		β	P value	β	P value	β	P value
TM6SF2	total cholesterol	0.008	0.674	−0.091	0.071	−0.034	0.293		−0.018	0.787	−0.049	0.639	−0.030	0.036
5’ flanking	LDL	−0.005	0.793	−0.019	0.700	0.001	0.986		0.024	0.724	−0.008	0.936	−0.019	0.181
T/c	HDL	0.037	0.019	−0.017	0.728	−0.038	0.211		0.024	0.721	−0.048	0.635	−0.005	0.716
	Log TG	−0.025	0.128	−0.098	0.038	−0.019	0.544		−0.147	0.028	−0.052	0.599	−0.031	0.019
rs1009136	MAF (P-HWE)	0.286 (0.757)		0.275 (0.706)		0.341 (0.911)			0.347 (0.128)		0.572 (0.966)
chr19:19329619		β	P value	β	P value	β	P value		β	P value	β	P value	β	P value
MAU2	total cholesterol	0.008	0.663	−0.088	0.084	−0.042	0.186		−0.019	0.783	−0.049	0.693	−0.030	0.041
intronic	LDL	−0.005	0.793	−0.005	0.915	−0.001	0.977		0.021	0.755	−0.008	0.936	−0.016	0.275
G/a	HDL	0.038	0.018	−0.009	0.855	−0.041	0.178		0.036	0.590	−0.048	0.635	−0.005	0.719
	Log TG	−0.026	0.113	−0.094	0.047	−0.031	0.313		−0.148	0.027	−0.058	0.599	−0.035	0.010
rs1858999	MAF (P-HWE)	0.276 (0.844)		0.253 (0.349)		0.335 (0.422)			0.370 (0.168)		0.5812 (0.994)
chr19:19386860		β	P-value	β	P-value	β	P-value		β	P-value	β	P-value	β	P-value
GATAD2A	total cholesterol	−0.003	0.853	−0.098	0.054	−0.047	0.139		−0.023	0.729	−0.053	0.610	−0.037	0.012
intronic	LDL	−0.019	0.289	−0.003	0.946	0.000	0.997		−0.008	0.909	−0.010	0.927	−0.022	0.121
G/c	HDL	0.046	0.004	0.008	0.866	−0.031	0.308		0.035	0.594	−0.067	0.501	0.001	0.997
	Log TG	−0.044	0.007	−0.110	0.021	−0.027	0.380		−0.112	0.096	−0.060	0.541	−0.042	0.002*
rs16996148	MAF (P-HWE)	0.119 (0.470)		0.069 (0.611)		0.099 (0.907)			0.132 (0.631)		0.308 (0.854)
chr19:19547663		β	P value	β	P value	β	P value		β	P value	β	P value	β	P value
CILP2	total cholesterol	−0.034	0.057	−0.049	0.336	−0.092	0.004		−0.106	0.116	0.024	0.820	−0.032	0.026
3’ flanking	LDL	−0.032	0.069	0.005	0.923	−0.073	0.024		−0.094	0.166	0.123	0.238	−0.016	0.276
G/t	HDL	0.009	0.554	0.030	0.538	−0.049	0.106		0.091	0.171	−0.080	0.421	0.001	0.948
	Log TG	−0.038	0.020	−0.065	0.175	−0.007	0.817		−0.181	0.007	−0.058	0.552	−0.037	0.006

Beta coefficient (β) and P values of copy numbers of minor alleles for each lipid parameter in multiple linear regression models of the indicated ethnic groups are shown. Minor alleles of each SNP are indicated by lowercase letters. Statistical significance is shown by an asterisk (*) on the threshold of <0.0025. MAF (P HWE): minor allele frequency (P value of Hardy-Weinberg equilibrium.)

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