Table 6. Comparison of association of validated SNPs with lipid and cholesterol phenotypes in JHS, JHS-AFR-2_LPL and JHS-EUR-2_LPL.

Trait	Gene	SNP	Type	p_all	p_all_int	effect_all±se	effect_afr±se	effect_eur±se	f_afr	f_eur	f_all
HDL-C	LIPC	rs1800588	Upstream	0.10	0.53	0.56±0.34	0.55±0.34	1.3±0.8	0.50	0.58	0.50
HDL-C	LIPG	rs2156552	Intergenic	0.011	0.84	−2.5±0.9	−3.5±2.2	−2.3±1.3	0.97	0.91	0.97
HDL-C	CETP	rs3764261	Downstream	2.7E-09	0.86	−2.1±0.3	−2.0±0.3	−2.1±0.8	0.67	0.67	0.67
HDL-C	ABCA1	rs3890182	Intronic	0.14	0.06	0.75±0.50	0.85±0.51	−1.2±1.1	0.88	0.86	0.88
HDL-C	LIPC	rs4775041	Intergenic	7.2E-03	0.21	−1.4±0.5	−1.1±0.5	−1.7±0.9	0.88	0.90	0.88
LDL-C	PCSK9	rs11591147	Coding (Non-Syn)	1.2E-03	0.12	−31.4±9.6	NA	−24.9±12.1	1.00	1.00	1.00
LDL-C	HMGCR	rs12654264	Intronic	0.085	0.54	1.9±1.1	1.4±1.2	3.4±2.2	0.68	0.68	0.68
LDL-C	LDLR	rs6511720	Intronic	1.4E-06	0.79	−7.0±1.4	−7.0±1.5	−7.1±3.1	0.86	0.87	0.86
LDL-C	ApoB	rs693	Coding (Syn)	0.21	0.17	−1.6±1.3	−0.78±1.58	−3.7±2.3	0.79	0.67	0.78
TG	ApoA5	rs3135506	Coding (Non-Syn)	1.6E-06	0.39	13.6±2.6	11.9±0.9	14.8±7.0	0.95	0.98	0.94
TG	ApoA5	rs662799	5′-UTR	0.069	0.03	3.5±1.9	1.1±1.0	21.5±5.5	0.88	0.86	0.88
TG	GCKR	rs780094	Intronic	3.8E-04	0.56	6.4±1.7	5.5±1.1	8.4±3.2	0.83	0.82	0.82
TG	LPL	rs328	Nonsense	7.1E-05	0.05	10.2±2.4	4.5±3.4	18.6±4.5	0.94	0.86	0.93

P-values for association of TG, LDL-C or HDL-C with genotype in the total population (p_all) and p-value for interaction (p_all_int) are shown (p≤0.05 is shown in bold). The percent change in TG or change in HDL-C or LDL-C level (mg/dL) per allele is shown with standard error for the total population (effect_all), JHS-AFR-2_LPL (effect_afr) and JHS-EUR-1_2_LPL (effect_eur). The SNP frequencies in the total population (f_all), JHS-AFR-2_LPL (f_afr) and JHS-EUR-2_LPL (f_eur) are also shown.