Table 5. Effect size of LPL variants on HDL-C levels.

SNP	Position	f_afr	f_eur	f_overall	p_hdl_all	p_int_hdl	effect_all±se	effect_afr±se	effect_eur±se
rs13702	19868772	0.43	0.66	0.48	1.2E-04	0.73	−1.28±0.33	−1.69±0.44	−0.59±0.69
rs328	19864004	0.94	0.86	0.93	6.7E-04	0.23	2.24±0.64	1.57±0.95	1.79±1.10
rs15285	19868947	0.43	0.67	0.48	6.9E-04	0.44	1.12±0.32	1.62±0.44	0.16±0.67
rs325	19863608	0.94	0.86	0.93	9.5E-04	0.17	−2.15±0.63	−1.38±0.93	−2.13±1.10
rs343	19855067	0.95	0.94	0.95	1.2E-03	0.85	−2.43±0.72	−2.80±1.05	−1.77±1.31
rs10096633	19875201	0.50	0.82	0.57	1.4E-03	0.71	1.10±0.34	1.20±0.44	0.60±0.76
rs17482753	19876926	0.95	0.85	0.94	1.4E-03	0.23	2.19±0.67	1.45±0.99	1.97±1.12
rs327	19863816	0.55	0.68	0.59	1.6E-03	0.52	−1.08±0.33	−1.30±0.45	−1.05±0.71
rs3289	19867472	0.92	1.00	0.92	2.0E-03	0.58	2.12±0.67	2.64±0.83	1.92±1.79
rs2197089	19870653	0.15	0.41	0.21	2.1E-03	0.84	−1.29±0.41	−1.99±0.62	−0.73±0.71
rs1011685	19875049	0.95	0.87	0.93	2.4E-03	0.34	2.07±0.66	1.43±0.98	1.68±1.10
rs3916027	19869148	0.55	0.69	0.58	3.4E-03	0.41	−0.99±0.33	−1.11±0.45	−1.20±0.68
rs12679834	19864713	0.92	0.86	0.91	3.7E-03	0.21	−1.73±0.58	−1.12±0.83	−1.63±1.07
rs10105606	19872128	0.26	0.66	0.34	4.5E-03	0.82	−1.03±0.36	−1.48±0.50	−0.66±0.70
rs331	19864685	0.56	0.68	0.60	6.1E-03	0.69	−0.92±0.32	−1.13±0.44	−0.71±0.70
rs1569209	19874450	1.00	0.90	0.98	7.7E-03	0.78	−3.38±1.24	−7.60±8.22	−2.80±1.38
rs295	19860518	0.57	0.73	0.61	8.3E-03	0.64	0.92±0.34	1.19±0.46	0.92±0.72
rs301	19861214	0.66	0.74	0.68	8.8E-03	0.82	−0.94±0.35	−1.20±0.47	−0.61±0.73

P-values for association of HDL-C with genotype in the total population (p_hdl_all) and for the significance of the genotype×local ancestry term in the linear regression model (p_int_hdl). SNPs with p<0.0006 are shown in bold. The change in HDL-C level (mg/dL) per LPL 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, as well as the chromosomal position in bases.