Table 1

The results for the 19 variants after the meta-analysis of all discovery cohorts, all replication cohorts and all cohorts combined

					Discovery cohorts					Replication cohorts					All cohorts combined
Trait	Chr:Position	rs identifier	nearest gene	A1/A2	Freq	N	β	SE_β	p Value	Freq	N	β	SE_β	p Value	Freq	β	SE_β	p Value
HDL-C	3:72 067 255	rs75909755	PROL2-EIF4E3	T/C	0.03	62 607	1.593	0.275	7.27E-09	0.03	86 252	−0.019	0.031	5.45E-01	0.03	0.002	0.031	9.57E-01
TC	6:31 272 261	rs6457374	HLA-B	T/C	0.75	46 839	2.339	0.339	5.32E-12	0.81	74 417	0.057	0.016	4.23E-04	0.81	0.062	0.016	1.18E-04
LDL-C	6:31 325 323	rs9266229	HLA-B	C/G	0.53	37 981	−2.201	0.344	1.62E-10	0.41	61 582	−0.025	0.014	7.37E-02	0.41	−0.029	0.014	4.04E-02
TG	6:36 648 275	–	CDKN1A	CAG/C	0.45	53 425	−0.019	0.003	7.63E-09	0.49	59 018	−0.003	0.004	5.20E-01	0.46	−0.013	0.003	5.93E-07
TG	6:13 983 949 8	rs608736	–	C/G	0.48	53 425	−0.019	0.003	5.67E-09	0.49	73 512	−0.008	0.003	2.67E-02	0.48	−0.013	0.002	9.10E-09
TG	6:16 085 176 6	rs376563	SLC22A3	T/C	0.46	47 036	−0.02	0.003	3.37E-09	0.46	73 512	−0.001	0.003	8.22E-01	0.46	−0.010	0.002	1.36E-05
LDL-C	6:16 111 170 0	rs186696265	LPA-PLG	T/C	0.01	49 221	11.247	1.241	1.31E-19	0.01	59 497	0.263	0.076	5.42E-04	0.01	0.304	0.076	6.17E-05
TC	6:16 111 170 0	rs186696265	LPA-PLG	T/C	0.01	59 859	10.004	1.162	7.20E-18	0.01	75 821	0.238	0.075	1.46E-03	0.01	0.278	0.075	1.93E-04
HDL-C	7:80 492 357	rs60839105	SEMA3C	T/C	0.07	7882	3.355	0.571	4.26E-09	0.08	4971	1.067	1.228	3.85E-01	0.07	2.948	0.518	1.25E-08
TC	8:68 351 787	rs151198427	CPA6	A/G	0.11	17 361	6.552	1.147	1.12E-08	0.13	1419	−2.858	2.396	2.33E-01	0.11	4.797	1.035	3.56E-06
LDL-C	9:78 728 065	rs146369471	PCSK5	T/C	0.99	43 398	8.529	1.449	3.99E-09	0.99	51 367	0.068	0.103	5.11E-01	0.99	0.110	0.103	2.84E-01
TC	9:78 728 065	rs146369471	PCSK5	T/C	0.99	53 787	7.978	1.413	1.64E-08	0.99	70 241	0.015	0.103	8.84E-01	0.99	0.057	0.103	5.79E-01
TC	12:51 207 704	rs829112	ATF1	A/G	0.68	56 924	1.448	0.258	2.02E-08	0.73	87 659	0.009	0.012	4.63E-01	0.73	0.012	0.012	3.18E-01
TG	13:11 454 402 4	rs7140110	GAS6	T/C	0.71	48 221	−0.021	0.004	3.65E-08	0.72	60 437	−0.006	0.005	2.68E-01	0.72	−0.015	0.003	5.13E-07
TG	15:43 726 625	rs150844304	TP53BP1	A/C	0.97	52 720	−0.083	0.01	2.52E-17	0.95	63 884	−0.026	0.015	8.85E-02	0.96	−0.066	0.008	9.52E-16
TC	17:18 046 290	rs8065026	MYO15A	T/C	0.79	56 924	−1.644	0.292	1.76E-08	0.81	76 913	−0.026	0.013	4.93E-02	0.81	−0.029	0.013	2.66E-02
HDL-C	17:41 840 849	rs77697917	SOST-DUSP3	T/C	0.02	45 052	−2.717	0.407	2.38E-11	0.03	67 843	−0.222	0.036	4.27E-10	0.03	−0.241	0.035	1.04E-11
TG	19:8 429 323	rs116843064	ANGPTL4	A/G	0.03	35 643	−0.101	0.016	6.46E-11	0.03	44 194	−0.065	0.019	4.53E-04	0.03	−0.087	0.012	3.83E-13
TC	20:17 844 684	rs2618566	BANF2-SNX5	T/G	0.65	63 300	−1.566	0.251	4.68E-10	0.60	88 946	−0.024	0.011	2.83E-02	0.60	−0.027	0.011	1.38E-02

The variants in bold are the significantly replicated variants.
A1 is allele 1 and A2 is allele 2, Freq is the frequency of A1, β is the effect of A1.
HDL-C, high-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; TC, total cholesterol; TG, triglycerides.