Table 2.

A selection of top signals from association and linkage analysis.

SNP	Chr:pos(hg19)	Allelesa	RAFb	function	Gene	P-value	Beta±SE	LOD	Trait
rs3832063	2:238944441	A/ACT	0.39	ncRNA_intronic	UBE2F-SCLY	3.50E-05	−0.27±0.066	2.70	LDL
rs201606363	2:238962655	A/ATG	0.43	ncRNA_intronic	UBE2F-SCLY	4.73E-04	−0.23±0.065	3.67	LDL
rs201606363	2:238962655	A/ATG	0.43	ncRNA_intronic	UBE2F-SCLY	1.39E-03	−0.16±0.051	4.60	APOB
rs201606363	2:238962655	A/ATG	0.43	ncRNA_intronic	UBE2F-SCLY	1.35E-02	−0.022±0.0090	3.80	CHOL
rs200229736	6:77298727	C/CTTA	0.22	intergenic	IMPG1-HTR1B	1.60E-06	−0.11±0.024	2.80	SI
rs201447751	7:67151523	ACC/A	0.29	intergenic	LINC01372-LOC102723427	8.99E-02	0.037±0.022	5.21	SI
rs149336631	7:67152121	C/CTG	0.30	intergenic	LINC01372-LOC102723427	1.16E-01	0.034±0.022	5.30	SI
rs60560566	7:67153704	T/TG	0.30	intergenic	LINC01372-LOC102723427	1.19E-01	0.034±0.022	5.36	SI
rs200122735	8:16588076	TA/T	0.39	intergenic	MSR1-FGF20	4.01E-01	0.047±0.056	4.50	APOB
rs201639667	8:16588078	AC/A	0.39	intergenic	MSR1-FGF20	4.34E-01	0.044±0.056	4.69	APOB
rs201639667	8:16588078	AC/A	0.39	intergenic	MSR1-FGF20	8.04E-01	−0.0025±0.010	3.70	CHOL
rs138536353	9:9513612	C/CAT	0.13	intronic	PTPRD	8.59E-06	−0.36±0.080	3.00	APOB
rs5896378	9:10194679	TTACA/T	0.16	intronic	PTPRD	6.38E-01	−0.033±0.070	3.90	APOB
rs201315549	12:108590892	ACCC/A	0.02	intronic	WSCD2	1.75E-06	0.39±0.081	1.79	SI
rs59849892	12:108593020	AT/A	0.02	intronic	WSCD2	1.20E-07	0.41±0.077	2.00	SI
rs36229491	16:56994244	TA/T	0.27	intergenic	HERPUD1-CETP	3.06E-12	0.092±0.013	1.52	HDL
rs66512242	16:56996645	G/GCC	0.46	intronic	CETP	3.00E-05	0.050±0.012	2.00	HDL
rs12720908	16:57001254	TCACA/T	0.18	intronic	CETP	2.70E-05	−0.065±0.016	2.01	HDL
rs35874588	16:57009651	TC/T	0.45	intronic	CETP	5.50E-04	0.042±0.012	4.30	HDL
rs5825825	18:65832839	A/AT	0.33	intergenic	LOC643542-TMX3	6.13E-01	0.013±0.025	5.11	ADP_G45R

^aReference/Other allele with minor allele on the left

^bReference allele frequency based on the entire population.