A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study

Kathiresan, Sekar; Manning, Alisa K; Demissie, Serkalem; D'Agostino, Ralph B; Surti, Aarti; Guiducci, Candace; Gianniny, Lauren; Burtt, Nöel P; Melander, Olle; Orho-Melander, Marju; Arnett, Donna K; Peloso, Gina M; Ordovas, Jose M; Cupples, L Adrienne

doi:10.1186/1471-2350-8-S1-S17

BMC Medical Genetics

Table 5 Association Results for 40 SNPs Attempted for Replication in Three Stages

From: A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study

SNP	Chr	Gene	Allele*	Trait	Stage I – FHS 100K			Stage II – FHS Unrelated			Joint P	Stage III – MDC			Stage III – GOLDN			Joint Stages I, II, & III
					P	Beta^†	SE	P	Beta	SE	Stages I & II	P	Beta	SE	P	Beta	SE	P	Beta	SE
rs7231460	18		C	MeanHDL-C	4.3*10^-4	-0.145	0.041	2.4*10^-4	-0.131	0.036	3.7*10^-7	0.50	0.013	0.020	0.60	0.023	0.044	0.03	-0.033	0.015
rs966376	18		C	MeanHDL-C	2.5*10^-4	-0.148	0.040	4.8*10^-4	-0.125	0.036	4.5*10^-7	0.43	0.016	0.020	0.56	0.026	0.044	0.04	-0.031	0.015
rs744134	13	L10374	C	MeanLDL-C	5.4*10^-4	0.168	0.048	4.7*10^-4	0.124	0.036	1.1*10^-6	0.67	0.009	0.020	0.20	0.062	0.048	0.0007	0.053	0.016
rs7233386	18		T	MeanHDL-C	2.4*10^-4	0.149	0.041	0.005	0.100	0.036	6.3*10^-6	0.32	-0.020	0.020	0.61	-0.023	0.046	0.11	0.024	0.015
rs1428445	5		A	MeanHDL-C	3.0*10^-4	-0.187	0.052	0.01	-0.113	0.044	1.8*10^-5	0.24	-0.028	0.024	0.77	0.016	0.054	0.002	-0.058	0.018
rs2304589	2	LOC130502	A	MeanLDL-C	6.4*10^-4	0.187	0.055	0.006	0.124	0.045	1.8*10^-5	0.47	-0.020	0.027	0.09	-0.101	0.060	0.18	0.027	0.020
rs2278528	2	LOC130502	G	MeanLDL-C	6.7*10^-4	0.180	0.053	0.007	0.122	0.045	2.0*10^-5	0.51	-0.018	0.027	0.12	-0.092	0.060	0.14	0.029	0.020
rs2142136	10	PTEN	G	MeanTG	8.1*10^-6	0.228	0.051	0.14	0.077	0.052	2.4*10^-5	0.38	-0.026	0.029	0.85	0.011	0.061	0.06	0.040	0.021
rs1555173	6		C	MeanLDL-C	1.0*10^-5	-0.243	0.055	0.10	-0.083	0.050	2.7*10^-5	0.31	-0.027	0.027	0.03	0.143	0.066	0.01	-0.051	0.021
rs6053754	20	FLJ25067	C	MeanLDL-C	3.1*10^-4	0.166	0.046	0.02	0.090	0.037	3.4*10^-5	0.46	0.017	0.022	0.99	-0.001	0.050	0.003	0.049	0.017
rs8032553	15	KIF7	A	MeanLDL-C	3.0*10^-5	0.171	0.041	0.08	0.061	0.034	5.5*10^-5	0.09	0.033	0.020	Failed	Failed	Failed	0.0002	0.060	0.016
rs1741662	6	RFXDC1	T	MeanTG	7.2*10^-5	0.198	0.050	0.07	0.083	0.046	5.9*10^-5	0.15	-0.037	0.026	0.03	-0.131	0.061	0.58	0.011	0.020
rs1741660	6	RFXDC1	T	MeanTG	7.8*10^-5	0.197	0.050	0.07	0.084	0.046	6.1*10^-5	Failed^‡	Failed	Failed	Failed	Failed	Failed	6E-05	0.136	0.034
rs890945	5		A	MeanHDL-C	5.4*10^-4	-0.181	0.052	0.03	-0.099	0.044	8.0*10^-5	0.18	-0.033	0.024	0.79	0.014	0.053	0.002	-0.057	0.018
rs10512297	9		T	MeanLDL-C	2.1*10^-4	-0.235	0.064	0.05	-0.108	0.054	8.6*10^-5	0.71	-0.011	0.030	0.44	0.056	0.072	0.03	-0.051	0.023
rs541326	9	TRPM3	G	MeanHDL-C	3.6*10^-5	-0.201	0.049	0.28	-0.061	0.056	1.3*10^-4	0.10	0.048	0.029	0.02	-0.159	0.069	0.08	-0.038	0.022
rs719829	5		G	MeanTG	1.3*10^-4	-0.156	0.041	0.11	-0.062	0.039	1.4*10^-4	0.66	0.009	0.022	0.58	0.028	0.050	0.08	-0.028	0.016
rs10509384	10	KCNMA1	G	MeanLDL-C	7.7*10^-4	-0.148	0.044	0.04	-0.076	0.038	1.9*10^-4	0.02	0.050	0.021	Failed	Failed	Failed	0.79	-0.005	0.017
rs688933	9	TRPM3	T	MeanHDL-C	3.1*10^-6	-0.232	0.050	0.80	-0.015	0.059	2.0*10^-4	0.17	0.041	0.030	0.01	-0.172	0.069	0.05	-0.044	0.022
rs1122080	5		A	MeanHDL-C	3.4*10^-4	-0.202	0.056	0.07	-0.084	0.047	2.5*10^-4	0.44	-0.020	0.025	0.47	-0.041	0.058	0.005	-0.055	0.019
rs6743779	2	KLF7	C	MeanLDL-C	2.4*10^-5	-0.181	0.043	0.24	-0.043	0.036	2.8*10^-4	0.69	0.009	0.022	Failed	Failed	Failed	0.05	-0.033	0.017
rs950828	4		A	MeanHDL-C	9.1*10^-4	-0.151	0.046	0.06	-0.080	0.043	2.9*10^-4	0.58	0.012	0.022	Failed	Failed	Failed	0.10	-0.030	0.018
rs1365032	8		C	MeanLDL-C	1.4*10^-4	-0.161	0.042	0.12	-0.053	0.034	3.2*10^-4	0.01	-0.056	0.020	0.11	0.077	0.048	0.0002	-0.055	0.015
rs287474	13		T	MeanLDL-C	8.1*10^-6	0.209	0.047	0.16	0.056	0.040	3.4*10^-4	0.97	0.001	0.020	0.62	-0.023	0.046	0.05	0.030	0.016
rs10507756	13		C	MeanLDL-C	6.0*10^-5	0.202	0.050	0.22	0.052	0.043	4.2*10^-4	0.24	0.032	0.028	0.89	-0.008	0.060	0.003	0.059	0.020
rs1507203	13		C	MeanLDL-C	1.9*10^-4	0.172	0.046	0.15	0.057	0.039	4.3*10^-4	0.23	0.027	0.023	0.32	-0.052	0.052	0.01	0.044	0.017
rs4941236	18	SERPINB8	C	MeanLDL-C	4.7*10^-4	0.151	0.043	0.09	0.059	0.034	4.3*10^-4	0.83	-0.004	0.020	0.18	-0.065	0.048	0.02	0.022	0.015
rs544543	19		G	MeanHDL-C	4.8*10^-6	-0.185	0.040	0.61	-0.019	0.038	4.7*10^-4	0.95	-0.001	0.021	0.78	-0.013	0.047	0.03	-0.033	0.016
rs3763188	6	REPS1	C	MeanTG	5.2*10^-4	-0.191	0.055	0.12	-0.076	0.048	5.1*10^-4	0.13	0.042	0.028	0.02	-0.153	0.063	0.09	-0.035	0.021
rs717987	6	RUNX2	G	MeanHDL-C	8.0*10^-5	0.250	0.063	0.26	0.063	0.057	5.4*10^-4	0.06	0.058	0.031	0.87	0.011	0.067	0.0007	0.079	0.023
rs10508997	10		G	MeanTG	4.1*10^-4	-0.165	0.047	0.15	-0.062	0.043	5.6*10^-4	0.10	0.039	0.023	Failed	Failed	Failed	0.51	-0.012	0.019
rs2395833	7	PRKAR2B	T	MeanHDL-C	6.2*10^-4	-0.145	0.042	0.12	-0.060	0.038	5.6*10^-4	0.99	0.000	0.021	0.06	-0.090	0.049	0.01	-0.041	0.016
rs6677589	1	JUN	G	MeanTG	1.9*10^-4	-0.145	0.039	0.27	-0.042	0.037	7.1*10^-4	0.18	0.028	0.021	0.84	-0.010	0.048	0.30	-0.016	0.016
rs10513320	3		A	MeanTG	1.3*10^-4	-0.190	0.050	0.31	-0.046	0.045	9.0*10^-4	0.24	0.028	0.024	0.21	0.068	0.054	0.61	-0.010	0.018
rs508969	18	CETN1	A	MeanLDL-C	6.8*10^-4	-0.144	0.042	0.18	-0.053	0.040	9.5*10^-4	0.31	0.023	0.023	0.64	0.025	0.054	0.29	-0.018	0.017
rs7858099	9		G	MeanLDL-C	6.9*10^-4	-0.140	0.041	0.15	-0.051	0.035	9.6*10^-4	0.53	-0.013	0.021	0.31	-0.049	0.048	0.006	-0.043	0.016
rs4134425	14		T	MeanLDL-C	6.6*10^-4	-0.156	0.046	0.13	-0.055	0.036	9.8*10^-4	0.14	0.032	0.021	0.16	-0.068	0.048	0.24	-0.019	0.016
rs7021834	9	AL136545	T	MeanHDL-C	4.3*10^-5	-0.174	0.043	0.65	-0.021	0.045	9.9*10^-4	0.05	0.045	0.023	1.00	0.000	0.057	0.72	-0.006	0.018
rs10500770	11		T	MeanLDL-C	3.9*10^-4	-0.157	0.044	0.17	-0.049	0.036	0.001	0.41	0.017	0.021	0.90	0.006	0.050	0.22	-0.019	0.016
rs10516430	4	RAP1GDS1	T	MeanHDL-C	7.2*10^-4	-0.139	0.041	0.20	-0.052	0.040	0.001	0.64	-0.010	0.022	Failed	Failed	Failed	0.02	-0.041	0.017

*The allele on the positive strand of the reference genome was modeled in all analyses.
^†Beta refers to the proportion of 1 standard deviation unit change in phenotype (phenotype is sex-specific residual adjusted for age and age²) per copy of the allele modeled.
^‡"Failed" refers to SNP genotype failure in the sample.

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