Table 3.

Validation of Genes in Independent NOMAS Cohort of 301 Dominicans

Chr	Gene	Discovery SNP	Validation SNP	Function	Position (MB)	D’	Minor Allele	MAF	P Value*	OR (95% CI)†
Thick Plaque
2	TNFSF4	rs1234313	rs10489269	intron	171.427	1.00	A	0.08	0.049	2.26 (1.00-5.11)
			rs2840317	upstream	171.493	0.08	A	0.22	0.015	2.01 (1.14-3.54)
			rs2901716	upstream	171.494	0.06	A	0.21	0.021	1.97 (1.11-3.48)
			rs2022449	upstream	171.505	0.12	T	0.25	6.46E-03	2.15 (1.24-3.72)
			rs844665	upstream	171.516	0.57	T	0.13	0.035	0.44 (0.20-0.94)
			rs10912580	upstream	171.523	0.08	C	0.20	9.49E-03	2.17 (1.21-3.90)
			rs947505	upstream	171.569	0.77	A	0.18	0.014	2.20 (1.17-4.14)
			rs1539259	upstream	171.579	0.13	C	0.19	0.024	1.96 (1.10-3.52)
			rs1539256	upstream	171.579	1.00	G	0.07	7.88E-03	3.20 (1.36-7.55)
			rs16845685	upstream	171.581	1.00	A	0.08	5.37E-04	4.49 (1.92-10.51)
			rs7550607	upstream	171.582	1.00	G	0.07	7.88E-03	3.20 (1.36-7.55)
			rs16845722	upstream	171.594	1.00	T	0.07	7.88E-03	3.20 (1.36-7.55)
			rs6701066	upstream	171.619	0.07	C	0.32	9.21E-05	0.32 (0.18-0.57)
			rs4916219	upstream	171.640	0.19	T	0.29	0.015	1.87 (1.13-3.11)
			rs10798277	upstream	171.640	0.35	C	0.35	1.74E-03	2.14 (1.33-3.45)
			rs7526628	upstream	171.644	0.05	T	0.48	0.012	1.84 (1.15-2.96)
			rs3934575	upstream	171.665	0.14	A	0.15	0.044	0.46 (0.22-0.98)
22	PPARA	rs4253655	rs4253617	intron	44.927	1	G	0.11	4.22E-03	0.27 (0.11-0.66)
			rs4253655	intron	44.948	1	A	0.08	0.047	2.37 (1.01-5.56)
Irregular Plaque
9	TLR4	rs752998	rs1930706	downstream	119.709	0.32	G	0.25	0.011	0.40 (0.20-0.81)
			rs2151370	downstream	119.765	0.27	C	0.28	0.018	2.02 (1.13-3.62)
			rs12335791	downstream	119.560	0.04	G	0.13	0.018	2.28 (1.15-4.50)
			rs2780244	downstream	119.768	0.27	T	0.29	0.018	2.02 (1.13-3.62)
			rs10983777	downstream	119.566	0.06	C	0.14	0.022	2.19 (1.12-4.27)
			rs6478338	downstream	119.748	0.47	G	0.25	0.028	0.51 (0.28-0.93)
			rs488101	downstream	119.747	0.40	C	0.24	0.031	1.93 (1.06-3.51)
			rs4837527	downstream	119.718	0.06	C	0.37	0.032	1.88 (1.06-3.35)
			rs1927910	intron	119.510	0.69	A	0.06	0.044	0.18 (0.04-0.95)
22	PPARA	rs4253655	rs4253617	intron	44.927	1.00	G	0.11	4.30E-03	0.20 (0.07-0.60)
Calcified Plaque
5	ITGA2	rs1991013	rs4865756	intron	52.349	0.44	A	0.36	0.031	0.22 (0.05-0.87)
			rs3797497	intron	52.370	0.00	T	0.36	0.049	0.28 (0.08-1.00)
10	HABP2	rs932650	rs4918818	upstream	115.159	0.01	A	0.11	0.046	5.09 (1.03-25.17)
			rs11196327	upstream	115.169	0.02	A	0.11	0.013	4.81 (1.39-16.60)
			rs1416131	upstream	115.183	0.02	C	0.36	0.046	0.27 (0.07-0.97)
			rs10509977	upstream	115.184	0.06	T	0.12	0.018	4.39 (1.29-14.96)
			rs11196335	upstream	115.200	0.03	A	0.19	0.022	3.42 (1.20-9.73)
			rs10885459	upstream	115.200	0.05	C	0.19	0.021	3.43 (1.21-9.74)
			rs8181320	upstream	115.207	0.01	A	0.14	5.94E-03	5.01 (1.59-15.80)
			rs7909440	upstream	115.270	0.15	C	0.16	0.040	3.29 (1.05-10.29)
			rs10885476	intron	115.321	0.94	T	0.13	0.035	3.06 (1.08-8.62)
			rs3121494	downstream	115.419	0.13	C	0.34	0.034	0.23 (0.06-0.89)
22	PPARA	rs4253655	rs5768939	upstream	44.913	0.03	G	0.11	0.024	3.94 (1.20-13.00)

^*adjusted for baseline age, sex, and smoking, hypertension, dislipidemia, diabetes, and number of years between baseline and phenotype measurement

^**Odds ratio is measuring the risk of the minor allele

MAF = Minor Allele Frequency

D’ and R2 are the measures of linkage disequilibrium between the SNP from the discovery analysis and the SNP from the validation analysis