Table 4.

Comparison of top association hits for analysis of a dichotomous phenotype for African Americans samples from the Multi-Ethnic Study of Atherosclerosis.

Chr	SNP	MAF	Gene	Position (bp)	GEE: GC 1.02	MQLS: GC 1.0	Logistic: GC 1.07
16	rs247617	0.26	CETP	56990716	3.8 × 10−10	2.5 × 10−8	1.2 × 10−10
12	rs10770291	0.42	RERGL	18108048	4.6 × 10−7	1.4 × 10−5	3.7 × 10−7
1	rs12407335	0.21	PRMT6	107299585	5.5 × 10−7	2.2 × 10−6	4.4 × 10−7
1	rs12409858	0.20	PRMT6	107299233	1.1 × 10−6	4.9 × 10−6	9.6 × 10−7
12	rs701069	0.16	FLJ37505	128026678	1.8 × 10−6	4.3 × 10−6	1.4 × 10−6
7	rs6974174	0.40	WIPF3	29914469	2.5 × 10−6	1.4 × 10−5	2.7 × 10−6
1	rs11184981	0.25	PRMT6	107299263	3.2 × 10−6	1.0 × 10−5	2.5 × 10−6
2	rs3940409	0.43	PARD3B	205115659	3.4 × 10−6	1.5 × 10−5	4.3 × 10−6
7	rs10251970	0.49	DYNC1I1	95596832	3.5 × 10−6	6.2 × 10−6	1.6 × 10−6
9	rs2806687	0.36	INVS	103005815	3.7 × 10−6	2.8 × 10−6	2.6 × 10−6
10	rs7086818	0.08	ANKRD30A	36893908	3.7 × 10−6	4.4 × 10−5	3.1 × 10−6
12	rs7971307	0.45	RERGL	18118930	4.2 × 10−6	5.9 × 10−5	2.7 × 10−6
10	rs7096919	0.09	ANKRD30A	36889214	4.6 × 10−6	4.2 × 10−5	2.8 × 10−6
9	rs1529191	0.32	ERP44	102845908	9.0 × 10−6	3.3 × 10−6	5.4 × 10−6
15	rs10518973	0.10	LIPC	58651580	1.8 × 10−5	1.9 × 10−6	3.1 × 10−5
2	rs13384421	0.25	NMUR1	232464308	2.0 × 10−5	2.2 × 10−6	2.7 × 10−5

Results are shown for all SNPs with p-value ≤ 5 × 10⁻⁶ by GEE or M_QLS binary trait analyses, with corresponding results by logistic regression shown for comparison. GEE and logistic regression were performed with adjustment for covariates age, gender, study site, and a single principal component of ancestry, while M_QLS was performed with no covariates due to a practical limitation of the method. Minor allele frequency (MAF) is shown for each SNP, and genomic control (GC) numbers are indicated for each test, with no adjustment for GC inflation in the presented association results. SNP annotation was obtained using Human Genome build 37.1 from dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/).