Table 3.

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

Chr	SNP	MAF	Gene	Position (bp)	LME: GC 1.02	fastAssoc: GC 1.0	robustAssoc: GC 0.95	Linear regression: GC 1.11
16	rs247617	0.26	CETP	56990716	3.7 × 10−15	9.0 × 10−15	7.4 × 10−15	3.2 × 10−15
10	rs10826964	0.37	ZEB1	31857752	7.2 × 10−7	2.3 × 10−6	2.6 × 10−6	6.5 × 10−7
2	rs340619	0.03	APOB	21035081	3.6 × 10−6	4.5 × 10−6	8.5 × 10−5	1.8 × 10−6
10	rs1314013	0.45	ZEB1	31565355	3.7 × 10−6	5.8 × 10−6	6.6 × 10−6	2.5 × 10−6
15	rs16976466	0.29	PRTG	55972797	4.3 × 10−6	5.4 × 10−6	5.7 × 10−6	1.1 × 10−6
10	rs161259	0.34	ZEB1	3172158	4.5 × 10−6	1.4 × 10−5	1.4 × 10−5	6.8 × 10−6

Results are shown for all SNPs with p-value ≤ 5 × 10⁻⁶ for LME (Chen and Yang 2010), fastAssoc (Chen and Abecasis 2007) or robustAssoc (Chen et al. 2009) quantitative trait analyses. All quantitative trait analyses were performed with adjustment for covariates age, gender, study site, and a single principal component of ancestry. 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/).