Table 4.

T2D-GENES + METSIM Studies: Meta-analysis of all 4 lipid traits. This table lists the SNPs exclusively detected by metaUSAT only. Only the independent SNPs (pairwise distance > 500 kb and r² < 0.1) are listed. We also report the empirical p-values of metaUSAT based on 8.5 × 10⁹ Monte Carlo simulations. P-values exceeding the genome-wide threshold of 5 × 10⁻⁸ have been bold-faced. The known association results are based on previously reported GWAS associations within 500 kb of and r² > 0.7 with any of our SNPs from the NHGRI GWAS catalog (Welter et al., 2014) and our in-house GWAS catalog.

rsID	chr	position	p-value		empirical p-value metaUSAT	Known association result
			meta-USAT	meta-MANOVA
rs2483205	1	55518316	2.5 × 10−8	1.1 × 10−7	3.2 × 10−8	Lipids, Lipoprotein fractions1
rs1367117†	2	21263900	1.5 × 10−9	2.3 × 10−7	2.8 × 10−9	Lipids, Lipoprotein fractions2
rs2304130	19	19789528	1.5 × 10−9	1.8 × 10−6	3.3 × 10−9	Lipids, Lipoprotein fractions, T2D3

¹near many known GWAS hits for lipids (Surakka et al., 2015), lipoprotein fractions (Kettunen et al., 2012), cardiovascular endpoints (Kathiresan et al., 2009).

^†Illumina OmniExpress Exome Chip ID is exm176096.

²known GWAS hit for lipids (Teslovich et al., 2010; Willer et al., 2013; Surakka et al., 2015)

³known GWAS hit for lipids (Kristiansson et al., 2012; Willer et al., 2013)