Table 4. Top MixMAP and single SNP evidence for IBC array locus association with LDL-C in PennCAC.

		Position			PennCAC Results			Top GLGC Findings		Supporting
Locus	Chr	Start	Stop	Gene Name	Single SNP*1	MixMAP*2	# of SNPs	SNP	p-value	Evidence§
ELA2A	1	15653807	15669301	ELA2A	+	-	8	rs10927787	0.048	None
RGS7	1	239219450	239268557	RGS7	+	-	38	rs628208	0.008	None
MFSD7	4	671940	671940	MFSD7	+	-	1	rs9991613	0.671	None
ESR1	6	152167137	152467893	ESR1	+	-	149	rs9341052	1.83E-04	A [53]–[56]
APOA5-A4-C3-A1	11	116024949	116145447	BUD13	+	-	16	rs6589565	5.37E-16	A [1]
	11	116157417	116170289	APOA5	+	-	6	rs2075290	2.32E-16	A [1]
YY1	14	99795191	99809982	YY1	+	-	2	rs4905941	0.232	C [57]–[59]
FEM1B	15	66348570	66371610	FEM1B	+	-	7	rs16951723	0.352	None
SORT1	1	109590236	109623689	CELSR2	-	+	23	rs629301	9.70E-171	A [1]
IL1R2	2	101970201	102010893	IL1R2	-	+	37	rs2236927	0.086	A [39]; B [40]; C [41]
TNIP3	4	122257475	122313818	TNIP3	-	+	14	rs17051298	0.058	None
FGF2	4	123975987	124033758	FGF2	-	+	25	rs308406	0.039	None
LPA	6	160873025	161011583	LPA	-	+	28	rs10455872	1.36E-15	A [1]
GRM3	7	86106844	86327561	GRM3	-	+	32	rs10245069	0.058	None
VPS13B	8	100143528	100936497	VPS13B	-	+	30	rs7841688	3.57E-04	A† [42]

For the 31585 SNPs in 2944 genes interrogated in PennCAC, MixMAP identifies loci in PennCAC that are not identified by single SNP analysis. Of these gene/loci, SNPs in reach genome wide significance in GLGC (SORT1 and LPA) and are also MixMAP significant in GLGC; is MixMAP significant but single SNP non-significant in GLGC (VPS13B), and 2 have animal model data supporting modulation of lipid metabolism (VPS13B and IL1R2). ^†No association with plasma lipids but implicated in Cohen syndrome in which truncal obesity is a feature; indicates corresponding gene detected and – indicates corresponding gene not detected; IBC array threshold (); Bonferroni correction based on the number of genes (); Based on published literature (see corresponding citations): A: human data; B: mouse/animal data; and C: cell biology.