Table 3. MixMAP in GLGC identifies IBC array loci that lack single SNP evidence for LDL-C association.

		Position						Single SNP p-values			Supporting
Locus	Chr	Start	Stop	Gene Name	Single SNP*1	MixMAP*2	# of SNPs	Min	Median	Max	Evidence§
PKN2	1	88918822	89073711	PKN2	-	+	21	0.003906	0.06777	0.6081	None
FN1	2	215938326	216066837	FN1	-	+	44	1.56E-05	0.1254	0.9993	†B [49], [50]
UGT1A1	2	234255355	234346384	UGT1A1	-	+	20	3.53E-06	0.070225	0.9471	A [18]–[20]; B [21]
PPARG	3	12309416	12450557	PPARG	-	+	49	1.35E-05	0.1021	0.9917	?A,B,C[22]–[25]
DMDGH	5	78331610	78402461	DMGDH	-	+	19	0.002283	0.08308	0.6427	‡A [51]
PPARD	6	35419966	35503982	PPARD	-	+	45	0.002272	0.1943	0.8976	A [31]–[34]; B [52]
CDK6	7	92074765	92304241	CDK6	-	+	43	0.0006457	0.1083	0.8932	None
VPS13B	8	100143528	100936497	VPS13B	-	+	30	0.0003567	0.101375	0.861	**A [42]
GAD2	10	26552050	26631994	GAD2	-	+	22	0.006998	0.06269	0.3543	None
GAB2	11	77604417	77802894	GAB2	-	+	13	1.65E-05	0.0005164	0.9401	None
APOH	17	61629102	61657177	APOH	-	+	25	2.10E-05	0.1556	0.9846	A [26]–[29]
NPC1	18	19366772	19415132	NPC1	-	+	16	0.014	0.04201	0.3832	A,B,C [35]–[38]

For the 31827 SNPs in 2960 genes interrogated in Global Lipids Genetic Consortium (GLGC) summary data [1], novel loci are detected by MixMAP alone. The median p-values for these genes tend to be lower than expected by chance. ^†No association with plasma lipids but mouse models support role in atherosclerosis; ^‡No association with plasma lipids but cause of inborn error of choline metabolism; ^**No association with plasma lipids but implicated in Cohen syndrome in which truncal obesity is a feature; ?PPARG is a prominent gene for insulin resistance, type-2 diabetes mellitus, lipodystrophy and obesity; some data link PPARG to lipoprotein abnormalities; indicates corresponding gene detected and – indicates corresponding gene not detected; genome wide significant 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.