Table 2. MetS SNP association with phenotypes and their gene annotation at 3q27 QTL.

SNPs within 1 LOD reduction from the linkage peak were tested against the 42 phenotypes. For phenotypic abbreviations, see Table 1. SNPs were mapped to genes and the known functions of these genes summarized, based on data from the NCBI build 36 human genome assembly. Annotations were determined at the position and within 250kb up- and downstream of the associated SNP. Data shown in column “−Log10(p)” are levels of the highest association. The QTL-specific significance threshold based on the effective number of SNPs was p_0.05=1.32×10⁻⁵, −log(p-value)=4.941. Prioritized biologically relevant genes are shaded in gray and SNP associations that exceed statistical QTL-specific significance threshold are bolded. MAF, minor allele frequency.

	Variant	Minor Allele	MAF	−Log10(p)	Associated phenotype	Nearest gene	Location	Annotation
Body composition and insulin responsiveness	rs6443434	A	0.43	3.76	Weight	TBL1XR1	upstream	signal transduction
	rs11710431	A	0.19	4.55	Height	TBL1XR1	intergenic	signal transduction
	rs6443434	A	0.43	3.49	BMI	TBL1XR1	upstream	signal transduction
	rs6772734	A	0.02	3.82	WC	LOC131583	intergenic	unknown function
	rs13068101	T	0.28	3.06	HC	C3orf59	intergenic	unknown function
	rs12639517	T	0.33	4.03	WHR	IGF2BP2	intergenic	controls IGF translation
	rs11708240	G	0.14	3.54	Fatkg	NAALADL2	intergenic	dipeptidase
	rs13098487	G	0.22	3.59	Fatpct	NLGN1	intronic	brain synapses
	rs569221	A	0.19	4.47	Leankg	NLGN1	intronic	brain synapses
	rs301177	C	0.23	3.39	Leanpct	TBL1XR1	intergenic	signal transduction
	rs4074869	C	0.44	3.70	SubQF	EPHB3	intergenic	ephrinB receptor
	rs7433602	T	0.29	5.03	VF	NAALADL2	intronic	dipeptidase
	rs12496403	A	0.01	3.76	TAF	TBL1XR1	intergenic	signal transduction
	rs13324849	T	0.09	4.39	RQ	NAALADL2	intergenic	dipeptidase
	rs6443434	A	0.43	3.51	REE	TBL1XR1	upstream	signal transduction
	rs4074869	C	0.44	4.47	REE/weight	EPHB3	intergenic	ephrinB receptor
	rs13321995	A	0.40	4.89	REE/Leanmass	C3orf21	intronic	unknown function
	rs6807927	A	0.27	3.96	FG	SENP2	intronic	SUMO protease
	rs10933727	G	0.32	4.43	FI	LOC100131551	intergenic	unknown function
	rs2513	A	0.10	3.57	IGR	AK091265	downstream	unknown function
	rs10933727	G	0.32	5.93	HOMA	LOC100131551	intergenic	unknown function
	rs9814412	T	0.27	3.90	SI	HRG	5’UTR	thrombosis
	rs1463332	C	0.32	3.29	SG	TBL1XR1	intergenic	signal transduction
	rs6785028	T	0.26	3.87	AIR	LPP	intronic	cell adhesion
	rs937589	T	0.02	3.70	DI	C3orf59	intronic	unknown function
Lipids/lipoprotein profiles and cardiovascular performance	rs10804867	A	0.26	3.74	TG	TBL1XR1	intergenic	signal transduction
	rs1895070	A	0.10	4.66	TC	mRNA FLJ31690	downstream	unknown function
	rs1895070	A	0.10	4.25	LDL-c	mRNA FLJ31690	downstream	unknown function
	rs1895070	A	0.10	4.57	cal.LDL-c	mRNA FLJ31690	downstream	unknown function
	rs4452373	G	0.00	3.90	HDL-c	mRNA HQ448050	intergenic	unknown function
	rs9716	C	0.24	3.55	HMED	ST6GAL1	downstream	glycosyltransferase
	rs6793161	T	0.01	3.62	LMEDn	mRNA AF338197	intergenic	unknown function
	rs2700839	C	0.12	3.70	LDLppd	ATP11B	intergenic	ATPase
	rs10937009	G	0.00	5.14	BMED	NDUFB5	intergenic	repiratory chain
	rs260589	G	0.33	3.27	sBP	TPRG1	intergenic	tumor protein regulated
	rs6444517	G	0.10	4.64	dBP	OSTN	intergenic	osteoblastic differentiation
	rs7631640	C	0.09	4.51	Pulse	MCF2L2	downstream	guanine exchange factor
Adipokine and cytokines	rs17427594	C	0.10	3.60	Adiponectin	CLDN1	intergenic	cell junction
	rs6772734	A	0.02	3.45	Leptin	FAM43A	intergenic	unknown function
	rs13070418	T	0.36	5.06	TNFalfa	SOX2	intergenic	transcription factor
	rs9877500	C	0.22	4.11	IL-1β	IQCG	intronic	unknown function
	rs6807480	A	0.36	3.60	IL-6	FGF12	intronic	fibroblast growth factor