A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation

Zhang, Yi; Kent, Jack W; Olivier, Michael; Ali, Omar; Cerjak, Diana; Broeckel, Ulrich; Abdou, Reham M; Dyer, Thomas D; Comuzzie, Anthony; Curran, Joanne E; Carless, Melanie A; Rainwater, David L; Göring, Harald H H; Blangero, John; Kissebah, Ahmed H

doi:10.1186/1755-8794-6-14

Table 2 MetS SNP association with phenotypes and their gene annotation at 5p14 QTL

From: A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation

Variant	Minor allele	MAF	-LOG(p)	Associated phenotypes	Nearest gene	Location	Annotation
rs10061119	T	0.26	5.07	Weight	CDH18	intron	Cell Cell adhesion
rs13357704	A	0.26	5.07	Weight	CDH18	intron	Cell Cell adhesion
rs10805723	G	0.25	5.03	Weight	CDH18	intron	Cell Cell adhesion
rs16887308	T	0.26	5.03	Weight	CDH18	intron	Cell Cell adhesion
rs4386736	A	0.26	5.03	Weight	CDH18	intron	Cell Cell adhesion
rs6879762	C	0.26	5.03	Weight	CDH18	intron	Cell Cell adhesion
rs10062513	G	0.25	4.68	Weight	CDH18	intron	Cell Cell adhesion
rs13355121	C	0.25	4.68	Weight	CDH18	intron	Cell Cell adhesion
rs10062864	A	0.25	4.57	Weight	CDH18	intron	Cell Cell adhesion
rs163282	A	0.26	4.27	Height	FAM134B	intron	Neuron maintenance
rs10061119	T	0.26	4.82	BMI	CDH18	intron	Cell Cell adhesion
rs13357704	A	0.26	4.82	BMI	CDH18	intron	Cell Cell adhesion
rs10805723	G	0.25	4.77	BMI	CDH18	intron	Cell Cell adhesion
rs16887308	T	0.26	4.77	BMI	CDH18	intron	Cell Cell adhesion
rs4386736	A	0.26	4.77	BMI	CDH18	intron	Cell Cell adhesion
rs6879762	C	0.26	4.77	BMI	CDH18	intron	Cell Cell adhesion
rs13355121	C	0.25	4.52	BMI	CDH18	intron	Cell Cell adhesion
rs10062864	A	0.25	4.43	BMI	CDH18	intron	Cell Cell adhesion
rs10061119	T	0.26	4.66	WC	CDH18	intron	Cell Cell adhesion
rs13357704	A	0.26	4.66	WC	CDH18	intron	Cell Cell adhesion
rs10805723	G	0.25	4.57	WC	CDH18	intron	Cell Cell adhesion
rs16887308	T	0.26	4.57	WC	CDH18	intron	Cell Cell adhesion
rs4386736	A	0.26	4.57	WC	CDH18	intron	Cell Cell adhesion
rs6879762	C	0.26	4.57	WC	CDH18	intron	Cell Cell adhesion
rs995021	C	0.49	3.57	HC	CDH18	intron	Cell Cell adhesion
rs1864220	G	0.07	3.45	WHR	FBXL7	intron	Protein sorting
rs860545	T	0.16	2.89	Fatkg	MARCH11	intergenic	Protein sorting
rs10223312	T	0.01	3.52	Fatpct	mRNA BC033144	intergenic	unknown function
rs17707882	A	0.04	4.47	Leankg	MYO10	intron	Cell Cell adhesion
rs10223312	T	0.01	3.54	Leanpct	mRNA BC033144	intergenic	unknown function
rs1840870	C	0.44	2.44	SubQF	EST BG220738	intergenic	unknown function
rs11134371	T	0.33	4.04	VF	LOC285692	intron	unknown function
rs17275322	G	0.03	2.82	TAF	LOC285692	intron	unknown function
rs12652510	C	0.19	3.11	RQ	CDH18	intron	Cell Cell adhesion
rs10065719	G	0.14	2.74	REE	AY330599	intergenic	tumor antigen
rs6859862	C	0.41	3.61	REE/weight	DNAH5	intron	motor protein
rs1809880	G	0.06	3.16	REE/Lean	ROPN1L	intron	sperm protein
rs7721328	G	0.17	3.57	FG	mRNA TAG1	intron	tumor antigen
rs2582660	C	0.18	2.88	FI	MARCH11	intergenic	Protein sorting
rs16902967	A	0.03	3.77	IGR	DNAH5	intergenic	motor protein
rs4327597	A	0.14	3.25	HOMA	TAG	intron	tumor antigen
rs831657	G	0.14	3.23	SI	MARCH11	intergenic	protein sorting
rs1551936	T	0.15	3.44	SG	FAM134B	intron	Neuron maintenance
rs2929724	C	0.50	3.30	AIR	LOC285696	intron	unknown function
rs10805650	G	0.33	3.11	DI	EST BM682321	intergenic	unknown function
rs16887451	C	0.07	3.10	TG	mRNA BC028204	intron	unknown function
rs17839277	T	0.03	3.55	TC	mRNA BC028204	intergenic	unknown function
rs12659663	A	0.25	4.17	LDL-c	mRNA BC028204	intron	unknown function
rs12659663	A	0.25	3.87	cal. LDL-c	mRNA BC028204	intron	unknown function
rs6883134	G	0.06	3.25	HDL-c	TRIO mRNA	intron	protein interaction
rs10065719	G	0.14	4.48	HMED	AY330599	intergenic	tumor antigen
rs10079252	G	0.49	4.30	LMEDn	mRNA U92022	intergenic	transposon Hsmar2
rs10073730	C	0.01	3.77	LDLppd	MYO10	intron	Cell Cell adhesion
rs6894869	C	0.01	5.13	BMED	CTNND2	intron	Cell Cell adhesion
rs5745297	A	0.07	3.58	sBP	DAP	3’ UTR	cell death
rs6450583	G	0.21	3.27	dBP	mRNA BC028204	intergenic	unknown function
rs1971391	A	0.44	3.10	Pulse	mRNA AK130861	intergenic	unknown function
rs31509	G	0.28	3.33	Adiponectin	MYO10	intron	Cell Cell adhesion
rs404639	G	0.06	4.29	Leptin	CDH12	intron	Cell Cell adhesion
rs6893920	G	0.22	4.04	TNF-alpha	mRNA U92022	intergenic	transposon Hsmar2
rs7730897	T	0.10	3.47	IL-1β	MARCH11	intergenic	protein sorting
rs17707882	A	0.04	3.77	IL-6	MYO10	intron	Cell Cell adhesion

SNPs within 1 LOD reduction from the linkage peak were tested for associations against the 42 phenotypes. Annotated genes and their known function were derived 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. SNP associations that exceed statistical QTL-specific significance threshold are bolded.

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ISSN: 1755-8794

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