Table 3.

Significantly-associated MetS QTNs with functional annotation

Ethnic group	Trait	Gene (distance in basepairs) from refGene	Function (refGene)	CHR	Basepair (hg19)	rsid	Alleles	Functional annotations with thresholds^a
Ethnic group	Trait	Gene (distance in basepairs) from refGene	Function (refGene)	CHR	Basepair (hg19)	rsid	Alleles	FATHMM-MLK (noncoding > 0.50)	GWAVA (TSS) > 0.40	CADD v1.3 (phred-scaled) > 10	EIGEN > 0
AA	log(TG)	FAM89A(120,755) TRIM67(1919)	Intergenic	1	231,296,755	rs75219957	G/C	0.20	0.62	4.48	0.38
AA	log(TG)	MIR4283-1(273,158) ZNF722P(104,479)	Intergenic	7	63,354,705	rs73123056	A/C	0.97	0.21	3.38	0.61
EA	log(TG)	GCKR	Exonic-NSV^b	2	27,730,940	rs1260326	T/C	0.02^c	0.20	0.11	0.29
EA	Weight	GLI2(86,646) TFCP2L1(137,289)	Intergenic	2	121,836,875	rs139940998	A/G	0.63	0.46	19.05	0.69
JA	Weight	QRFPR	Intronic	4	122,258,149	rs2302308^d	G/T	0.12	0.34	3.83	0.02
JA	Weight	QRFPR	Intronic	4	122,260,042	rs17051338	G/T	0.23	0.31	7.28	0.33
JA	Weight	QRFPR	Intronic	4	122,264,692	rs77438622	G/C	0.12	0.21	6.40	0.09
JA	Weight	QRFPR	Intronic	4	122,270,900	rs77006299	C/A	0.21	0.22	1.33	0.03
JA	Waist	STIM1	Intronic	11	3,972,232	rs146792726	A/G	0.14	0.12	4.48	0.08
JA	Waist	STIM1	Intronic	11	4,063,916	rs147605117	G/C	0.15	0.17	10.86	0.28
MA	Glucose	NR3C2(195,478) LOC105377480(300,770)	Intergenic	4	149,561,328	rs76209611	G/T	0.18	0.2	6.35	0.08

AA African Americans, EA, European Americans, JA, Japanese Americans, MA, Mexican Americans

^aBolded scores beyond recommended thresholds indicate QTNs with a deleterious or functional role

^bExonic, nonsynonymous variant

^cFATHMM-MLK coding score shown

^dRegSNPs-intron probability of disease-causing was 0.79 and only annotated for variant rs2302308