Table 2.

cis eQTLs among GWAS Results for Metabolic Traits

					SNP -- Gene		SNP -- Trait
Gene	Chr.	eQTL	SNP location	* $h_{\mathit{\text{geneExp}}}^2$	eSNP-Pval	† $r{h}_{eQTL}^2$	‡GWAS-p value	§ $r{h}_{\mathit{\text{trait}}-SNP}^2$	GWAS- Trait
GSTM4	chr1	rs4970843	Intronic (SORT1)	0.55	7.26E-63	0.11	9.77E-23	0.002	LDL/TC
RHD	chr1	rs926438	Intronic (RHCE)	0.52	5.19E-289	0.47	1.68E-09	5.01E-7	LDL/TC
DOCK7	chr1	rs1748195	Intronic (DOCK7)	0.23	2.73E-162	0.60	2.43E-42	0.004	LDL/TG/TC
GSTM4	chr1	rs4970843	Intronic (SORT1)	0.55	7.26E-63	0.11	9.77E-23	0.001	LDL/TC
CLCN6	chr1	rs1256713 6	Intronic (CLCN6)	0.21	6.68E-52	0.21	3.41E-10	0.007	SBP/DBP
C4B	chr6	rs2072633	Intronic (CFB)	0.21	1.56E-40	0.16	2.67E-08	0	TC
HLA-B	chr6	rs437179	Coding(SKI V2L)	0.46	1.38E-59	0.11	6.98E-12	5.60E-4	TC
HLA-B	chr6	rs2524095	Unknown	0.46	4.88E-113	0.22	3.02E-08	0.001	TG
LOC10051 0059	chr6	rs2894254	Intronic (C6orf10)	0.74	1.65E-218	0.24	8.92E-10	0.004	TG
HCP5	chr6	rs2596565	Unknown	0.29	5.63E-28	0.13	1.55E-10	0.004	TG/TC
NCRNA00 243	chr6	rs3130544	Unknown	0.26	3.70E-100	0.37	4.84E-10	0.003	TG/TC
FLOT1				0.25	1.39E-59	0.23
SLC44A4	chr6	rs486416	Intronic (EHMT2)	0.56	0	0.87	1.99E-14	0.006	TG/TC
CSGALNA CT1	chr8	rs1967103	Intronic (CSGALNA CT1)	0.55	5.97E-218	0.35	5.78E-09	0.006	HDL/TG
GRINA	chr8	rs6985603	5' upstream (SPATC1)	0.26	1.10E-104	0.35	3.39E-10	0.002	LDL
C11orf10	chr11	rs174534	Intronic (C11orf9)	0.32	2.01E-255	0.65	2.68E-18	0.005	HDL/LDL/T G/TC
FADS2	chr11	rs174549	Intronic (FADS1)	0.74	0	0.54	2.08E-20	0.004	HDL/LDL/T G/TC
SIDT2	chr11	rs6589597	Unknown	0.53	2.17E-297	0.46	7.22E-14	0.003	TC
SIDT2	chr11	rs7107152	Intronic (SIDT2)	0.53	0	0.68	7.13E-10	0.001	TG
POC1B	chr12	rs1110532 8	Intergenic	0.35	2.53E-41	0.11	1.08E-09	0.003	SBP/DBP
MAP2K5	chr15	rs1290281 2	Intronic (MAP2K5)	0.24	1.40E-198	0.73	1.33E-08	1.49E-4	BMI
APOB48R	chr16	rs1244388 1	Intronic (ATXN2L)	0.60	0	0.72	5.32E-10	2.06E-4	BMI
GSDMB	chr17	rs1293623 1	Intronic (ZPBP2)	0.35	0	0.92	2.47E-09	1.48E-4	HDL
ORMDL3				0.24	1.34E-92	0.34
LILRB3	chr19	rs431420	Unknown	0.44	3.50E-160	0.33	7.51E-13	8.22E-5	HDL
LILRB2				0.34	5.93E-124	0.31
SLC44A2	chr19	rs2288904	Coding (SLC44A2)	0.27	2.37E-48	0.16	5.72E-10	0.005	LDL
PVRL2	chr19	rs8104483	Intronic (PVRL2)	0.58	1.13E-271	0.40	1.94E-20	2.90E-4	LDL/TC

^*$h_{\mathit{\text{geneExp}}}^2$ is the proportion of total phenotypic variance that can be explained by the additive genetic components$(h_{\mathit{\text{geneExp}}}^2={\sigma }_A^2/{\sigma }_{\mathit{\text{geneExp}}}^2)$

^†$r{h}_{eQTL}^2$ is the ratio of the proportion of variance explained by a peak eQTL to the heritability of a gene expression trait $(r{h}_{eQTL}^2=h_{eQTL}^2/h_{\mathit{\text{geneExp}}}^2)$

^‡GWAS-p value: the minimum trait-associated SNP p value in NHGRI GWAS Catalog (Hindorff et al. 2009)

^§$r{h}_{\mathit{\text{trait}}-SNP}^2$ is the ratio of the proportion of variance explained by a SNP to the heritability of a clinical trait$(r{h}_{\mathit{\text{trait}}-SNP}^2=h_{SNP}^2/h_{\mathit{\text{trait}}}^2)$. $r{h}_{\mathit{\text{trait}}-SNP}^2$ is calculated from FHS samples along.