Predicting gene targets from integrative analyses of summary data from GWAS and eQTL studies for 28 human complex traits

Table 2 Seventeen novel genes identified in the SMR Analysis. Novel genes are genes that have passed both the SMR and HEIDI tests (P _SMR <8.4E-06 and P _HEIDI ≥ 005), have not previously been identified as GWS, and no GWS loci within 1 Mb window reported in the primary GWAS paper (full results are given in Additional file 1: Table S4)

Trait	Probe ID	Gene	Top cis-eQTL	Allele Freq	P _eQTL	P _GWAS	P _SMR	P _HEIDI	nsnp
BIP1	ILMN_1665280	SPCS1	rs998909	0.420	2.1E-39	6.8E-07	3.4E-06	0.15	155
CAD	ILMN_1713380	EIF2B2	rs175016	0.475	1.8E-278	4.7E-06	5.6E-06	0.23	189
CAD	ILMN_1712430	ATP5G1	rs1962412	0.281	1.3E-44	7.4E-07	3.0E-06	0.27	127
CD	ILMN_1718852	PLCL1	rs2117339	0.486	6.7E-30	8.0E-07	6.0E-06	0.14	216
	ILMN_2122952	CISD1	rs1199098	0.214	<1.0E-300	1.5E-06	1.7E-06	0.17	241
	ILMN_2122953	CISD1	rs1550773	0.212	<1.0E-300	2.0E-06	2.2E-06	0.13	217
COLLEGE	ILMN_1723684	DARC	rs12075	0.456	4.8E-107	3.3E-06	5.4E-06	0.47	110
EDUYEARS	ILMN_1718023	APEH	rs3197999	0.291	1.1E-27	5.7E-07	5.5E-06	0.08	88
	ILMN_2343048	ABCB9	rs1615350	0.248	9.1E-43	2.0E-06	7.2E-06	0.75	53
	ILMN_1738369	TUFM	rs8049439	0.405	<1.0E-300	1.5E-07	1.7E-07	0.11	37
HDL	ILMN_1684227	GPR146	rs1997243	0.155	2.2E-300	2.4E-07	3.1E-07	0.22	130
IBD	ILMN_1697409	TNFRSF14	rs734999	0.483	2.1E-90	2.3E-07	5.4E-07	0.98	64
	ILMN_1727709	GPBAR1	rs2292550	0.405	8.3E-43	6.3E-08	4.9E-07	0.24	109
	ILMN_1684628	ZFP90	rs1182968	0.219	<1.0E-300	3.3E-06	3.6E-06	0.90	311
LDL	ILMN_1718706	ERAL1	rs901975	0.202	6.5E-46	2.2E-06	6.9E-06	0.19	66
UC	ILMN_1744713	PARK7	rs3766606	0.173	1.1E-53	5.7E-08	3.0E-07	0.09	195
	ILMN_1727709	GPBAR1	rs2292550	0.405	8.3E-43	1.2E-07	8.1E-07	0.12	109
	ILMN_1683811	TNPO3	rs3807306	0.496	1.4E-150	2.3E-06	3.3E-06	0.69	125

P _eQTL p value of the top associated cis-eQTL of the probe, P _GWAS GWAS p value of the top cis-eQTL, P _SMR p value for gene-trait association from the SMR test, P _HEIDI p value from HEIDI test to indicate whether the gene-trait association is due to a single shared genetic variant (the smaller P _HEIDI the more likely that there are more than one genetic variant)

ISSN: 1756-994X