Table 2 Summary results for most significant SNP–expression–BMI combination identified in Discovery (FHS) sample.

From: Integrating genetic and transcriptomic data to identify genes underlying obesity risk loci

Gene	CHR	POS (b38)	dbSNP ID	EA	OA	GWAS tag SNP	GWAS tag dbSNP ID	Study	P_BMI	N_BMI	BETA_BMI	P_SNP	N_SNP	BETA_SNP	P_META
GSTM3	chr1	109612066	rs17024393	C	T	Yes	rs17024393	FHS—Blood	2.67E−05	5619	0.003	9.30E−13	5257	0.123	3.89E−15
								CCHC—Blood	4.37E−01	934	−0.366	5.56E−03	769	0.757	1.70E−02
								Hypothalamus	9.48E−01	131	−7.858	–	–	–	–
								Nucleus accumbens	1.61E−01	198	−7.033	–	–	–	–
								Liver	7.06E−01	2225	0.007	6.56E−30		0.914	3.17E−28
								VAT	3.92E−03	657	−0.013	8.15E−05	657	0.484	5.09E−06
NT5C2	chr10	103154183	rs74233809	C	T	No	rs11191560	FHS—Blood	3.48E−16	5619	−0.004	5.82E−23	5257	0.072	1.16E−37
								CCHC—Blood	1.07E−01	934	−0.803	7.98E−49	769	0.363	9.76E−48
								Hypothalamus	2.02E−01	131	−7.037	4.30E−01	108	0.128	2.99E−01
								Nucleus accumbens	3.66E−01	198	−7.612	7.69E−04	170	0.276	2.59E−03
								Liver	6.40E−06	2225	−0.044	4.87E−02	2225	0.035	4.98E−06
								VAT	1.43E−01	657	0.007	5.90E−01	657	−0.031	2.94E−01
SNAPC3	chr9	15786904	rs10962158	A	T	No	rs4740619	FHS—Blood	4.71E−10	5619	0.002	2.97E−06	5257	0.015	3.66E−14
								CCHC—Blood	1.63E−02	934	−0.559	2.96E−03	769	0.091	5.28E−04
								Hypothalamus	6.41E−01	131	−7.751	2.88E−01	108	0.083	4.97E−01
								Nucleus accumbens	7.70E−01	198	−7.979	8.19E−01	170	0.011	9.21E−01
								Liver	4.03E−06	2225	−0.033	3.79E−02	2225	0.025	2.55E−06
								VAT	4.45E−06	657	−0.022	3.41E−01	657	0.019	2.18E−05
SPNS1	chr16	28814099	rs11860513	T	C	No	rs3888190	FHS—Blood	1.33E−05	5619	−0.001	1.03E−15	5257	0.019	4.59E−18
								CCHC—Blood	4.12E−02	934	−1.266	4.98E−38	769	0.293	1.85E−37
								Hypothalamus	6.62E−01	131	−7.764	2.38E−01	108	0.119	4.49E−01
								Nucleus accumbens	6.24E−01	198	−7.902	6.37E−01	170	−0.038	7.64E−01
								Liver	6.17E−01	2225	0.006	–	–	–	-
								VAT	1.13E−01	657	0.008	1.06E−04	657	0.088	1.48E−04
TMEM245	chr9	109170062	rs6477694	T	C	Yes	rs6477694	FHS—Blood	2.39E−23	5619	0.005	2.95E−36	5257	0.055	1.09E−57
								CCHC—Blood	3.91E−02	934	0.396	2.17E−20	769	0.337	4.20E−20
								Hypothalamus	7.22E−01	131	−7.796	5.13E−01	108	0.059	7.38E−01
								Nucleus accumbens	2.88E−01	198	−7.455	1.89E−01	170	0.062	2.13E−01
								Liver	1.72E−07	2225	−0.341	3.78E−34	2225	0.113	6.08E−39
								VAT	4.76E−01	657	−0.003	7.10E−13	657	−0.231	1.00E−11
YPEL3	chr16	29986879	rs4077410	G	A	No	rs4787491	FHS—Blood	3.19E−25	5619	0.007	1.68E−21	5257	0.057	5.98E−46
								CCHC—Blood	1.07E−01	934	−0.803	3.21E−02	769	0.037	2.30E−02
								Hypothalamus	3.22E−01	131	−7.365	1.07E−01	108	0.144	1.50E−01
								Nucleus accumbens	1.04E−01	198	−6.692	1.23E−02	170	0.156	9.79E−03
								Liver	1.09E−08	2225	−0.127	1.39E−52	2225	0.163	2.10E−58
								VAT	8.19E−02	657	0.008	3.89E−23	657	−0.294	1.76E−22
ZNF646	chr16	31077026	rs749671	A	G	No	rs9925964	FHS—Blood	9.68E−20	5619	−0.003	1.89E−09	5257	0.017	7.33E−26
								CCHC—Blood	3.91E−02	934	0.396	6.16E−01	769	−0.010	1.14E−01
								Hypothalamus	5.83E−01	131	−7.708	4.44E−01	108	−0.042	6.09E−01
								Nucleus accumbens	2.72E−01	198	−7.414	7.26E−02	170	−0.067	9.71E−02
								Liver	9.25E−03	2225	−0.020	7.32E−50	2225	−0.195	8.05E−50
								VAT	4.13E−02	657	0.010	9.75E−04	657	−0.081	4.48E−04

EA effect allele, OA other allele.
The bolded values in column “P_meta” means meeting significance criteria for generalization.

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Table 2 Summary results for most significant SNP–expression–BMI combination identified in Discovery (FHS) sample.

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