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chr4:146,598,342-149,011,707

Best TWAS P=1.466368e-09 · Best GWAS P=1.181753e-09 conditioned to 0.1440765

Associated models

#	Tissue	Gene	Modality	RNA phenotype	h2	eQTL R2	model	# weights	model R2	model R2 P	eQTL GWAS Z	TWAS Z	TWAS P	Top SNP corr	PP3	PP4	joint
1	Adipose	Atg7	alternative polyA	ENSRNOT00000067532	0.02	0.02	top1	1	0.02	2.2e-03	5.4	5.4	6.4e-08	0.96	0.07	0.03	FALSE
2	Adipose	Atg7	alternative polyA	ENSRNOT00000099380	0.04	0.04	top1	1	0.04	1.0e-05	5.4	-5.4	6.4e-08	-0.98	0.48	0.26	FALSE
3	Adipose	Atg7	alternative polyA	ENSRNOT00000067532	0.02	0.02	top1	1	0.02	9.8e-04	5.4	5.4	6.4e-08	0.96	0.08	0.04	FALSE
4	Adipose	Atg7	alternative polyA	ENSRNOT00000099380	0.07	0.05	top1	1	0.06	1.0e-06	5.4	-5.4	6.4e-08	-0.98	0.58	0.32	FALSE
5	Adipose	Vgll4	gene expression	ENSRNOG00000007822	0.02	0.01	blup	1519	0.01	1.1e-02	5.6	-5.8	5.3e-09	-0.96	0.31	0.51	FALSE
6	Adipose	Tamm41	gene expression	ENSRNOG00000007874	0.28	0.23	enet	208	0.27	1.8e-29	-4.4	5.4	5.7e-08	0.84	0.94	0.06	FALSE
7	Adipose	Timp4	gene expression	ENSRNOG00000007955	0.05	0.03	lasso	27	0.04	2.1e-05	-4.6	5.7	1.4e-08	0.87	0.38	0.61	FALSE
8	Adipose	Atg7	mRNA stability	ENSRNOG00000007486	0.04	0.04	top1	1	0.04	4.3e-05	5.7	-5.7	1.3e-08	-0.94	0.16	0.35	FALSE
9	Adipose	Tamm41	mRNA stability	ENSRNOG00000007874	0.19	0.17	top1	1	0.17	2.5e-18	5.6	5.6	1.9e-08	0.96	0.39	0.61	FALSE
10	BLA	Atg7	alternative polyA	ENSRNOT00000096019	0.06	0.02	blup	1953	0.02	2.2e-02	5.8	-5.1	2.9e-07	-0.95	0.28	0.52	FALSE
11	BLA	Vgll4	gene expression	ENSRNOG00000007822	0.25	0.15	blup	1519	0.16	5.6e-09	6.0	5.9	4.3e-09	0.96	0.30	0.70	FALSE
12	Brain	Atg7	alternative polyA	ENSRNOT00000096019	0.20	0.19	enet	32	0.20	2.5e-18	5.6	-5.5	4.7e-08	-0.97	0.33	0.67	FALSE
13	Brain	Atg7	alternative polyA	ENSRNOT00000109260	0.40	0.36	lasso	24	0.38	8.0e-37	5.6	5.7	1.2e-08	0.97	0.36	0.64	FALSE
14	Brain	Atg7	alternative polyA	ENSRNOT00000099380	0.16	0.19	top1	1	0.19	6.3e-17	5.6	-5.6	1.9e-08	-0.98	0.36	0.64	FALSE
15	Brain	Atg7	alternative polyA	ENSRNOT00000104390	0.08	0.05	top1	1	0.05	8.5e-06	5.6	-5.6	1.7e-08	-0.98	0.33	0.64	FALSE
16	Brain	Atg7	alternative polyA	ENSRNOT00000109260	0.34	0.33	enet	303	0.36	1.4e-34	5.6	5.8	8.9e-09	0.98	0.35	0.65	FALSE
17	Brain	Vgll4	gene expression	ENSRNOG00000007822	0.15	0.10	blup	1519	0.14	5.3e-13	5.6	5.5	3.0e-08	0.88	0.49	0.51	FALSE
18	Brain	Tamm41	gene expression	ENSRNOG00000007874	0.11	0.10	blup	1461	0.10	2.7e-09	5.7	5.9	4.0e-09	0.98	0.29	0.71	FALSE
19	Brain	Atg7	isoform ratio	ENSRNOT00000067532	0.04	0.05	top1	1	0.05	3.0e-05	5.7	-5.7	9.3e-09	-0.98	0.15	0.44	FALSE
20	Brain	Atg7	isoform ratio	ENSRNOT00000104390	0.05	0.04	top1	1	0.04	8.6e-05	5.6	-5.6	2.6e-08	-0.97	0.27	0.33	FALSE
21	Brain	Atg7	isoform ratio	ENSRNOT00000109260	0.25	0.27	lasso	18	0.27	2.1e-25	5.6	5.7	1.3e-08	0.98	0.36	0.64	FALSE
22	Brain	Slc6a11	mRNA stability	ENSRNOG00000005697	0.06	0.04	top1	1	0.04	7.9e-05	6.0	6.0	1.5e-09	0.90	0.03	0.86	TRUE
23	Eye	Atg7	isoform ratio	ENSRNOT00000067532	0.41	0.00	blup	1953	0.05	6.4e-02	-4.0	-5.8	5.0e-09	-0.93	0.21	0.18	FALSE
24	IL	Atg7	alternative polyA	ENSRNOT00000096019	0.16	0.08	top1	1	0.08	4.9e-03	5.6	-5.6	2.2e-08	-0.98	0.10	0.06	FALSE
25	IL	Vgll4	gene expression	ENSRNOG00000007822	0.21	0.10	blup	1518	0.12	8.4e-04	5.6	5.8	6.2e-09	0.94	0.31	0.51	FALSE
26	IL	Tamm41	gene expression	ENSRNOG00000007874	0.20	0.08	blup	1460	0.08	7.1e-03	5.7	5.9	4.0e-09	0.98	0.27	0.54	FALSE
27	LHb	Atg7	alternative polyA	ENSRNOT00000109260	0.20	0.05	blup	1950	0.09	3.7e-03	4.6	5.4	7.9e-08	0.96	0.37	0.31	FALSE
28	LHb	Atg7	alternative polyA	ENSRNOT00000109260	0.20	0.05	blup	1950	0.09	3.2e-03	4.6	5.4	6.9e-08	0.96	0.37	0.31	FALSE
29	LHb	Vgll4	gene expression	ENSRNOG00000007822	0.25	0.06	blup	1518	0.09	4.1e-03	5.8	5.7	1.3e-08	0.90	0.32	0.45	FALSE
30	LHb	Tamm41	gene expression	ENSRNOG00000007874	0.31	0.08	blup	1460	0.13	5.2e-04	5.6	5.8	6.0e-09	0.94	0.31	0.55	FALSE
31	Liver	Atg7	alternative polyA	ENSRNOT00000109260	0.18	0.14	lasso	45	0.17	8.0e-19	5.7	5.6	1.7e-08	0.93	0.27	0.73	FALSE
32	Liver	Atg7	alternative polyA	ENSRNOT00000104390	0.03	0.02	top1	1	0.02	8.9e-04	5.6	-5.6	2.0e-08	-0.98	0.07	0.05	FALSE
33	Liver	Atg7	alternative polyA	ENSRNOT00000109260	0.20	0.17	lasso	43	0.20	3.6e-22	5.6	5.6	2.8e-08	0.92	0.29	0.71	FALSE
34	Liver	Atg7	gene expression	ENSRNOG00000007486	0.10	0.13	lasso	52	0.14	5.7e-15	5.6	-5.6	2.8e-08	-0.99	0.28	0.72	FALSE
35	Liver	Vgll4	gene expression	ENSRNOG00000007822	0.05	0.04	blup	1519	0.04	8.5e-06	5.6	5.9	3.9e-09	0.99	0.29	0.71	FALSE
36	Liver	Tamm41	gene expression	ENSRNOG00000007874	0.23	0.13	enet	64	0.18	2.5e-19	6.0	5.8	6.8e-09	0.90	0.32	0.69	FALSE
37	Liver	Atg7	isoform ratio	ENSRNOT00000109260	0.09	0.08	enet	104	0.09	6.6e-10	-4.1	5.4	6.3e-08	0.87	0.76	0.23	FALSE
38	Liver	Tamm41	mRNA stability	ENSRNOG00000007874	0.04	0.03	top1	1	0.03	2.8e-04	5.7	5.7	9.9e-09	0.98	0.08	0.16	FALSE
39	NAcc	Vgll4	alternative TSS	ENSRNOT00000095273	0.19	0.03	top1	1	0.03	6.1e-02	5.5	5.5	2.9e-08	0.98	0.08	0.05	FALSE
40	NAcc	Vgll4	gene expression	ENSRNOG00000007822	0.50	0.26	lasso	4	0.27	1.0e-06	5.7	5.7	1.3e-08	0.97	0.30	0.69	FALSE
41	NAcc2	Atg7	alternative polyA	ENSRNOT00000067532	0.13	0.09	blup	1953	0.11	1.3e-06	4.5	-5.3	9.1e-08	-0.90	0.55	0.45	FALSE
42	NAcc2	Atg7	alternative polyA	ENSRNOT00000096019	0.06	0.03	blup	1953	0.04	3.9e-03	5.6	-5.5	3.3e-08	-0.95	0.35	0.53	FALSE
43	NAcc2	Atg7	alternative polyA	ENSRNOT00000109260	0.20	0.15	blup	1953	0.17	1.1e-09	5.6	5.7	1.2e-08	0.93	0.41	0.59	FALSE
44	NAcc2	Atg7	alternative polyA	ENSRNOT00000067532	0.09	0.06	blup	1953	0.08	4.3e-05	5.6	-5.6	2.0e-08	-0.94	0.38	0.61	FALSE
45	NAcc2	Atg7	alternative polyA	ENSRNOT00000099380	0.08	0.04	top1	1	0.04	4.0e-03	5.7	-5.7	1.4e-08	-0.89	0.09	0.07	FALSE
46	NAcc2	Atg7	alternative polyA	ENSRNOT00000109260	0.17	0.13	blup	1953	0.15	1.9e-08	4.5	5.7	1.4e-08	0.93	0.44	0.56	FALSE
47	NAcc2	Vgll4	gene expression	ENSRNOG00000007822	0.24	0.10	blup	1519	0.17	1.5e-09	5.7	5.8	7.0e-09	0.94	0.31	0.69	FALSE
48	NAcc2	Tamm41	gene expression	ENSRNOG00000007874	0.15	0.06	blup	1461	0.07	7.0e-05	5.7	5.8	5.8e-09	0.98	0.33	0.67	FALSE
49	NAcc2	Vgll4	mRNA stability	ENSRNOG00000007822	0.06	0.05	enet	61	0.06	3.1e-04	-4.6	-5.6	1.6e-08	-0.79	0.64	0.07	FALSE
50	OFC	Atg7	alternative polyA	ENSRNOT00000109260	0.17	0.11	top1	1	0.11	1.2e-03	5.6	5.6	2.3e-08	0.96	0.11	0.07	FALSE
51	OFC	Atg7	alternative polyA	ENSRNOT00000109260	0.17	0.11	blup	1950	0.12	1.1e-03	5.6	5.5	3.0e-08	0.92	0.41	0.48	FALSE
52	OFC	Vgll4	gene expression	ENSRNOG00000007822	0.19	0.12	top1	1	0.12	1.1e-03	5.6	5.6	2.1e-08	0.99	0.08	0.06	FALSE
53	OFC	Atg7	isoform ratio	ENSRNOT00000109260	0.14	0.04	blup	1950	0.04	4.0e-02	5.6	5.5	4.4e-08	0.94	0.29	0.37	FALSE
54	PL	Atg7	alternative polyA	ENSRNOT00000099380	0.26	0.11	enet	19	0.17	7.2e-05	-3.8	-5.2	1.5e-07	-0.87	0.53	0.41	FALSE
55	PL	Vgll4	gene expression	ENSRNOG00000007822	0.18	0.08	lasso	4	0.13	6.5e-04	-4.2	5.2	2.2e-07	0.76	0.44	0.30	FALSE
56	PL2	Atg7	alternative polyA	ENSRNOT00000096019	0.12	0.13	top1	1	0.13	2.7e-07	5.6	-5.6	2.3e-08	-0.96	0.35	0.51	FALSE
57	PL2	Atg7	alternative polyA	ENSRNOT00000109260	0.45	0.33	blup	1953	0.36	1.1e-20	5.7	5.8	5.4e-09	0.95	0.36	0.64	FALSE
58	PL2	Atg7	alternative polyA	ENSRNOT00000099380	0.39	0.27	blup	1953	0.28	1.0e-15	5.6	-5.8	5.9e-09	-0.97	0.36	0.64	FALSE
59	PL2	Atg7	alternative polyA	ENSRNOT00000109260	0.44	0.34	top1	1	0.34	2.4e-19	5.7	5.7	1.4e-08	0.97	0.30	0.70	FALSE
60	PL2	Slc6a1	gene expression	ENSRNOG00000006527	0.07	0.02	blup	2003	0.04	5.4e-03	5.5	5.2	1.9e-07	0.93	0.45	0.52	FALSE
61	PL2	Atg7	isoform ratio	ENSRNOT00000067532	0.06	0.02	blup	1953	0.04	1.7e-03	5.5	-5.3	1.0e-07	-0.89	0.44	0.43	FALSE
62	PL2	Atg7	isoform ratio	ENSRNOT00000109260	0.22	0.21	blup	1953	0.22	3.1e-12	5.6	5.7	9.0e-09	0.97	0.35	0.65	FALSE
63	PL2	Vgll4	isoform ratio	ENSRNOT00000010338	0.06	0.04	top1	1	0.04	2.6e-03	5.6	5.6	2.3e-08	0.98	0.06	0.04	FALSE

h2: Heritability estimate for the given transcriptomic model. PP3: Posterior probability of two distinct causal variants. PP4: Posterior probability of a single shared causal variant. joint: Whether the RNA phenotype is in the joint model.