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chr2:26,592,429-29,260,106

Best TWAS P=2.94e-41 · Best GWAS P=7.58e-40 conditioned to 1

Associated models

#	Study	Tissue	Gene	h2	eQTL R2	model	# weights	model R2	model R2 P	eQTL GWAS Z	TWAS Z	TWAS P	Top SNP corr	PP3	PP4	joint
88	The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	FNDC4	0.13	0.06	lasso	2	0.05	1.1e-03	13.21	-13.5	2.9e-41	-0.99	0.00	0.94	TRUE
50	GTEx	Thyroid	FNDC4	0.24	0.10	enet	23	0.16	2.2e-12	-7.43	-10.9	7.6e-28	-0.69	0.61	0.39	FALSE
95	The Cancer Genome Atlas	Thyroid Carcinoma	FNDC4	0.24	0.09	enet	9	0.17	1.9e-16	-7.82	-10.7	7.5e-27	-0.70	0.45	0.55	FALSE
48	GTEx	Testis	AC074117.10	0.14	0.08	lasso	6	0.12	4.5e-06	-6.12	10.5	9.4e-26	0.85	0.03	0.96	FALSE
96	The Cancer Genome Atlas	Thyroid Carcinoma	GCKR	0.18	0.08	enet	5	0.13	1.7e-12	-7.43	-9.7	3.6e-22	-0.64	0.88	0.12	FALSE
31	GTEx	Esophagus Muscularis	NRBP1	0.07	0.04	lasso	6	0.04	1.3e-03	-7.47	9.7	4.7e-22	0.82	0.03	0.95	FALSE
97	The Cancer Genome Atlas	Thyroid Carcinoma	IFT172	0.08	0.01	blup	43	0.02	6.1e-03	-7.70	-9.5	1.8e-21	-0.54	0.02	0.30	FALSE
47	GTEx	Testis	NRBP1	0.16	0.09	lasso	3	0.06	1.8e-03	-7.47	9.4	5.3e-21	0.80	0.03	0.96	FALSE
86	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	SUPT7L	0.05	0.02	blup	28	0.04	5.2e-05	-7.54	-9.1	8.4e-20	-0.40	0.07	0.70	FALSE
30	GTEx	Esophagus Mucosa	AC074117.10	0.12	0.14	lasso	8	0.14	2.1e-09	-7.47	9.1	9.6e-20	0.74	0.92	0.08	FALSE
40	GTEx	Ovary	AC074117.10	0.16	0.04	enet	9	0.05	2.0e-02	-5.95	8.9	4.1e-19	0.77	0.05	0.74	FALSE
2	CommonMind	Brain Pre-frontal Cortex	IFT172	0.06	0.09	enet	16	0.09	3.9e-11	-5.97	-8.6	1.1e-17	-0.75	0.42	0.58	FALSE
55	GTEx	Vagina	AC074117.10	0.14	0.04	enet	13	0.06	1.4e-02	-5.48	8.5	2.2e-17	0.72	0.10	0.47	FALSE
20	GTEx	Breast Mammary Tissue (Female)	ABHD1	0.17	0.01	enet	28	0.07	5.3e-03	-2.94	-8.5	2.7e-17	-0.52	0.02	0.70	FALSE
1	CommonMind	Brain Pre-frontal Cortex	GTF3C2	0.06	0.09	lasso	8	0.08	7.2e-10	-6.29	8.2	3.2e-16	0.72	0.42	0.58	FALSE
46	GTEx	Stomach	AC074117.10	0.06	0.01	lasso	7	0.01	7.8e-02	-7.47	-8.1	6.9e-16	-0.36	0.20	0.06	FALSE
78	The Cancer Genome Atlas	Breast Invasive Carcinoma	SNX17	0.08	0.01	blup	25	0.02	6.6e-05	-3.73	-7.8	9.1e-15	-0.55	0.02	0.34	FALSE
29	GTEx	Esophagus Gastroesophageal Junction	AC074117.10	0.12	0.13	enet	9	0.09	4.9e-04	-6.09	7.7	1.5e-14	0.64	0.47	0.23	FALSE
61	METSIM	Adipose	SLC5A6	0.03	0.02	bslmm	298	0.01	3.9e-03	-5.01	7.6	2.4e-14	0.43	0.24	0.08	FALSE
41	GTEx	Pituitary	AC074117.10	0.23	0.23	lasso	8	0.29	5.6e-08	-6.30	7.6	3.5e-14	0.66	0.45	0.44	FALSE
38	GTEx	Nerve Tibial	NRBP1	0.06	0.00	enet	9	0.02	2.0e-02	-7.47	7.6	4.0e-14	0.61	0.39	0.46	FALSE
60	METSIM	Adipose	NRBP1	0.06	0.09	lasso	3	0.08	1.6e-12	-7.47	7.5	4.7e-14	0.67	0.99	0.01	FALSE
81	The Cancer Genome Atlas	Glioblastoma Multiforme	NRBP1	0.15	0.10	lasso	2	0.10	5.8e-04	-7.47	7.5	9.2e-14	0.67	0.02	0.09	FALSE
66	ROSMAP	Brain Pre-frontal Cortex	FTH1P3	0.04	0.01	bslmm	280	0.02	2.8e-03	-7.47	7.4	1.2e-13	0.65	0.04	0.72	FALSE
73	The Cancer Genome Atlas	Bladder Urothelial Carcinoma	PPM1G	0.03	0.02	blup	31	0.02	8.8e-03	-6.46	7.3	2.4e-13	0.66	0.03	0.51	FALSE
16	GTEx	Artery Tibial	PPM1G	0.06	0.02	lasso	4	0.03	2.3e-03	-6.36	7.3	3.8e-13	0.66	0.28	0.15	FALSE
62	NTR	Blood	CGREF1	0.01	0.00	blup	307	0.01	5.7e-03	-3.47	-7.2	6.3e-13	-0.49	0.20	0.10	FALSE
5	GTEx	Adipose Subcutaneous	AC074117.10	0.06	0.04	lasso	5	0.02	4.8e-03	-7.47	7.2	8.1e-13	0.65	0.52	0.17	FALSE
33	GTEx	Esophagus Muscularis	AC074117.10	0.17	0.14	enet	5	0.09	6.6e-06	-7.47	7.1	9.4e-13	0.65	0.83	0.16	FALSE
67	YFS	Blood	EIF2B4	0.01	0.00	enet	9	0.00	8.5e-02	-4.09	-7.0	3.8e-12	-0.52	0.04	0.04	FALSE
22	GTEx	Cells EBV-transformed lymphocytes	NRBP1	0.11	0.13	enet	13	0.15	1.2e-05	-6.15	6.8	1.3e-11	0.62	0.57	0.10	FALSE
93	The Cancer Genome Atlas	Prostate Adenocarcinoma	NRBP1	0.03	0.03	blup	30	0.03	2.2e-04	-5.48	6.7	1.8e-11	0.64	0.67	0.08	FALSE
45	GTEx	Skin Sun Exposed Lower leg	SLC4A1AP	0.04	0.01	lasso	3	0.02	1.7e-02	-6.15	-6.7	2.1e-11	-0.60	0.21	0.11	FALSE
7	GTEx	Adipose Visceral Omentum	PPM1G	0.06	0.01	lasso	5	0.01	1.1e-01	-5.95	6.7	3.0e-11	0.64	0.11	0.28	FALSE
35	GTEx	Lung	AC074117.10	0.07	0.06	lasso	6	0.05	6.6e-05	-6.36	6.6	3.4e-11	0.63	0.78	0.21	FALSE
23	GTEx	Cells Transformed fibroblasts	NRBP1	0.09	0.08	lasso	3	0.08	7.8e-07	-5.87	6.6	4.2e-11	0.61	0.96	0.03	FALSE
75	The Cancer Genome Atlas	Breast Invasive Carcinoma	GPN1	0.06	0.02	lasso	6	0.02	7.2e-05	7.95	6.5	6.7e-11	0.54	0.01	0.95	FALSE
17	GTEx	Artery Tibial	AC074117.10	0.13	0.14	lasso	5	0.13	1.1e-10	-5.87	6.5	7.1e-11	0.62	1.00	0.00	FALSE
21	GTEx	Breast Mammary Tissue (Female)	AC074117.10	0.06	0.01	lasso	2	0.04	2.7e-02	-5.58	-6.5	8.7e-11	-0.23	0.04	0.06	FALSE
85	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	SNX17	0.02	0.01	blup	26	0.01	2.1e-02	-5.88	-6.5	9.0e-11	-0.62	0.13	0.18	FALSE
69	YFS	Blood	NRBP1	0.01	0.01	lasso	6	0.01	9.1e-06	-6.12	6.5	1.0e-10	0.61	0.99	0.01	FALSE
49	GTEx	Testis	RP11-195B17.1	0.13	0.00	lasso	4	0.02	4.5e-02	-6.36	6.4	1.3e-10	0.58	0.04	0.15	FALSE
18	GTEx	Brain Cerebellum	AC074117.10	0.13	0.08	enet	6	0.07	4.4e-03	-6.46	-6.4	1.4e-10	-0.60	0.11	0.35	FALSE
64	ROSMAP	Brain Pre-frontal Cortex	IFT172	0.07	0.02	blup	287	0.03	5.8e-05	-5.87	-6.4	1.4e-10	-0.63	0.43	0.49	FALSE
25	GTEx	Cells Transformed fibroblasts	AC074117.10	0.21	0.19	enet	23	0.18	1.6e-13	-7.47	6.4	1.9e-10	0.66	0.94	0.06	FALSE
27	GTEx	Colon Transverse	NRBP1	0.08	0.03	enet	14	0.00	2.0e-01	-7.45	6.4	2.0e-10	0.59	0.17	0.10	FALSE
8	GTEx	Adipose Visceral Omentum	KRTCAP3	0.10	0.07	lasso	4	0.06	5.2e-04	-6.29	-6.3	2.4e-10	-0.61	0.69	0.10	FALSE
99	The Cancer Genome Atlas	Thyroid Carcinoma	NRBP1	0.03	0.01	blup	30	0.02	5.3e-03	-7.47	6.3	2.4e-10	0.62	0.32	0.05	FALSE
14	GTEx	Artery Coronary	NRBP1	0.09	0.01	enet	14	0.03	4.4e-02	-3.92	6.3	2.7e-10	0.46	0.18	0.27	FALSE
42	GTEx	Prostate	AC074117.10	0.14	0.01	lasso	5	0.02	8.8e-02	-7.47	6.2	4.0e-10	0.61	0.07	0.51	FALSE
53	GTEx	Thyroid	AC074117.10	0.17	0.14	lasso	4	0.15	2.7e-11	-6.09	6.2	5.1e-10	0.61	1.00	0.00	FALSE
94	The Cancer Genome Atlas	Prostate Adenocarcinoma	PPM1G	0.03	0.02	blup	32	0.02	2.4e-03	-6.38	6.2	6.0e-10	0.61	0.16	0.05	FALSE
80	The Cancer Genome Atlas	Colon Adenocarcinoma	NRBP1	0.03	0.04	lasso	1	0.03	5.2e-03	-6.15	6.2	7.7e-10	0.59	0.04	0.11	FALSE
36	GTEx	Muscle Skeletal	SNX17	0.18	0.24	lasso	6	0.26	6.2e-26	-6.05	6.2	8.0e-10	0.61	1.00	0.00	FALSE
39	GTEx	Nerve Tibial	PPM1G	0.09	0.06	lasso	4	0.05	1.2e-04	-6.30	6.1	1.0e-09	0.57	0.49	0.28	FALSE
37	GTEx	Muscle Skeletal	KRTCAP3	0.08	0.06	lasso	4	0.04	3.1e-05	-6.15	-6.1	1.2e-09	-0.59	1.00	0.00	FALSE
10	GTEx	Adrenal Gland	KRTCAP3	0.11	0.16	lasso	4	0.15	4.9e-06	-6.15	-6.1	1.3e-09	-0.60	0.44	0.50	FALSE
6	GTEx	Adipose Visceral Omentum	NRBP1	0.05	0.05	lasso	4	0.04	2.5e-03	-5.95	6.1	1.4e-09	0.61	0.34	0.06	FALSE
26	GTEx	Colon Sigmoid	AC074117.10	0.13	0.18	lasso	3	0.14	1.1e-05	-5.87	6.0	1.5e-09	0.60	0.88	0.05	FALSE
9	GTEx	Adipose Visceral Omentum	AC074117.10	0.14	0.09	lasso	3	0.08	5.0e-05	-5.87	6.0	1.6e-09	0.60	0.87	0.05	FALSE
51	GTEx	Thyroid	PPM1G	0.06	0.06	lasso	3	0.06	2.2e-05	-5.95	6.0	1.6e-09	0.60	0.92	0.01	FALSE
57	GTEx	Whole Blood	KRTCAP3	0.12	0.05	enet	10	0.05	9.9e-06	-5.91	-6.0	1.6e-09	-0.63	0.97	0.02	FALSE
34	GTEx	Lung	NRBP1	0.05	0.05	enet	9	0.05	1.7e-04	-6.36	6.0	1.9e-09	0.61	0.76	0.14	FALSE
63	ROSMAP	Brain Pre-frontal Cortex	SNX17	0.27	0.35	lasso	10	0.34	7.9e-46	-5.95	-6.0	2.2e-09	-0.60	1.00	0.00	FALSE
58	METSIM	Adipose	ATRAID	0.11	0.09	bslmm	297	0.10	1.4e-14	-4.09	-6.0	2.6e-09	-0.47	1.00	0.00	FALSE
82	The Cancer Genome Atlas	Head and Neck Squamous Cell Carcinoma	IFT172	0.02	0.01	blup	43	0.02	2.7e-03	-5.73	6.0	2.7e-09	0.60	0.10	0.14	FALSE
24	GTEx	Cells Transformed fibroblasts	IFT172	0.04	0.04	lasso	2	0.02	8.1e-03	-5.82	-5.9	2.8e-09	-0.60	0.17	0.37	FALSE
68	YFS	Blood	KRTCAP3	0.12	0.18	bslmm	286	0.18	1.0e-55	-6.00	-5.9	3.2e-09	-0.59	1.00	0.00	FALSE
84	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	NRBP1	0.06	0.07	lasso	2	0.07	1.1e-08	-5.91	5.9	3.4e-09	0.60	1.00	0.00	FALSE
72	The Cancer Genome Atlas	Bladder Urothelial Carcinoma	NRBP1	0.05	0.06	lasso	2	0.05	6.0e-05	-5.85	5.8	5.0e-09	0.60	0.82	0.01	FALSE
44	GTEx	Skin Sun Exposed Lower leg	NRBP1	0.10	0.08	lasso	6	0.08	3.6e-07	-6.09	5.8	5.9e-09	0.58	1.00	0.00	FALSE
13	GTEx	Artery Aorta	AC074117.10	0.06	0.04	lasso	3	0.03	6.8e-03	-5.87	5.8	6.5e-09	0.58	0.26	0.08	FALSE
91	The Cancer Genome Atlas	Lung Adenocarcinoma	NRBP1	0.03	0.05	blup	30	0.05	3.7e-06	-5.91	5.8	9.2e-09	0.59	0.97	0.01	FALSE
43	GTEx	Skin Not Sun Exposed Suprapubic	NRBP1	0.19	0.15	lasso	7	0.16	6.0e-09	-6.36	5.7	1.0e-08	0.58	1.00	0.00	FALSE
4	GTEx	Adipose Subcutaneous	PPM1G	0.04	0.05	lasso	2	0.04	4.9e-04	-5.95	5.7	1.6e-08	0.59	0.59	0.03	FALSE
32	GTEx	Esophagus Muscularis	PPM1G	0.06	0.10	lasso	2	0.07	3.7e-05	-6.15	5.6	1.7e-08	0.57	0.39	0.50	FALSE
56	GTEx	Whole Blood	KHK	0.05	0.06	lasso	5	0.02	4.6e-03	-4.60	-5.6	2.2e-08	-0.28	0.50	0.24	FALSE
54	GTEx	Thyroid	AC109828.1	0.12	0.02	enet	24	0.04	4.3e-04	-5.73	5.6	2.5e-08	0.52	0.43	0.28	FALSE
77	The Cancer Genome Atlas	Breast Invasive Carcinoma	NRBP1	0.03	0.03	blup	29	0.03	1.2e-06	-5.73	5.5	2.9e-08	0.57	0.99	0.00	FALSE
83	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	KRTCAP3	0.02	0.01	blup	28	0.01	2.9e-02	-6.00	-5.5	3.8e-08	-0.57	0.08	0.05	FALSE
98	The Cancer Genome Atlas	Thyroid Carcinoma	KRTCAP3	0.04	0.04	lasso	1	0.03	3.4e-04	-5.48	-5.5	4.3e-08	-0.55	0.11	0.11	FALSE
15	GTEx	Artery Coronary	AC074117.10	0.13	0.17	enet	9	0.12	5.4e-05	-3.96	5.5	4.5e-08	0.47	0.13	0.66	FALSE
87	The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	C2orf28	0.05	0.00	lasso	1	0.01	4.8e-02	-5.44	-5.4	5.2e-08	-0.38	0.01	0.69	FALSE
92	The Cancer Genome Atlas	Lung Squamous Cell Carcinoma	C2orf28	0.02	0.01	blup	39	0.02	6.0e-03	-5.15	-5.4	5.2e-08	-0.32	0.01	0.52	FALSE
90	The Cancer Genome Atlas	Liver Hepatocellular Carcinoma	C2orf28	0.07	0.04	blup	47	0.04	4.1e-03	-5.11	-5.4	6.5e-08	-0.36	0.01	0.83	FALSE
89	The Cancer Genome Atlas	Brain Lower Grade Glioma	PPM1G	0.03	0.03	blup	32	0.02	9.3e-04	-5.88	5.4	7.0e-08	0.56	0.36	0.05	FALSE
59	METSIM	Adipose	BRE	0.03	0.00	blup	534	0.00	1.3e-01	0.13	5.3	8.8e-08	0.30	0.10	0.07	FALSE
74	The Cancer Genome Atlas	Breast Invasive Carcinoma	EIF2B4	0.08	0.01	lasso	2	0.01	1.0e-02	-3.73	-5.3	8.9e-08	-0.35	0.03	0.02	FALSE
19	GTEx	Brain Cortex	KRTCAP3	0.19	0.10	lasso	2	0.12	3.7e-04	-5.48	-5.3	1.1e-07	-0.54	0.27	0.26	FALSE
28	GTEx	Esophagus Gastroesophageal Junction	NRBP1	0.11	0.01	enet	23	0.02	7.7e-02	-5.82	5.3	1.2e-07	0.53	0.13	0.19	FALSE
70	YFS	Blood	SLC5A6	0.21	0.14	blup	296	0.14	4.1e-45	-5.10	5.3	1.2e-07	0.36	1.00	0.00	FALSE
65	ROSMAP	Brain Pre-frontal Cortex	KRTCAP3	0.06	0.05	blup	279	0.05	3.1e-07	-5.95	-5.2	1.7e-07	-0.58	1.00	0.00	FALSE
11	GTEx	Artery Aorta	NRBP1	0.06	0.07	enet	8	0.06	2.6e-04	-7.45	5.2	2.1e-07	0.51	0.50	0.04	FALSE
3	CommonMind	Brain Pre-frontal Cortex	PPM1G	0.03	0.01	bslmm	305	0.00	8.7e-02	-6.15	-5.2	2.3e-07	-0.50	0.59	0.07	FALSE
12	GTEx	Artery Aorta	ATRAID	0.31	0.15	lasso	13	0.11	9.2e-07	-5.10	-5.2	2.6e-07	-0.37	0.99	0.00	FALSE
76	The Cancer Genome Atlas	Breast Invasive Carcinoma	KRTCAP3	0.01	0.00	blup	27	0.00	8.7e-02	-5.48	-5.2	2.6e-07	-0.56	0.05	0.02	FALSE
79	The Cancer Genome Atlas	Colon Adenocarcinoma	C2orf28	0.07	0.09	lasso	1	0.08	1.6e-05	-5.15	-5.2	2.6e-07	-0.36	0.02	0.98	FALSE
71	The Cancer Genome Atlas	Bladder Urothelial Carcinoma	C2orf28	0.03	0.03	blup	47	0.02	7.7e-03	-5.13	-5.1	2.7e-07	-0.36	0.01	0.66	FALSE
52	GTEx	Thyroid	ATRAID	0.14	0.12	lasso	6	0.10	6.1e-08	-5.01	-5.1	3.0e-07	-0.36	1.00	0.00	FALSE