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chr3:51,539,688-53,778,875

Best TWAS P=8.34e-13 · Best GWAS P=1.73e-12 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
9	GTEx	Adrenal Gland	GLYCTK-AS1	0.16	0.14	lasso	4	0.09	5.1e-04	-7.1	-7.2	8.3e-13	0.99	0.00	0.98	TRUE
38	GTEx	Lung	NEK4	0.05	0.01	lasso	3	0.00	2.1e-01	5.7	-6.1	1.4e-09	0.65	0.21	0.73	TRUE
14	GTEx	Artery Tibial	PBRM1	0.16	0.20	enet	35	0.21	4.8e-16	6.6	5.8	6.3e-09	-0.70	0.08	0.92	TRUE
80	The Cancer Genome Atlas	Brain Lower Grade Glioma	NEK4	0.08	0.01	enet	14	0.05	1.2e-06	-3.1	-5.8	8.8e-09	0.32	0.05	0.90	TRUE
71	The Cancer Genome Atlas	Glioblastoma Multiforme	GNL3	0.17	0.06	blup	47	0.06	9.0e-03	6.0	-5.7	1.3e-08	0.60	0.03	0.82	TRUE
3	CommonMind	Brain Pre-frontal Cortex	PBRM1	0.04	0.00	bslmm	435	0.02	2.4e-03	5.8	5.2	2.6e-07	-0.08	0.13	0.09	TRUE
26	GTEx	Cells Transformed fibroblasts	NEK4	0.07	0.11	lasso	5	0.08	7.2e-07	-4.4	-5.1	2.9e-07	0.73	0.30	0.70	TRUE
58	NTR	Blood	WDR82	0.02	0.03	blup	325	0.03	4.9e-09	-6.5	7.2	8.6e-13	-0.85	0.08	0.92	FALSE
8	GTEx	Adrenal Gland	GLYCTK	0.14	0.05	enet	20	0.06	4.8e-03	-7.1	-7.1	1.6e-12	0.82	0.01	0.93	FALSE
66	YFS	Blood	PPM1M	0.07	0.06	lasso	4	0.07	3.8e-22	-6.5	-7.1	1.7e-12	0.92	0.08	0.92	FALSE
33	GTEx	Esophagus Muscularis	GLYCTK	0.09	0.10	lasso	4	0.08	9.7e-06	-6.5	-7.0	2.5e-12	0.95	0.02	0.98	FALSE
35	GTEx	Heart Atrial Appendage	GLYCTK	0.08	0.02	lasso	5	0.00	3.0e-01	-6.1	-6.8	8.5e-12	0.89	0.10	0.79	FALSE
15	GTEx	Artery Tibial	GLYCTK	0.04	0.02	enet	4	0.01	4.9e-02	-6.5	-6.8	1.2e-11	0.94	0.08	0.76	FALSE
18	GTEx	Brain Cerebellum	GLYCTK	0.15	0.10	lasso	12	0.11	3.2e-04	-6.5	6.7	1.6e-11	-0.84	0.05	0.90	FALSE
34	GTEx	Esophagus Muscularis	GLYCTK-AS1	0.05	0.00	lasso	4	0.01	9.6e-02	-6.3	-6.7	1.8e-11	0.96	0.04	0.83	FALSE
36	GTEx	Heart Atrial Appendage	GLYCTK-AS1	0.06	-0.01	lasso	2	0.00	6.1e-01	-6.1	-6.7	2.6e-11	0.89	0.12	0.61	FALSE
20	GTEx	Brain Hippocampus	GLYCTK	0.17	0.16	lasso	7	0.10	2.6e-03	6.2	-6.6	4.0e-11	0.67	0.12	0.54	FALSE
30	GTEx	Colon Sigmoid	GNL3	0.08	0.04	lasso	5	0.04	1.8e-02	6.6	-6.6	5.1e-11	0.67	0.10	0.57	FALSE
48	GTEx	Spleen	GLYCTK	0.56	0.14	enet	10	0.13	4.1e-04	-6.4	-6.6	5.4e-11	0.93	0.07	0.87	FALSE
61	ROSMAP	Brain Pre-frontal Cortex	WDR82	0.03	0.02	enet	11	0.03	1.2e-04	-6.0	6.6	5.4e-11	-0.86	0.06	0.93	FALSE
57	METSIM	Adipose	PPM1M	0.08	0.08	enet	17	0.08	1.4e-12	6.3	-6.5	6.3e-11	0.71	0.15	0.85	FALSE
27	GTEx	Cells Transformed fibroblasts	GNL3	0.10	0.12	lasso	8	0.10	3.0e-08	6.6	-6.5	6.5e-11	0.67	0.09	0.91	FALSE
41	GTEx	Lung	GLYCTK-AS1	0.11	0.09	lasso	5	0.09	3.0e-07	-6.5	-6.5	7.6e-11	0.91	0.06	0.94	FALSE
19	GTEx	Brain Cerebellum	GLYCTK-AS1	0.09	0.14	lasso	8	0.12	1.6e-04	-6.5	6.5	8.3e-11	-0.93	0.05	0.74	FALSE
53	GTEx	Thyroid	GLYCTK	0.13	0.19	lasso	3	0.17	7.1e-13	-6.5	-6.5	1.0e-10	0.93	0.09	0.91	FALSE
82	The Cancer Genome Atlas	Prostate Adenocarcinoma	LOC440957	0.05	0.02	lasso	9	0.02	4.3e-03	6.6	-6.5	1.0e-10	0.51	0.01	0.84	FALSE
24	GTEx	Breast Mammary Tissue (Female)	NEK4	0.02	-0.01	lasso	2	0.01	1.4e-01	-6.4	-6.5	1.1e-10	0.93	0.04	0.21	FALSE
32	GTEx	Esophagus Mucosa	GLYCTK	0.11	0.11	lasso	3	0.10	3.8e-07	-6.5	-6.5	1.1e-10	0.93	0.09	0.91	FALSE
62	ROSMAP	Brain Pre-frontal Cortex	GLYCTK	0.05	0.08	lasso	5	0.08	2.5e-10	-6.5	-6.5	1.1e-10	0.93	0.06	0.94	FALSE
1	CommonMind	Brain Pre-frontal Cortex	GLT8D1	0.07	0.10	lasso	1	0.09	5.2e-11	6.4	6.4	1.5e-10	-0.67	0.11	0.89	FALSE
54	GTEx	Thyroid	GLYCTK-AS1	0.08	0.07	enet	10	0.08	9.7e-07	-6.5	-6.4	1.5e-10	0.91	0.03	0.97	FALSE
81	The Cancer Genome Atlas	Prostate Adenocarcinoma	GNL3	0.04	0.05	lasso	12	0.05	9.0e-06	6.4	-6.4	1.5e-10	0.67	0.02	0.98	FALSE
83	The Cancer Genome Atlas	Prostate Adenocarcinoma	NEK4	0.13	0.07	lasso	4	0.06	4.0e-07	6.3	-6.4	1.5e-10	0.59	0.02	0.98	FALSE
4	GTEx	Adipose Subcutaneous	NEK4	0.04	0.01	lasso	3	0.00	1.2e-01	6.6	-6.4	1.6e-10	0.67	0.15	0.78	FALSE
22	GTEx	Brain Hippocampus	GLYCTK-AS1	0.17	0.25	lasso	6	0.15	1.9e-04	6.3	-6.4	1.6e-10	0.62	0.14	0.71	FALSE
64	YFS	Blood	GLYCTK	0.15	0.14	enet	17	0.13	1.1e-41	-6.5	-6.4	1.8e-10	0.93	0.09	0.91	FALSE
45	GTEx	Skin Sun Exposed Lower leg	NEK4	0.06	0.12	lasso	3	0.10	2.2e-08	6.4	-6.4	2.0e-10	0.67	0.22	0.78	FALSE
86	The Cancer Genome Atlas	Soft Tissue Sarcoma	NEK4	0.06	0.04	blup	69	0.03	8.2e-03	6.4	-6.4	2.1e-10	0.62	0.02	0.80	FALSE
7	GTEx	Adipose Visceral Omentum	NEK4	0.10	0.09	lasso	3	0.08	5.0e-05	6.4	-6.3	2.4e-10	0.70	0.16	0.83	FALSE
77	The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	NEK4	0.07	0.04	blup	69	0.03	8.6e-03	6.4	-6.3	2.4e-10	0.63	0.04	0.91	FALSE
85	The Cancer Genome Atlas	Soft Tissue Sarcoma	GNL3	0.07	0.01	blup	47	0.03	1.1e-02	6.4	-6.3	2.4e-10	0.57	0.02	0.78	FALSE
28	GTEx	Cells Transformed fibroblasts	PBRM1	0.03	0.04	lasso	3	0.02	1.6e-02	-6.3	-6.3	2.9e-10	0.94	0.10	0.71	FALSE
75	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	NEK4	0.06	0.09	lasso	3	0.08	1.1e-09	6.4	-6.3	3.0e-10	0.67	0.02	0.98	FALSE
40	GTEx	Lung	GLYCTK	0.12	0.09	lasso	6	0.08	1.5e-06	-6.5	-6.3	3.4e-10	0.91	0.08	0.92	FALSE
78	The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	PPM1M	0.10	0.07	lasso	4	0.05	1.2e-03	6.3	-6.3	3.7e-10	0.64	0.01	0.97	FALSE
16	GTEx	Brain Cerebellar Hemisphere	GNL3	0.13	0.19	enet	16	0.10	1.6e-03	6.4	-6.2	5.7e-10	0.71	0.11	0.84	FALSE
69	The Cancer Genome Atlas	Cervical Squamous Cell Carcinoma	NEK4	0.07	0.01	blup	69	0.04	5.8e-03	6.2	-6.2	5.7e-10	0.68	0.03	0.70	FALSE
6	GTEx	Adipose Subcutaneous	PPM1M	0.07	0.05	lasso	3	0.05	5.2e-05	5.9	-6.2	5.9e-10	0.69	0.17	0.75	FALSE
50	GTEx	Testis	GNL3	0.12	0.18	lasso	7	0.18	2.4e-08	6.6	-6.2	6.3e-10	0.65	0.13	0.87	FALSE
52	GTEx	Thyroid	PBRM1	0.19	0.33	lasso	7	0.31	2.7e-24	6.0	6.2	6.9e-10	-0.67	0.10	0.90	FALSE
39	GTEx	Lung	GNL3	0.05	0.03	lasso	6	0.03	3.0e-03	6.1	-6.1	8.1e-10	0.61	0.18	0.75	FALSE
31	GTEx	Esophagus Mucosa	NEK4	0.05	0.03	lasso	8	0.02	2.4e-02	-6.5	-6.1	8.9e-10	0.88	0.12	0.83	FALSE
51	GTEx	Thyroid	NEK4	0.09	0.09	lasso	4	0.10	4.1e-08	6.4	-6.1	8.9e-10	0.71	0.13	0.87	FALSE
56	METSIM	Adipose	GNL3	0.04	0.06	enet	25	0.05	4.5e-08	6.4	-6.1	8.9e-10	0.77	0.20	0.80	FALSE
87	The Cancer Genome Atlas	Thyroid Carcinoma	GNL3	0.03	0.03	blup	47	0.03	3.3e-04	6.4	-6.1	9.3e-10	0.67	0.03	0.96	FALSE
25	GTEx	Cells Transformed fibroblasts	SPCS1	0.22	0.03	lasso	2	0.01	9.4e-02	6.2	6.1	1.2e-09	-0.63	0.09	0.44	FALSE
67	YFS	Blood	SPCS1	0.04	0.03	enet	19	0.04	6.0e-12	5.7	6.1	1.3e-09	-0.55	0.22	0.78	FALSE
88	The Cancer Genome Atlas	Thyroid Carcinoma	NEK4	0.07	0.12	blup	69	0.12	6.3e-12	5.4	-6.1	1.3e-09	0.68	0.04	0.96	FALSE
68	The Cancer Genome Atlas	Breast Invasive Carcinoma	NEK4	0.01	0.00	enet	5	0.01	2.0e-02	6.1	-6.0	1.6e-09	0.37	0.03	0.51	FALSE
42	GTEx	Nerve Tibial	NEK4	0.06	0.06	enet	8	0.06	2.2e-05	5.4	-6.0	1.9e-09	0.66	0.32	0.68	FALSE
44	GTEx	Skin Not Sun Exposed Suprapubic	GLYCTK	0.07	0.01	enet	12	0.06	3.9e-04	-6.4	-6.0	2.7e-09	0.89	0.10	0.81	FALSE
29	GTEx	Cells Transformed fibroblasts	WDR82	0.05	0.02	lasso	5	0.02	1.8e-02	5.3	5.9	2.8e-09	-0.65	0.17	0.58	FALSE
13	GTEx	Artery Tibial	GNL3	0.08	0.06	lasso	3	0.06	3.0e-05	-5.0	-5.9	3.5e-09	0.77	0.32	0.67	FALSE
73	The Cancer Genome Atlas	Head and Neck Squamous Cell Carcinoma	ITIH4	0.04	0.02	blup	53	0.03	3.0e-04	6.1	5.9	3.9e-09	-0.68	0.02	0.95	FALSE
76	The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	GNL3	0.19	0.02	enet	9	0.04	2.0e-03	6.4	-5.9	4.5e-09	0.47	0.03	0.93	FALSE
49	GTEx	Spleen	GLYCTK-AS1	0.32	0.08	enet	18	0.09	2.2e-03	-6.4	-5.8	5.1e-09	0.85	0.07	0.74	FALSE
74	The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	GNL3	0.03	0.03	enet	6	0.04	3.6e-05	5.4	-5.8	5.6e-09	0.64	0.04	0.95	FALSE
37	GTEx	Liver	GNL3	0.14	0.02	lasso	5	0.04	3.0e-02	6.3	-5.8	5.7e-09	0.43	0.11	0.29	FALSE
79	The Cancer Genome Atlas	Brain Lower Grade Glioma	GNL3	0.15	0.08	enet	20	0.11	3.0e-12	5.4	-5.8	7.7e-09	0.50	0.04	0.96	FALSE
2	CommonMind	Brain Pre-frontal Cortex	NEK4	0.07	0.11	enet	69	0.11	1.0e-13	6.3	-5.8	8.0e-09	0.71	0.16	0.84	FALSE
84	The Cancer Genome Atlas	Rectum Adenocarcinoma	ITIH4	0.12	0.09	blup	53	0.06	1.4e-02	6.1	5.6	2.1e-08	-0.68	0.02	0.68	FALSE
55	METSIM	Adipose	ALAS1	0.05	0.03	lasso	8	0.02	1.9e-03	-5.3	5.6	2.2e-08	-0.80	0.83	0.08	FALSE
47	GTEx	Small Intestine Terminal Ileum	RP5-966M1.6	0.14	0.03	lasso	7	0.00	2.5e-01	6.3	5.6	2.5e-08	-0.59	0.07	0.37	FALSE
65	YFS	Blood	GNL3	0.02	0.03	enet	11	0.03	2.9e-09	5.9	-5.6	2.6e-08	0.71	0.18	0.82	FALSE
63	ROSMAP	Brain Pre-frontal Cortex	RP5-1157M23.2	0.03	0.02	blup	320	0.01	5.1e-03	-6.1	-5.5	3.2e-08	0.87	0.02	0.98	FALSE
43	GTEx	Pituitary	SFMBT1	0.16	0.01	enet	9	0.02	1.2e-01	6.3	5.5	4.6e-08	-0.61	0.10	0.58	FALSE
46	GTEx	Skin Sun Exposed Lower leg	NT5DC2	0.21	0.19	enet	12	0.18	2.0e-14	4.7	-5.4	5.3e-08	0.71	0.96	0.04	FALSE
10	GTEx	Artery Aorta	GNL3	0.12	0.15	lasso	5	0.14	4.7e-08	6.3	-5.4	5.5e-08	0.63	0.15	0.85	FALSE
21	GTEx	Brain Hippocampus	TMEM110	0.17	0.11	lasso	7	0.13	5.1e-04	6.1	5.4	5.7e-08	-0.54	0.08	0.14	FALSE
60	ROSMAP	Brain Pre-frontal Cortex	SFMBT1	0.07	0.02	bslmm	340	0.03	2.9e-04	6.1	5.4	8.1e-08	-0.43	0.33	0.46	FALSE
5	GTEx	Adipose Subcutaneous	GNL3	0.04	0.05	enet	28	0.04	2.4e-04	5.6	-5.4	8.3e-08	0.40	0.20	0.72	FALSE
17	GTEx	Brain Cerebellum	GNL3	0.14	0.07	enet	43	0.09	1.3e-03	6.3	-5.2	1.5e-07	0.69	0.13	0.79	FALSE
23	GTEx	Brain Nucleus accumbens basal ganglia	TMEM110	0.13	0.07	lasso	3	0.05	1.5e-02	5.3	5.2	1.8e-07	-0.56	0.12	0.23	FALSE
72	The Cancer Genome Atlas	Glioblastoma Multiforme	ITIH4	0.10	0.02	blup	53	0.05	1.2e-02	3.9	5.2	1.8e-07	-0.56	0.03	0.42	FALSE
11	GTEx	Artery Aorta	TMEM110	0.19	0.08	enet	16	0.10	6.0e-06	3.9	5.2	1.9e-07	-0.58	0.55	0.43	FALSE
12	GTEx	Artery Coronary	ITIH4-AS1	0.11	0.12	enet	20	0.16	5.5e-06	3.9	5.2	2.0e-07	-0.49	0.30	0.60	FALSE
59	ROSMAP	Brain Pre-frontal Cortex	SPCS1	0.04	0.03	blup	357	0.04	6.6e-06	6.1	5.2	2.1e-07	-0.65	0.20	0.80	FALSE
70	The Cancer Genome Atlas	Colon Adenocarcinoma	NT5DC2	0.04	0.02	blup	50	0.03	9.7e-03	5.6	-5.2	2.6e-07	0.63	0.02	0.57	FALSE