TWAS hub - HbA1C

#	chr	p0	p1	# assoc genes	# joint genes	best TWAS P	best SNP P	cond SNP P	% var exp	joint genes
1	4	69713	383530	1	1	2.1e-07	8.6e-04	1.5e-02	46	ZNF595
2	10	70332066	71859953	1	1	1.2e-12	3.2e-25	2.1e-14	46	HK1
3	12	111645043	113036817	1	1	1.1e-07	3.8e-06	9.7e-01	100	ADAM1A
4	17	79977970	81051007	6	1	3.1e-25	1.6e-26	8.4e-03	94	FN3K
5	22	37157240	37673781	2	1	2.5e-11	2.7e-14	1.7e-04	76	TST

Trait	chisq ratio	# genes⁺	# genes⁺⁺	% genes⁺⁺	corr	corr P	genes
Blood Red Count	7.4	3	3	6.7	0.00	1.00	ADAM1A HK1 TST
Blood Platelet Count	6.0	4	2	4.4	0.48	0.52	ADAM1A FN3K HK1 TST
Heart attack/myocardial infarction (self-reported)	4.2	1	0	0.0	0.00	1.00	HK1
Fasting Glucose	3.6	1	0	0.0	0.00	1.00	ZNF595
Pulse wave Arterial Stiffness index	3.4	1	0	0.0	0.00	1.00	ADAM1A
Pulse wave peak to peak time	3.4	1	0	0.0	0.00	1.00	ADAM1A
Sensitivity / hurt feelings	2.9	1	0	0.0	0.00	1.00	TST
Supplements: Glucosamine	2.9	1	0	0.0	0.00	1.00	TST
Medication: Levothyroxine sodium	2.5	1	0	0.0	0.00	1.00	ADAM1A
Hayfever, allergic rhinitis or eczema	2.4	1	0	0.0	0.00	1.00	ADAM1A
Birth weight of first child	2.4	1	0	0.0	0.00	1.00	HK1
Cardiovascular Disease	2.3	1	0	0.0	0.00	1.00	ADAM1A
Allergy	2.3	1	0	0.0	0.00	1.00	HK1
Birth weight	2.3	1	0	0.0	0.00	1.00	ADAM1A
Blood White Count	2.2	1	1	2.2	0.00	1.00	ADAM1A
Past tobacco smoking	2.2	1	0	0.0	0.00	1.00	ADAM1A
Hypertension (Self-reported)	2.2	1	0	0.0	0.00	1.00	ADAM1A
Blood Eosinophil Count	2.1	1	1	2.2	0.00	1.00	ADAM1A
Allergy or Eczema	2.1	1	0	0.0	0.00	1.00	ADAM1A
High blood pressure	2.0	1	0	0.0	0.00	1.00	ADAM1A
Smoking Status	1.9	1	0	0.0	0.00	1.00	ADAM1A
Neuroticism score	1.9	1	0	0.0	0.00	1.00	TST
Vascular/heart problems diagnosed by doctor	1.8	1	0	0.0	0.00	1.00	ADAM1A
Systolic Blood Pressure	1.5	1	1	2.2	0.00	1.00	ADAM1A
Diastolic blood pressure, automated reading	1.4	1	0	0.0	0.00	1.00	ADAM1A
Height	0.3	1	0	0.0	0.00	1.00	FN3K

study	tissue	# hits	% hits/tests	avg chisq
GTEx	Adipose Visceral Omentum	1	0.050	1.2
GTEx	Adrenal Gland	1	0.069	1.2
GTEx	Artery Coronary	1	0.085	1.2
GTEx	Brain Caudate basal ganglia	0	0.000	1.2
GTEx	Brain Cortex	3	0.292	1.2
GTEx	Brain Frontal Cortex BA9	1	0.109	1.2
GTEx	Brain Hippocampus	1	0.192	1.2
GTEx	Brain Nucleus accumbens basal ganglia	0	0.000	1.2
GTEx	Cells EBV-transformed lymphocytes	2	0.142	1.2
GTEx	Colon Sigmoid	1	0.069	1.2
GTEx	Esophagus Gastroesophageal Junction	1	0.070	1.2
GTEx	Heart Atrial Appendage	1	0.064	1.2
GTEx	Heart Left Ventricle	0	0.000	1.2
GTEx	Liver	1	0.140	1.2
GTEx	Ovary	1	0.111	1.2
GTEx	Pituitary	0	0.000	1.2
GTEx	Prostate	0	0.000	1.2
GTEx	Uterus	1	0.178	1.2
GTEx	Vagina	1	0.159	1.2
NTR	Blood	2	0.083	1.2
The Cancer Genome Atlas	Bladder Urothelial Carcinoma	2	0.123	1.2
The Cancer Genome Atlas	Breast Invasive Carcinoma	3	0.069	1.2
The Cancer Genome Atlas	Cervical Squamous Cell Carcinoma	1	0.093	1.2
The Cancer Genome Atlas	Esophageal Carcinoma	0	0.000	1.2
The Cancer Genome Atlas	Glioblastoma Multiforme	1	0.100	1.2
The Cancer Genome Atlas	Head and Neck Squamous Cell Carcinoma	2	0.075	1.2
The Cancer Genome Atlas	Liver Hepatocellular Carcinoma	1	0.092	1.2
The Cancer Genome Atlas	Pheochromocytoma and Paraganglioma	2	0.154	1.2
The Cancer Genome Atlas	Rectum Adenocarcinoma	1	0.147	1.2
The Cancer Genome Atlas	Soft Tissue Sarcoma	2	0.192	1.2
The Cancer Genome Atlas	Skin Cutaneous Melanoma	1	0.192	1.2
The Cancer Genome Atlas	Testicular Germ Cell Tumors	1	0.080	1.2
The Cancer Genome Atlas	Uterine Corpus Endometrial Carcinoma	1	0.201	1.2
GTEx	Adipose Subcutaneous	2	0.058	1.1
GTEx	Artery Aorta	1	0.034	1.1
GTEx	Artery Tibial	1	0.027	1.1
GTEx	Brain Cerebellar Hemisphere	0	0.000	1.1
GTEx	Brain Cerebellum	0	0.000	1.1
GTEx	Brain Hypothalamus	1	0.170	1.1
GTEx	Brain Putamen basal ganglia	0	0.000	1.1
GTEx	Breast Mammary Tissue	1	0.051	1.1
GTEx	Breast Mammary Tissue (Male)	0	0.000	1.1
GTEx	Breast Mammary Tissue (Female)	1	0.062	1.1
GTEx	Cells Transformed fibroblasts	1	0.024	1.1
GTEx	Colon Transverse	1	0.049	1.1
GTEx	Esophagus Mucosa	2	0.061	1.1
GTEx	Esophagus Muscularis	1	0.031	1.1
GTEx	Lung	1	0.035	1.1
GTEx	Muscle Skeletal	1	0.035	1.1
GTEx	Nerve Tibial	2	0.047	1.1
GTEx	Pancreas	1	0.062	1.1
GTEx	Skin Not Sun Exposed Suprapubic	1	0.041	1.1
GTEx	Skin Sun Exposed Lower leg	1	0.028	1.1
GTEx	Small Intestine Terminal Ileum	0	0.000	1.1
GTEx	Spleen	1	0.071	1.1
GTEx	Stomach	1	0.069	1.1
GTEx	Testis	1	0.032	1.1
GTEx	Thyroid	2	0.051	1.1
GTEx	Whole Blood	2	0.101	1.1
METSIM	Adipose	1	0.022	1.1
YFS	Blood	1	0.022	1.1
CommonMind	Brain Pre-frontal Cortex	1	0.019	1.1
The Cancer Genome Atlas	Colon Adenocarcinoma	2	0.099	1.1
The Cancer Genome Atlas	Kidney Renal Clear Cell Carcinoma	2	0.050	1.1
The Cancer Genome Atlas	Kidney Renal Papillary Cell Carcinoma	1	0.050	1.1
The Cancer Genome Atlas	Brain Lower Grade Glioma	1	0.024	1.1
The Cancer Genome Atlas	Lung Adenocarcinoma	2	0.070	1.1
The Cancer Genome Atlas	Lung Squamous Cell Carcinoma	2	0.081	1.1
The Cancer Genome Atlas	Ovarian Serous Cystadenocarcinoma	1	0.064	1.1
The Cancer Genome Atlas	Pancreatic Adenocarcinoma	1	0.061	1.1
The Cancer Genome Atlas	Prostate Adenocarcinoma	3	0.066	1.1
The Cancer Genome Atlas	Stomach Adenocarcinoma	1	0.060	1.1
The Cancer Genome Atlas	Thyroid Carcinoma	3	0.059	1.1
ROSMAP	Brain Pre-frontal Cortex	0	0.000	1.0

Hub : Traits :

HbA1C

Significant Loci

Pleiotropic Associations

Associations by panel