Hub : Genes

Arfgap3

Models

All models for this gene with cis-heritability P-value <0.01 were tested and are shown here. In each tissue, a gene can have zero, one, or multiple RNA phenotypes for each RNA modality. After the heritability statistics, subsequent columns show cross-validation performance (R² and P-value) of each modeling method. The best-performing method for each models is used for TWAS.

#	Tissue	Modality	RNA phenotype	h2	h2 SE	h2 P	xQTL R2	BLUP R2	ENET R2	LASSO R2	xQTL P	BLUP P	ENET P	LASSO P
1	Adipose	gene expression	ENSRNOG00000046472	0.25	0.16	2.0e-09	0.06	0.05	0.06	0.06	6.8e-07	2.0e-06	1.0e-06	4.9e-07
2	PL	mRNA stability	ENSRNOG00000046472	0.03	0.03	9.6e-03	0.01	0.01	0	0	3.0e-02	1.1e-01	1.2e-01	2.0e-01

Trait associations

The numbered columns correspond to the numbered models in the table above. They contain the TWAS Z-score for each trait-model pair. Colors indicate strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait	Avg chi2 ratio	Avg chi2	Max chi2	1	2
BMI with tail	1.6	5.2	5.5	-2.4	2.2
BMI without tail	0.6	1.2	1.7	-1.3	0.9
Body weight	1.8	7.5	8.6	-2.9	2.5
Epididymis fat weight	1.8	4.2	5.1	-1.8	2.2
Glucose	0.6	0.9	1.0	1.0	-0.9
Heart weight	2.9	4.1	4.4	-2.1	1.9
Left kidney weight	16.3	46.6	48.0	-6.7	6.9
Right kidney weight	17.0	48.6	49.2	-7.0	6.9
Tail length	0.0	0.1	0.1	-0.3	-0.2
Length with tail	0.4	1.4	1.4	-1.2	1.2
Length without tail	0.6	1.2	1.7	-0.9	1.3
Liver weight, left	0.4	0.7	0.9	-0.7	0.9
Liver weight, right	0.8	1.3	1.9	-0.9	1.4
Parametrial fat weight	0.1	0.1	0.1	0.2	-0.4
Retroperitoneal fat weight	1.6	5.4	6.4	-2.1	2.5
Intraocular pressure	0.2	0.3	0.5	-0.7	0.4
Extensor digitorum longus weight	0.1	0.2	0.4	-0.2	-0.6
Soleus weight	0.0	0.1	0.2	-0.4	-0.2
Tibialis anterior weight	0.6	2.1	3.1	1.0	-1.7
Tibia length	1.1	3.2	3.8	-1.6	2.0
Number of licking bursts	0.2	0.2	0.2	0.3	-0.5
Food consumed during 24 hour testing period	2.3	2.7	3.2	-1.8	1.5
Times rat made contact with spout	1.5	1.8	2.8	-1.7	0.9
Mean time between licks in bursts	1.1	1.6	1.7	1.2	-1.3
Mean num. licks in bursts	1.8	2.2	2.8	-1.7	1.3
Std. dev. time between licks in bursts	0.5	0.6	0.9	1.0	-0.5
Water consumed over 24 hours	3.7	4.4	6.4	-2.5	1.6
Indifference point 0 sec	0.1	0.1	0.1	0.4	-0.3
Indifference point AUC	0.1	0.1	0.2	0.5	-0.1
Indifference point function ln k	1.3	1.9	2.6	-1.6	1.1
Indifference point function log k	1.3	1.9	2.6	-1.6	1.1
Delay discounting total patch changes 0 sec	0.1	0.2	0.2	0.5	-0.4
Delay discounting total patch changes 12 sec	0.2	0.2	0.4	-0.0	0.7
Delay discounting total patch changes 18 sec	0.0	0.1	0.1	0.1	0.3
Delay discounting total patch changes 24 sec	0.2	0.3	0.4	0.6	-0.4
Delay discounting total patch changes 6 sec	0.0	0.0	0.1	-0.0	0.2
Delay discounting time to switch 0 sec	0.2	0.3	0.7	0.8	-0.0
Delay discounting water rate 0 sec	0.3	0.5	0.9	-1.0	0.2
Delay discounting water rate 12 sec	0.2	0.3	0.7	-0.8	-0.1
Delay discounting water rate 18 sec	0.0	0.0	0.1	0.1	-0.3
Delay discounting water rate 24 sec	2.3	3.2	4.1	-2.0	1.5
Delay discounting water rate 6 sec	0.1	0.2	0.2	0.4	-0.5
Locomotor activity	3.1	4.9	5.7	-2.0	2.4
Locomotor testing distance	0.0	0.0	0.0	0.2	0.1
Locomotor testing rearing	0.6	0.9	1.2	-0.8	1.1
Light reinforcement 1	0.6	1.0	1.4	-0.8	1.2
Light reinforcement 2	0.7	1.0	1.0	-1.0	1.0
Reaction time number correct	1.3	1.8	2.0	1.3	-1.4
Reaction time mean minus median	0.2	0.3	0.4	-0.7	0.5
Reaction time mean minus median AUC	0.5	0.7	0.9	-0.9	0.7
Reaction time num false alarms	0.1	0.1	0.1	-0.3	0.3
Reaction time num false alarms AUC	0.1	0.1	0.1	-0.3	0.4
Reaction time trials correct on left	1.3	1.8	2.0	1.3	-1.4
Reaction time trials on left	1.3	1.9	2.1	1.3	-1.4
Reaction time mean	0.0	0.0	0.0	0.2	-0.1
Reaction time mean AUC	0.0	0.0	0.0	0.2	-0.1
Median of all reaction times	0.1	0.2	0.2	0.5	-0.4
Reaction time omissions	0.1	0.2	0.2	0.5	-0.4
Reaction time false alarm rate	0.5	0.6	0.7	-0.8	0.8
Reaction time premature initiation rate	0.2	0.2	0.4	0.2	0.6
Reaction time premature initiations	0.2	0.2	0.5	0.7	-0.1
Std. dev. reaction times	0.4	0.5	0.6	-0.7	0.8
Reaction time trials completed	1.3	1.9	2.1	1.3	-1.4
Reaction time trials AUC	0.9	1.3	1.4	1.1	-1.2
Social response proportion	0.2	0.2	0.3	-0.6	0.2
Social responses	0.1	0.1	0.1	0.2	0.4
Social time	2.1	2.7	3.2	1.8	-1.5
Conditioned locomotion	0.1	0.2	0.2	-0.3	0.5
Cocaine response after cond. corrected	0.0	0.0	0.0	0.1	-0.0
Cocaine response after cond. not corrected	0.0	0.0	0.0	0.1	0.1
Cocaine response before conditioning	0.0	0.1	0.1	0.3	-0.2
Saline control response	0.4	0.5	0.6	-0.6	0.8
Condit. Reinf. active minus inactive responses	0.2	0.2	0.3	-0.2	0.6
Condit. Reinf. active-inactive response ratio	0.3	0.4	0.6	-0.3	0.8
Condit. Reinf. active responses	1.1	1.5	2.1	-1.0	1.5
Condit. Reinf. inactive responses	0.9	1.1	1.4	-0.9	1.2
Condit. Reinf. lever presses	0.1	0.2	0.3	0.6	-0.0
Condit. Reinf. lever reinforcers received	0.5	0.7	1.3	-0.4	1.1
Pavlov. Cond. lever latency	0.2	0.2	0.4	-0.7	-0.0
Pavlov. Cond. magazine entry latency	3.2	3.7	5.0	2.2	-1.5
Pavlov. Cond. change in total contacts	0.2	0.3	0.4	0.7	0.4
Pavlov. Cond. index score	1.3	1.7	2.6	1.6	-0.9
Pavlov. Cond. latency score	1.7	2.1	3.1	1.7	-1.1
Pavlov. Cond. lever contacts	0.2	0.3	0.5	0.7	0.1
Pavlov. Cond. magazine entry number	1.8	2.2	3.5	-1.9	1.0
Pavlov. Cond. intertrial magazine entries	2.2	2.8	4.2	-2.0	1.2
Pavlov. Cond. lever-magazine prob. diff.	1.5	2.0	3.1	1.7	-1.0
Pavlov. Cond. response bias	0.4	0.6	1.1	1.1	-0.1
Conditioned reinforcement - actives	0.1	0.1	0.2	0.4	0.0
Conditioned reinforcement - inactives	0.1	0.1	0.1	0.2	-0.3
Conditioned locomotion	0.8	1.0	1.1	-0.9	1.1
Intermittent access intake day 1-15 change	0.4	0.4	0.4	0.7	-0.6
Intermittent access intake escalation	0.3	0.3	0.3	0.5	-0.5
Intermittent access intake escalation 2	0.1	0.1	0.1	0.3	-0.2
Intermitt. access day 1 inactive lever presses	0.6	0.7	0.9	-0.7	0.9
Intermitt. access day 15 inactive lever presses	0.7	0.8	0.9	-0.8	1.0
Intermitt. access escalation Index	0.1	0.1	0.1	0.3	-0.2
Intermittent access day 1 total infusions	0.7	0.8	0.8	-0.9	0.9
Intermittent access day 15 total infusions	0.0	0.0	0.1	-0.3	0.1
Intermittent access terminal intake (last 3 days)	0.0	0.0	0.0	0.1	0.0
Intermittent access total infusions	0.1	0.1	0.1	-0.3	0.3
Intermittent access day 1 locomotion	0.1	0.1	0.1	-0.3	0.3
Intermittent access day 15 total locomotion	0.1	0.1	0.2	-0.4	0.1
Intermittent access total locomotion	0.1	0.1	0.2	-0.5	0.2
Intermittent access standard deviation	0.5	0.5	0.6	-0.6	0.8
Cocaine induced anxiety	1.9	2.2	3.0	-1.7	1.2
Post-drug Anxiety	1.7	1.8	2.5	-1.6	1.1
Baseline Anxiety	1.3	1.3	1.5	1.2	-1.1
Lifetime Intake	0.4	0.4	0.5	-0.7	0.6
Incentive Sensitization - Responses	0.1	0.1	0.2	-0.5	0.0
Incentive Sensitization - Breakpoint	0.2	0.2	0.4	-0.6	0.2
Progressive ratio test 1 active lever presses	0.1	0.1	0.1	-0.2	0.3
Progressive ratio test 1 breakpoint	0.0	0.0	0.0	0.1	-0.0
Progressive ratio test 1 inactive lever presses	0.0	0.0	0.0	-0.0	0.2
Progressive ratio test 2 active lever presses	0.0	0.0	0.0	-0.2	-0.1
Progressive ratio test 2 breakpoint	0.1	0.1	0.1	-0.3	0.2
Progressive ratio test 2 inactive lever presses	0.0	0.0	0.1	0.1	-0.3
Total sessions with >9 infusions	0.7	0.8	0.9	-0.8	0.9
Short access day 1 total inactive lever presses	2.5	2.8	3.2	-1.8	1.6
Short access day 10 total inactive lever presses	2.3	2.6	2.9	-1.7	1.5
Short access day 1 total infusions	1.2	1.3	1.3	-1.1	1.1
Short access day 10 total infusions	0.0	0.0	0.0	0.0	0.1
Short access total infusions	1.1	1.2	1.3	-1.1	1.1
Short access day 1 locomotion	0.0	0.0	0.1	0.2	-0.2
Short access day 10 total locomotion	0.8	0.8	1.1	1.1	-0.7
Short access total locomotion	0.1	0.1	0.2	-0.0	0.4
Compulsive drug intake	0.6	0.6	0.7	0.9	-0.6
One hour access (0.3 mA shock)	0.4	0.5	0.6	0.6	-0.8
One hour access (shock baseline)	0.3	0.4	0.6	0.4	-0.8
Number of responses in last shaping day	0.8	0.8	0.9	0.8	-1.0
Context. condit. distance diff. score	4.5	5.4	6.6	-2.6	2.1
Locomotion velocity, session 1	0.9	1.0	1.3	-0.8	1.1
Locomotion distance, session 1	0.7	0.9	1.0	0.9	-1.0
Locomotion velocity, session 2	1.0	1.1	1.5	-0.9	1.2
Locomotion distance, session 2	1.3	1.9	2.5	1.6	-1.1
Locomotion velocity, session 3	0.3	0.4	0.5	-0.7	0.5
Locomotion distance, session 3	1.8	2.0	2.8	1.1	-1.7
Stereotopy head waving bouts, day 3	1.4	1.6	2.1	-1.1	1.4
Stereotopy head waving duration, day 3	6.4	7.7	8.6	-2.6	2.9
Locomotion velocity, session 7	0.0	0.0	0.0	0.1	-0.0
Locomotion distance, session 7	1.4	1.7	2.0	1.4	-1.2
Stereotopy head waving bouts, day 7	6.7	7.6	8.8	-2.5	3.0
Stereotopy head waving duration, day 7	4.3	5.3	5.8	-2.2	2.4
Locomotion velocity, session 8	6.3	7.6	7.6	-2.8	2.7
Locomotion distance, session 8	0.7	1.0	1.1	-1.0	1.0
Degree of sensitization distance	1.3	1.3	1.9	-0.8	1.4
Degree of sensitization stereotypy	4.2	4.6	4.8	-2.1	2.2
Condit. Reinf. active minus inactive responses	0.8	0.9	1.6	1.2	-0.4
Condit. Reinf. active-inactive response ratio	0.3	0.3	0.7	-0.1	0.8
Condit. Reinf. active responses	2.9	3.6	4.7	2.2	-1.6
Condit. Reinf. inactive responses	4.5	5.3	5.5	2.3	-2.3
Incentive salience index mean	1.5	1.9	2.8	1.7	-1.0
Condit. Reinf. lever presses	1.8	2.4	3.5	1.9	-1.2
Time in familiar zone, hab. session 1	0.1	0.1	0.1	-0.4	0.2
Time in novel zone, hab. session 1	1.1	1.1	1.1	-1.1	1.0
Total zone transitions, hab. session 1	2.0	2.9	3.1	1.6	-1.7
Total locomotion distance, hab. session 1	0.3	0.4	0.5	0.7	-0.6
Locomotion velocity, hab. session 1	0.6	0.8	1.0	1.0	-0.9
Time in familiar zone, hab. session 2	0.1	0.1	0.2	0.1	-0.4
Time in novel zone, hab. session 2	0.8	0.8	0.8	-0.9	0.9
Total zone transitions, hab. session 2	0.1	0.1	0.2	0.4	-0.2
Total locomotion distance, hab. session 2	0.2	0.2	0.2	0.4	-0.5
Locomotion velocity, hab. session 2	0.5	0.7	0.7	0.8	-0.9
Novel to familiar place preference ratio	3.6	3.8	4.2	-2.1	1.8
Novelty place preference	4.6	4.8	5.3	-2.3	2.1
Time in novel zone, NPP test	6.0	6.3	7.0	-2.6	2.4
Total zone transitions, NPP test	0.8	1.2	1.3	1.0	-1.1
Total locomotion distance, NPP test	0.3	0.4	0.5	0.6	-0.7
Locomotion velocity, NPP test	1.3	1.9	2.0	1.3	-1.4
Pavlov. Cond. lever latency	2.2	2.8	3.7	-1.9	1.4
Pavlov. Cond. magazine entry latency	2.2	2.8	3.1	1.8	-1.6
Pavlov. Cond. change in total contacts	2.2	2.3	2.7	1.6	-1.4
Pavlov. Cond. index score	1.5	1.9	2.4	1.5	-1.2
Pavlov. Cond. latency score	1.1	1.5	1.9	1.4	-1.0
Pavlov. Cond. lever contacts	2.8	3.3	3.9	2.0	-1.7
Pavlov. Cond. magazine entry number	2.0	2.5	2.6	-1.6	1.6
Pavlov. Cond. intertrial magazine entries	0.5	0.6	0.6	0.8	-0.8
Pavlov. Cond. lever-magazine prob. diff.	2.2	2.7	3.2	1.8	-1.5
Pavlov. Cond. response bias	3.1	3.8	4.4	2.1	-1.8
Bone: apparent density	0.2	0.3	0.5	0.7	-0.5
Bone surface	0.1	0.2	0.4	-0.1	0.6
Bone volume	0.0	0.1	0.2	-0.0	0.4
Bone: connectivity density	0.0	0.0	0.1	0.3	-0.1
Bone: cortical apparent density	1.2	1.5	1.8	1.3	-1.1
Bone: cortical area	1.8	2.7	2.9	-1.7	1.6
Bone: cortical porosity	0.5	0.5	0.6	-0.8	0.7
Bone: cortical porosity	1.4	1.5	1.7	-1.1	1.3
Bone: cortical thickness	0.1	0.1	0.2	-0.5	0.0
Bone: cortical thickness	0.2	0.3	0.5	-0.7	0.2
Bone: cortical tissue density	1.1	1.4	1.7	1.3	-1.1
Bone: elastic displacement	1.2	1.3	1.4	-1.2	1.1
Bone: elastic work	4.6	6.0	6.2	-2.4	2.5
Bone: endosteal estimation	2.1	4.5	5.8	-1.8	2.4
Bone: endosteal perimeter	2.3	4.7	5.8	-1.9	2.4
Bone: final force	1.1	1.8	2.1	-1.2	1.5
Bone: final moment	1.7	2.8	3.1	-1.6	1.8
Bone: marrow area	2.3	4.9	6.4	-1.9	2.5
Bone: maximum diameter	5.8	10.7	10.8	-3.3	3.3
Bone: maximum force	2.9	5.1	5.3	-2.2	2.3
Bone: maximum moment	3.8	6.6	6.7	-2.5	2.6
Bone: minimum diameter	1.0	1.8	2.2	-1.2	1.5
Bone: periosteal estimation	2.8	5.8	6.6	-2.2	2.6
Bone: periosteal perimeter	3.9	6.5	7.2	-2.4	2.7
Bone: post-yield work	0.6	0.8	0.9	-0.9	0.8
Bone: stiffness	1.2	1.9	1.9	-1.4	1.4
Bone: tissue strength	0.6	0.6	0.9	-0.5	1.0
Bone: trabecular number	0.1	0.1	0.2	0.4	-0.2
Bone: trabecular spacing	0.8	1.0	1.0	-1.0	1.0
Bone: trabecular thickness	0.2	0.2	0.3	0.6	-0.2
Bone: trabecular tissue density	0.7	0.9	1.1	1.0	-0.9
Breakpoint value in progressive ratio session	0.1	0.1	0.2	-0.4	0.3
Distance traveled before self-admin	0.2	0.2	0.2	0.4	-0.4
Distance traveled after self-admin	0.1	0.2	0.2	-0.4	0.4
Delta time in closed arm before/after self-admin	0.1	0.1	0.2	-0.0	0.4
Delta time in open arm before/after self-admin	0.0	0.0	0.0	-0.1	-0.2
Diff in mean of infusions in LGA sessions	0.8	0.9	1.2	1.1	-0.8
Extinction: sum of active levers before priming	0.2	0.2	0.4	0.6	-0.3
Active lever presses in extinction session 6	0.4	0.4	0.4	-0.6	0.6
Delta distance traveled before/after self-admin	2.2	2.3	2.4	-1.5	1.5
Delta ambulatory time before/after self-admin	3.7	4.0	4.1	-2.0	2.0
Time in closed arm before self-admin	3.4	3.9	4.7	1.8	-2.2
Time in closed arm after self-admin	0.0	0.0	0.0	0.1	0.2
Time in open arm before self-admin	0.1	0.1	0.1	0.3	-0.3
Time in open arm after self-admin	0.2	0.2	0.4	0.3	-0.6
Sum of active levers in priming session hrs 5-6	0.1	0.1	0.1	0.3	0.0
Time to tail flick, vehicle, before self-admin	0.4	0.4	0.6	-0.5	0.8
Time to tail flick, vehicle, after self-admin	0.3	0.3	0.5	0.7	-0.3
Time to tail flick, test, before self-admin	0.0	0.0	0.0	-0.2	0.2
Time to tail flick, test, after self-admin	3.7	3.8	4.0	2.0	-1.9
Delta time to tail flick, vehicle, before/after SA	0.1	0.1	0.1	0.4	-0.2
Delta time to tail flick, test, before/after SA	4.1	3.7	3.8	2.0	-1.9
Ambulatory time before self-admin	0.1	0.1	0.1	0.2	-0.3
Ambulatory time after self-admin	0.0	0.0	0.1	-0.3	0.1
Total heroin consumption	0.3	0.3	0.4	-0.5	0.6
Area under the delay curve	1.6	1.7	2.0	1.4	-1.2
Delay disc. indifference point, 0s delay	0.2	0.2	0.3	-0.4	0.5
Delay disc. indifference point, 16s delay	2.9	3.0	3.7	1.9	-1.5
Delay disc. indifference point, 2s delay	0.5	0.6	0.7	0.7	-0.8
Delay disc. indifference point, 24s delay	0.4	0.4	0.5	0.7	-0.5
Delay disc. indifference point, 4s delay	0.1	0.1	0.2	0.4	-0.3
Delay disc. indifference point, 8s delay	2.8	2.9	3.1	1.8	-1.6
Delay discount exponential model param	1.5	1.6	1.9	-1.4	1.2
Delay discount hyperbolic model param	1.1	1.2	1.4	-1.2	1.0
Fecal boli incidents, locomotor time 1	0.3	0.4	0.4	0.6	-0.6
Change in fecal boli incidents, locomotor task	0.9	0.9	1.0	-0.9	1.0
Time >=10cm from walls, locomotor time 1	0.0	0.0	0.1	0.3	0.1
Bouts of movement, locomotor time 1	0.0	0.1	0.1	0.3	-0.2
Total resting periods, locomotor time 1	0.3	0.3	0.3	0.5	-0.5
Rest time, locomotor task time 1	0.1	0.1	0.1	0.3	-0.4
Distance moved, locomotor task time 1	0.3	0.4	0.5	-0.5	0.7
Vertical activity count, locomotor time 1	0.1	0.1	0.1	-0.2	0.3
Time >=10cm from walls, locomotor time 2	0.4	0.4	0.4	0.7	-0.5
Bouts of movement, locomotor time 2	0.1	0.1	0.1	0.3	0.0
Total resting periods, locomotor time 2	0.0	0.0	0.1	0.3	0.0
Rest time, locomotor task time 2	0.1	0.2	0.2	0.4	-0.5
Distance moved, locomotor task time 2	0.6	0.6	0.7	-0.8	0.8
Vertical activity count, locomotor time 2	0.8	0.8	0.9	-0.9	0.9
Weight adjusted by age	0.1	0.1	0.1	-0.3	0.2
Seeking ratio, delayed vs. immediate footshock	3.5	4.1	4.7	1.8	-2.2
Locomotion in novel chamber	0.2	0.3	0.5	0.7	-0.3
Locomotion in novel chamber post-restriction	1.1	1.3	1.5	1.2	-1.1
Progressive ratio	0.1	0.1	0.1	0.4	0.2
Food seeking constrained by brief footshock	1.1	1.4	1.7	-1.1	1.3
Seeking ratio, punishment vs. effort	0.3	0.4	0.5	-0.7	0.5
Run reversals in cocaine runway, females	1.2	1.2	1.5	1.2	-1.0
Run reversals in cocaine runway, males	1.2	1.1	1.2	-1.1	1.0
Latency to leave start box in cocaine runway	0.2	0.3	0.4	-0.7	0.3
Latency to leave start box in cocaine runway, F	0.2	0.2	0.2	0.3	-0.5
Latency to leave start box in cocaine runway, M	1.5	1.4	1.9	-1.4	1.0
Cd content in liver	1.5	1.6	2.4	-1.5	0.9
Co content in liver	0.5	0.6	1.1	-1.1	0.4
Cu content in liver	4.7	5.6	7.1	2.7	-2.0
Fe content in liver	0.7	0.8	1.1	-0.7	1.1
K content in liver	0.2	0.2	0.4	0.6	0.0
Mg content in liver	0.5	0.5	0.9	1.0	-0.3
Mn content in liver	0.1	0.1	0.2	-0.1	0.4
Na content in liver	2.2	2.4	2.7	1.4	-1.7
Rb content in liver	0.2	0.2	0.4	-0.1	0.7
Se content in liver	0.8	1.0	1.6	1.3	-0.7
Sr content in liver	1.5	1.4	2.3	0.7	-1.5
Zn content in liver	0.6	0.7	0.7	0.8	-0.8