Hub : Genes

Angptl3

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	Liver	intron excision ratio	chr5_118822056_118822310	0.14	0.17	4.0e-04	0.02	0.01	0	0.01	4.5e-03	1.3e-02	3.0e-01	2.8e-02
2	Liver	intron excision ratio	chr5_118822405_118824571	0.12	0.13	6.4e-06	0.03	0.03	0.02	0.02	1.5e-04	4.1e-04	3.8e-03	1.0e-03

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 strength of Z-scores: cells with lower negative Z-scores are darker blue, cells with higher positive Z-scores are darker red. Significant associations have white and bolded text.

Trait	Avg chi2 ratio	Avg chi2	Max chi2	1	2
Bone: apparent density	0.4	0.7	0.7	0.8	-0.8
Area under the delay curve	0.1	0.1	0.1	0.3	-0.3
BMI with tail	0.5	1.6	1.6	-1.3	1.3
BMI without tail	1.2	3.6	3.6	-1.9	1.9
Body weight	0.1	0.6	0.6	-0.8	0.8
Weight adjusted by age	1.1	1.7	1.7	-1.3	1.3
Bone surface	1.6	2.9	2.9	-1.7	1.7
Bone volume	0.3	0.5	0.5	-0.7	0.7
Breakpoint value in progressive ratio session	0.6	0.7	0.7	0.9	-0.9
Number of licking bursts	0.1	0.1	0.1	-0.3	0.3
Context. condit. distance diff. score	2.4	2.9	2.9	1.7	-1.7
Locomotion velocity, session 1	0.0	0.0	0.0	-0.2	0.2
Locomotion distance, session 1	0.8	1.1	1.1	1.0	-1.0
Locomotion velocity, session 2	0.0	0.0	0.0	-0.2	0.2
Locomotion distance, session 2	0.1	0.1	0.1	-0.4	0.4
Locomotion velocity, session 3	0.0	0.0	0.0	0.2	-0.2
Locomotion distance, session 3	0.0	0.0	0.0	-0.2	0.2
Stereotopy head waving bouts, day 3	0.5	0.6	0.6	0.8	-0.8
Stereotopy head waving duration, day 3	1.3	1.5	1.5	1.2	-1.2
Locomotion velocity, session 7	0.5	0.6	0.6	0.8	-0.8
Locomotion distance, session 7	0.2	0.3	0.3	0.5	-0.5
Stereotopy head waving bouts, day 7	0.5	0.5	0.5	-0.7	0.7
Stereotopy head waving duration, day 7	0.7	0.8	0.8	-0.9	0.9
Locomotion velocity, session 8	0.2	0.2	0.2	0.5	-0.5
Locomotion distance, session 8	0.8	1.1	1.1	1.1	-1.1
Degree of sensitization distance	0.0	0.0	0.0	-0.1	0.1
Degree of sensitization stereotypy	0.7	0.8	0.8	-0.9	0.9
Conditioned locomotion	0.1	0.1	0.1	0.4	-0.4
Cocaine response after cond. corrected	0.3	0.4	0.4	-0.6	0.6
Cocaine response after cond. not corrected	0.2	0.3	0.3	-0.5	0.5
Cocaine response before conditioning	0.0	0.0	0.0	-0.0	0.0
Saline control response	0.0	0.0	0.0	0.1	-0.1
Bone: connectivity density	1.3	2.0	2.0	-1.4	1.4
Bone: cortical apparent density	6.2	8.5	8.5	2.9	-2.9
Bone: cortical area	0.2	0.4	0.4	-0.6	0.6
Bone: cortical porosity	0.3	0.3	0.3	-0.6	0.6
Bone: cortical porosity	0.5	0.5	0.5	-0.7	0.7
Bone: cortical thickness	0.3	0.4	0.4	0.7	-0.7
Bone: cortical thickness	0.2	0.2	0.2	0.4	-0.4
Bone: cortical tissue density	6.2	8.5	8.5	2.9	-2.9
Condit. Reinf. active minus inactive responses	0.3	0.4	0.4	-0.6	0.6
Condit. Reinf. active-inactive response ratio	0.0	0.0	0.0	-0.1	0.1
Condit. Reinf. active responses	1.1	1.3	1.3	-1.1	1.1
Condit. Reinf. inactive responses	0.6	0.7	0.7	-0.8	0.8
Incentive salience index mean	0.3	0.4	0.4	-0.7	0.7
Condit. Reinf. lever presses	0.0	0.0	0.0	0.0	-0.0
Condit. Reinf. active minus inactive responses	0.9	1.2	1.2	1.1	-1.1
Condit. Reinf. active-inactive response ratio	0.3	0.3	0.3	0.6	-0.6
Condit. Reinf. active responses	0.5	0.7	0.7	0.8	-0.8
Condit. Reinf. inactive responses	1.0	1.3	1.3	1.1	-1.1
Condit. Reinf. lever presses	2.0	2.7	2.7	-1.6	1.6
Condit. Reinf. lever reinforcers received	0.2	0.2	0.2	0.5	-0.5
Conditioned reinforcement - actives	0.0	0.1	0.1	0.3	-0.3
Conditioned reinforcement - inactives	0.1	0.1	0.1	0.4	-0.4
Conditioned locomotion	0.2	0.2	0.2	0.5	-0.5
Patch foraging indifference point 0 sec	5.8	10.6	10.6	-3.3	3.3
Patch foraging indifference point AUC	0.8	1.1	1.1	-1.1	1.1
Delay disc. indifference point, 0s delay	2.3	2.5	2.5	1.6	-1.6
Delay disc. indifference point, 16s delay	1.8	2.0	2.0	-1.4	1.4
Delay disc. indifference point, 2s delay	0.0	0.0	0.0	0.0	-0.0
Delay disc. indifference point, 24s delay	0.0	0.0	0.0	0.1	-0.1
Delay disc. indifference point, 4s delay	1.3	1.4	1.4	1.2	-1.2
Delay disc. indifference point, 8s delay	0.8	1.0	1.0	1.0	-1.0
Indifference point function ln k	0.2	0.4	0.4	0.6	-0.6
Indifference point function log k	0.2	0.4	0.4	0.6	-0.6
Patch foraging total patch changes 0 sec	5.3	9.9	9.9	-3.1	3.1
Patch foraging total patch changes 12 sec	1.4	1.8	1.8	-1.3	1.3
Patch foraging total patch changes 18 sec	1.9	2.9	2.9	-1.7	1.7
Patch foraging total patch changes 24 sec	1.0	1.7	1.7	-1.3	1.3
Patch foraging total patch changes 6 sec	2.6	4.0	4.0	-2.0	2.0
Patch foraging time to switch 0 sec	0.7	1.4	1.4	1.2	-1.2
Patch foraging water rate 0 sec	1.0	2.0	2.0	-1.4	1.4
Patch foraging water rate 12 sec	2.2	4.7	4.7	-2.2	2.2
Patch foraging water rate 18 sec	0.2	0.3	0.3	-0.6	0.6
Patch foraging water rate 24 sec	0.0	0.0	0.0	0.0	-0.0
Patch foraging water rate 6 sec	0.0	0.0	0.0	-0.1	0.1
Seeking ratio, delayed vs. immediate footshock	0.0	0.0	0.0	-0.2	0.2
Distance traveled before self-admin	0.5	0.6	0.6	-0.8	0.8
Distance traveled after self-admin	1.2	1.5	1.5	-1.2	1.2
Extensor digitorum longus weight	0.6	2.2	2.2	1.5	-1.5
Bone: elastic displacement	0.8	0.9	0.9	0.9	-0.9
Bone: elastic work	1.6	2.1	2.1	1.5	-1.5
Bone: endosteal estimation	0.8	1.8	1.8	-1.4	1.4
Bone: endosteal perimeter	1.7	3.5	3.5	-1.9	1.9
Epididymis fat weight	0.1	0.2	0.2	0.4	-0.4
Delta time in closed arm before/after self-admin	0.0	0.0	0.0	0.1	-0.1
Delta time in open arm before/after self-admin	2.3	2.2	2.2	-1.5	1.5
Diff in mean of infusions in LGA sessions	0.0	0.0	0.0	0.0	-0.0
Delay discount exponential model param	0.1	0.1	0.1	-0.3	0.3
Extinction: sum of active levers before priming	0.4	0.4	0.4	0.6	-0.6
Active lever presses in extinction session 6	0.0	0.0	0.0	-0.0	0.0
Bone: final force	0.2	0.4	0.4	0.6	-0.6
Bone: final moment	0.0	0.0	0.0	0.1	-0.1
Food consumed during 24 hour testing period	0.1	0.1	0.1	0.3	-0.3
Glucose	0.0	0.0	0.0	0.0	-0.0
Heart weight	3.0	4.6	4.6	2.1	-2.1
Delay discount hyperbolic model param	0.0	0.0	0.0	-0.2	0.2
Intermittent access intake day 1-15 change	0.1	0.2	0.2	0.5	-0.5
Intermittent access intake escalation	0.3	0.6	0.6	0.8	-0.8
Intermittent access intake escalation 2	0.2	0.2	0.2	0.4	-0.4
Intermitt. access day 1 inactive lever presses	0.0	0.0	0.0	-0.1	0.1
Intermitt. access day 15 inactive lever presses	1.2	2.4	2.4	1.6	-1.6
Intermitt. access escalation Index	0.0	0.1	0.1	-0.3	0.3
Intermittent access day 1 total infusions	0.8	1.3	1.3	1.2	-1.2
Intermittent access day 15 total infusions	1.3	1.9	1.9	1.4	-1.4
Intermittent access terminal intake (last 3 days)	0.4	0.6	0.6	0.8	-0.8
Intermittent access total infusions	1.7	2.0	2.0	1.4	-1.4
Intermittent access day 1 locomotion	0.1	0.1	0.1	0.3	-0.3
Intermittent access day 15 total locomotion	0.0	0.0	0.0	0.1	-0.1
Intermittent access total locomotion	0.1	0.1	0.1	0.4	-0.4
Intermittent access standard deviation	0.7	1.5	1.5	1.2	-1.2
Left kidney weight	0.1	0.3	0.3	0.6	-0.6
Right kidney weight	0.2	0.8	0.8	0.9	-0.9
Cocaine induced anxiety	0.0	0.0	0.0	-0.2	0.2
Post-drug Anxiety	0.0	0.0	0.0	0.1	-0.1
Baseline Anxiety	0.0	0.0	0.0	0.1	-0.1
Tail length	0.0	0.1	0.1	0.4	-0.4
Length with tail	0.0	0.1	0.1	0.3	-0.3
Length without tail	0.0	0.0	0.0	0.1	-0.1
Times rat made contact with spout	0.0	0.0	0.0	0.0	-0.0
Lifetime Intake	1.6	2.0	2.0	1.4	-1.4
Liver weight, left	3.0	4.9	4.9	2.2	-2.2
Liver weight, right	2.1	3.7	3.7	1.9	-1.9
Locomotor activity	0.0	0.0	0.0	-0.1	0.1
Locomotor testing distance	1.3	2.4	2.4	-1.5	1.5
Locomotor testing rearing	0.0	0.0	0.0	0.0	-0.0
Locomotion in novel chamber	1.5	1.9	1.9	-1.4	1.4
Locomotion in novel chamber post-restriction	0.5	0.8	0.8	0.9	-0.9
Fecal boli incidents, locomotor time 1	0.1	0.1	0.1	0.3	-0.3
Change in fecal boli incidents, locomotor task	0.1	0.1	0.1	0.3	-0.3
Time >=10cm from walls, locomotor time 1	0.3	0.3	0.3	-0.6	0.6
Bouts of movement, locomotor time 1	0.1	0.1	0.1	-0.2	0.2
Total resting periods, locomotor time 1	0.1	0.1	0.1	-0.3	0.3
Rest time, locomotor task time 1	0.4	0.5	0.5	-0.7	0.7
Distance moved, locomotor task time 1	0.1	0.1	0.1	0.3	-0.3
Vertical activity count, locomotor time 1	0.0	0.1	0.1	-0.3	0.3
Time >=10cm from walls, locomotor time 2	1.9	2.8	2.8	1.7	-1.7
Bouts of movement, locomotor time 2	0.5	0.8	0.8	-0.9	0.9
Total resting periods, locomotor time 2	0.5	0.9	0.9	-0.9	0.9
Rest time, locomotor task time 2	0.5	0.7	0.7	-0.8	0.8
Distance moved, locomotor task time 2	1.6	1.9	1.9	1.4	-1.4
Vertical activity count, locomotor time 2	0.4	0.6	0.6	0.8	-0.8
Light reinforcement 1	0.1	0.1	0.1	0.4	-0.4
Light reinforcement 2	0.1	0.2	0.2	0.5	-0.5
Bone: marrow area	0.7	1.5	1.5	-1.2	1.2
Bone: maximum diameter	0.6	1.2	1.2	-1.1	1.1
Bone: maximum force	0.0	0.0	0.0	0.1	-0.1
Bone: maximum moment	0.2	0.3	0.3	-0.5	0.5
Mean time between licks in bursts	3.2	7.9	7.9	2.8	-2.8
Mean num. licks in bursts	0.0	0.0	0.0	0.2	-0.2
Cd content in liver	0.8	0.8	0.8	-0.9	0.9
Co content in liver	0.1	0.1	0.1	0.3	-0.3
Cu content in liver	1.0	1.2	1.2	1.1	-1.1
Fe content in liver	0.1	0.1	0.1	0.3	-0.3
K content in liver	2.1	2.0	2.0	1.4	-1.4
Mg content in liver	0.3	0.3	0.3	-0.6	0.6
Mn content in liver	0.0	0.1	0.1	-0.2	0.2
Na content in liver	3.3	3.6	3.6	1.9	-1.9
Rb content in liver	0.5	0.6	0.6	0.8	-0.8
Se content in liver	0.1	0.2	0.2	-0.4	0.4
Sr content in liver	1.2	1.1	1.1	-1.0	1.0
Zn content in liver	0.6	0.7	0.7	-0.8	0.8
Bone: minimum diameter	1.7	3.0	3.0	-1.7	1.7
Time in familiar zone, hab. session 1	2.4	2.3	2.3	1.5	-1.5
Time in novel zone, hab. session 1	5.9	5.9	5.9	-2.4	2.4
Total zone transitions, hab. session 1	1.3	1.8	1.8	1.3	-1.3
Total locomotion distance, hab. session 1	0.1	0.1	0.1	0.3	-0.3
Locomotion velocity, hab. session 1	0.1	0.1	0.1	0.4	-0.4
Time in familiar zone, hab. session 2	0.4	0.5	0.5	0.7	-0.7
Time in novel zone, hab. session 2	0.7	0.7	0.7	-0.8	0.8
Total zone transitions, hab. session 2	5.2	6.6	6.6	2.6	-2.6
Total locomotion distance, hab. session 2	2.8	3.6	3.6	1.9	-1.9
Locomotion velocity, hab. session 2	2.2	2.9	2.9	1.7	-1.7
Novel to familiar place preference ratio	0.5	0.6	0.6	-0.8	0.8
Novelty place preference	0.2	0.3	0.3	-0.5	0.5
Time in novel zone, NPP test	0.4	0.4	0.4	-0.7	0.7
Total zone transitions, NPP test	2.0	2.9	2.9	1.7	-1.7
Total locomotion distance, NPP test	0.3	0.4	0.4	0.7	-0.7
Locomotion velocity, NPP test	0.4	0.5	0.5	0.7	-0.7
Intraocular pressure	0.0	0.0	0.0	0.1	-0.1
Delta distance traveled before/after self-admin	0.5	0.5	0.5	-0.7	0.7
Delta ambulatory time before/after self-admin	0.3	0.4	0.4	-0.6	0.6
Parametrial fat weight	6.0	14.0	14.0	-3.7	3.7
Pavlov. Cond. lever latency	0.5	0.7	0.7	0.8	-0.8
Pavlov. Cond. magazine entry latency	0.2	0.3	0.3	0.5	-0.5
Pavlov. Cond. change in total contacts	0.6	0.6	0.6	-0.8	0.8
Pavlov. Cond. index score	0.0	0.0	0.0	-0.2	0.2
Pavlov. Cond. latency score	0.1	0.1	0.1	-0.3	0.3
Pavlov. Cond. lever contacts	0.2	0.2	0.2	-0.4	0.4
Pavlov. Cond. magazine entry number	0.6	0.7	0.7	-0.9	0.9
Pavlov. Cond. intertrial magazine entries	0.3	0.3	0.3	0.6	-0.6
Pavlov. Cond. lever-magazine prob. diff.	0.1	0.1	0.1	-0.3	0.3
Pavlov. Cond. response bias	0.0	0.0	0.0	0.2	-0.2
Pavlov. Cond. lever latency	1.3	1.8	1.8	1.3	-1.3
Pavlov. Cond. magazine entry latency	1.7	2.0	2.0	-1.4	1.4
Pavlov. Cond. change in total contacts	1.3	2.1	2.1	-1.4	1.4
Pavlov. Cond. index score	1.3	1.7	1.7	-1.3	1.3
Pavlov. Cond. latency score	1.0	1.4	1.4	-1.2	1.2
Pavlov. Cond. lever contacts	1.5	2.1	2.1	-1.4	1.4
Pavlov. Cond. magazine entry number	0.5	0.6	0.6	0.8	-0.8
Pavlov. Cond. intertrial magazine entries	1.3	1.9	1.9	1.4	-1.4
Pavlov. Cond. lever-magazine prob. diff.	1.4	1.8	1.8	-1.3	1.3
Pavlov. Cond. response bias	1.3	1.7	1.7	-1.3	1.3
Time in closed arm before self-admin	0.0	0.0	0.0	0.2	-0.2
Time in closed arm after self-admin	0.2	0.2	0.2	0.4	-0.4
Time in open arm before self-admin	0.0	0.0	0.0	-0.2	0.2
Time in open arm after self-admin	3.2	3.5	3.5	-1.9	1.9
Bone: periosteal estimation	0.7	1.5	1.5	-1.2	1.2
Bone: periosteal perimeter	0.7	1.1	1.1	-1.1	1.1
Bone: post-yield work	1.2	1.7	1.7	-1.3	1.3
Progressive ratio test 1 active lever presses	3.7	4.6	4.6	2.1	-2.1
Progressive ratio test 1 breakpoint	4.3	5.2	5.2	2.3	-2.3
Progressive ratio test 1 inactive lever presses	3.0	4.4	4.4	2.1	-2.1
Progressive ratio test 2 active lever presses	0.3	0.3	0.3	0.6	-0.6
Progressive ratio test 2 breakpoint	0.6	0.6	0.6	0.8	-0.8
Progressive ratio test 2 inactive lever presses	0.2	0.3	0.3	0.6	-0.6
Incentive Sensitization - Responses	0.1	0.1	0.1	-0.3	0.3
Incentive Sensitization - Breakpoint	0.2	0.3	0.3	-0.5	0.5
Sum of active levers in priming session hrs 5-6	0.4	0.3	0.3	0.6	-0.6
Progressive ratio	0.2	0.3	0.3	0.6	-0.6
Food seeking constrained by brief footshock	5.3	6.5	6.5	2.5	-2.5
Seeking ratio, punishment vs. effort	1.0	1.4	1.4	1.2	-1.2
Retroperitoneal fat weight	0.3	1.3	1.3	-1.1	1.1
Reaction time number correct	0.0	0.0	0.0	-0.1	0.1
Reaction time mean minus median	0.2	0.5	0.5	-0.7	0.7
Reaction time mean minus median AUC	0.0	0.0	0.0	-0.2	0.2
Reaction time num false alarms	0.2	0.3	0.3	-0.5	0.5
Reaction time num false alarms AUC	0.6	1.0	1.0	-1.0	1.0
Reaction time trials correct on left	0.0	0.0	0.0	-0.1	0.1
Reaction time trials on left	0.0	0.0	0.0	-0.2	0.2
Reaction time mean	0.4	0.7	0.7	-0.8	0.8
Reaction time mean AUC	0.2	0.2	0.2	-0.5	0.5
Median of all reaction times	0.5	0.7	0.7	-0.9	0.9
Reaction time omissions	0.4	0.6	0.6	-0.8	0.8
Reaction time false alarm rate	0.9	1.2	1.2	-1.1	1.1
Reaction time premature initiation rate	0.2	0.2	0.2	0.5	-0.5
Reaction time premature initiations	0.2	0.4	0.4	0.6	-0.6
Std. dev. reaction times	1.1	2.0	2.0	-1.4	1.4
Reaction time trials completed	0.0	0.0	0.0	-0.2	0.2
Reaction time trials AUC	0.0	0.0	0.0	-0.2	0.2
Run reversals in cocaine runway, females	0.1	0.1	0.1	0.3	-0.3
Run reversals in cocaine runway, males	0.7	0.7	0.7	-0.8	0.8
Latency to leave start box in cocaine runway	0.5	0.5	0.5	0.7	-0.7
Latency to leave start box in cocaine runway, F	0.0	0.0	0.0	-0.0	0.0
Latency to leave start box in cocaine runway, M	0.8	0.7	0.7	0.8	-0.8
Std. dev. time between licks in bursts	0.0	0.0	0.0	0.0	-0.0
Total sessions with >9 infusions	1.7	2.1	2.1	1.5	-1.5
Short access day 1 total inactive lever presses	0.3	0.4	0.4	0.6	-0.6
Short access day 10 total inactive lever presses	0.9	2.1	2.1	-1.5	1.5
Short access day 1 total infusions	0.4	0.5	0.5	0.7	-0.7
Short access day 10 total infusions	1.6	2.1	2.1	1.4	-1.4
Short access total infusions	0.9	1.2	1.2	1.1	-1.1
Short access day 1 locomotion	0.2	0.2	0.2	0.5	-0.5
Short access day 10 total locomotion	0.0	0.1	0.1	-0.2	0.2
Short access total locomotion	0.4	0.5	0.5	0.7	-0.7
One hour access (0.3 mA shock)	0.0	0.0	0.0	0.1	-0.1
Compulsive drug intake	3.5	4.1	4.1	-2.0	2.0
One hour access (shock baseline)	1.6	2.4	2.4	1.6	-1.6
Social response proportion	0.2	0.2	0.2	-0.5	0.5
Social responses	0.7	0.9	0.9	1.0	-1.0
Social time	0.0	0.1	0.1	0.3	-0.3
Soleus weight	0.0	0.1	0.1	0.3	-0.3
Bone: stiffness	0.0	0.0	0.0	0.0	-0.0
Tibialis anterior weight	8.6	29.0	29.0	-5.4	5.4
Time to tail flick, vehicle, before self-admin	1.7	1.8	1.8	-1.3	1.3
Time to tail flick, vehicle, after self-admin	1.3	1.7	1.7	-1.3	1.3
Time to tail flick, test, before self-admin	0.0	0.0	0.0	-0.1	0.1
Time to tail flick, test, after self-admin	0.2	0.2	0.2	0.4	-0.4
Delta time to tail flick, vehicle, before/after SA	0.2	0.2	0.2	0.4	-0.4
Delta time to tail flick, test, before/after SA	0.2	0.2	0.2	-0.4	0.4
Tibia length	2.9	8.0	8.0	2.8	-2.8
Ambulatory time before self-admin	0.1	0.1	0.1	-0.4	0.4
Ambulatory time after self-admin	1.1	1.3	1.3	-1.1	1.1
Bone: tissue strength	0.2	0.2	0.2	-0.4	0.4
Total heroin consumption	0.8	1.0	1.0	1.0	-1.0
Bone: trabecular number	0.2	0.3	0.3	0.5	-0.5
Bone: trabecular spacing	0.0	0.0	0.0	-0.1	0.1
Bone: trabecular thickness	0.2	0.3	0.3	0.5	-0.5
Bone: trabecular tissue density	14.5	21.3	21.3	4.6	-4.6
Water consumed over 24 hours	0.0	0.0	0.0	-0.1	0.1
Number of responses in last shaping day	0.0	0.0	0.0	0.2	-0.2