Hub : Genes

Smc3

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	NAcc	gene expression	Smc3	0.02	0.01	7.4e-03	0.01	0.01	0.01	0.01	2.4e-02	1.1e-02	5.6e-03	1.6e-02
2	Liver	gene expression	Smc3	0.03	0.02	7.5e-03	0.01	0.01	0.01	0.02	1.5e-02	2.4e-02	2.7e-02	5.8e-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	1.7	2.9	4.9	-2.2	1.0
Area under the delay curve	1.5	1.7	3.3	-1.8	0.4
BMI with tail	2.0	6.9	13.3	-3.6	0.7
BMI without tail	0.9	2.8	5.6	-2.4	-0.2
Body weight	3.3	14.4	26.4	-5.1	1.6
Weight adjusted by age	0.5	0.7	1.4	-1.2	0.2
Bone surface	0.1	0.2	0.3	-0.5	0.2
Bone volume	1.7	3.1	4.8	-2.2	1.2
Breakpoint value in progressive ratio session	0.7	0.9	1.5	-1.2	0.5
Number of licking bursts	1.4	2.3	3.3	-1.2	1.8
Context. condit. distance diff. score	0.7	0.8	1.6	1.3	-0.3
Locomotion velocity, session 1	0.5	0.6	0.8	0.6	0.9
Locomotion distance, session 1	0.2	0.2	0.3	0.6	0.3
Locomotion velocity, session 2	0.3	0.4	0.5	0.7	-0.5
Locomotion distance, session 2	1.1	1.5	2.8	-0.5	1.7
Locomotion velocity, session 3	0.5	0.6	0.6	0.7	0.7
Locomotion distance, session 3	1.5	1.6	2.8	0.6	1.7
Stereotopy head waving bouts, day 3	0.7	0.8	1.1	0.7	-1.1
Stereotopy head waving duration, day 3	0.9	1.1	1.3	1.0	-1.1
Locomotion velocity, session 7	0.6	0.7	1.1	0.5	1.0
Locomotion distance, session 7	0.9	1.1	1.5	1.2	0.8
Stereotopy head waving bouts, day 7	0.2	0.2	0.3	0.5	0.4
Stereotopy head waving duration, day 7	0.1	0.1	0.2	-0.0	0.4
Locomotion velocity, session 8	0.2	0.2	0.3	0.6	-0.3
Locomotion distance, session 8	0.3	0.4	0.4	0.7	0.6
Degree of sensitization distance	0.6	0.6	0.9	0.6	-1.0
Degree of sensitization stereotypy	0.5	0.6	1.0	0.3	1.0
Conditioned locomotion	0.7	0.8	1.4	0.4	1.2
Cocaine response after cond. corrected	3.9	4.6	5.5	2.4	-1.9
Cocaine response after cond. not corrected	5.1	6.0	8.2	2.9	-1.9
Cocaine response before conditioning	0.2	0.2	0.4	0.7	0.0
Saline control response	1.3	1.7	2.6	1.6	-0.9
Bone: connectivity density	0.1	0.2	0.4	-0.6	-0.3
Bone: cortical apparent density	0.7	1.0	1.7	1.3	-0.5
Bone: cortical area	1.4	2.2	4.2	-0.5	2.1
Bone: cortical porosity	0.1	0.1	0.1	-0.2	-0.4
Bone: cortical porosity	0.3	0.4	0.5	-0.7	0.4
Bone: cortical thickness	0.9	1.5	2.8	0.4	1.7
Bone: cortical thickness	0.6	0.7	1.3	0.2	1.2
Bone: cortical tissue density	0.7	1.0	1.7	1.3	-0.6
Condit. Reinf. active minus inactive responses	0.5	0.6	0.9	1.0	0.5
Condit. Reinf. active-inactive response ratio	0.8	0.9	1.5	1.2	-0.5
Condit. Reinf. active responses	0.7	0.9	1.4	0.6	1.2
Condit. Reinf. inactive responses	0.7	0.9	1.6	-0.4	1.3
Incentive salience index mean	0.6	0.8	1.1	1.0	0.7
Condit. Reinf. lever presses	0.4	0.5	1.0	0.1	1.0
Condit. Reinf. active minus inactive responses	1.1	1.5	2.3	0.8	1.5
Condit. Reinf. active-inactive response ratio	1.2	1.4	2.4	1.5	0.7
Condit. Reinf. active responses	1.1	1.6	3.2	0.2	1.8
Condit. Reinf. inactive responses	1.1	1.4	1.9	-0.9	1.4
Condit. Reinf. lever presses	1.3	1.8	3.2	0.7	1.8
Condit. Reinf. lever reinforcers received	0.9	1.3	2.3	0.5	1.5
Conditioned reinforcement - actives	0.2	0.3	0.5	-0.7	-0.1
Conditioned reinforcement - inactives	0.6	0.9	1.6	-0.4	1.3
Conditioned locomotion	0.9	1.2	1.8	-1.4	-0.7
Patch foraging indifference point 0 sec	0.6	1.2	1.6	1.3	-0.8
Patch foraging indifference point AUC	1.6	2.4	4.4	-0.5	2.1
Delay disc. indifference point, 0s delay	0.9	1.0	1.5	-1.2	0.7
Delay disc. indifference point, 16s delay	0.4	0.5	0.9	-1.0	-0.1
Delay disc. indifference point, 2s delay	1.1	1.2	1.6	-1.3	0.9
Delay disc. indifference point, 24s delay	3.2	3.6	6.0	-2.4	1.1
Delay disc. indifference point, 4s delay	0.9	1.0	1.1	-1.0	0.9
Delay disc. indifference point, 8s delay	1.7	2.0	3.9	-2.0	0.2
Indifference point function ln k	0.6	1.0	1.7	0.6	-1.3
Indifference point function log k	0.6	1.0	1.7	0.6	-1.3
Patch foraging total patch changes 0 sec	0.2	0.5	0.8	0.9	-0.3
Patch foraging total patch changes 12 sec	0.8	1.0	2.0	-0.2	1.4
Patch foraging total patch changes 18 sec	0.7	1.1	2.2	-0.1	1.5
Patch foraging total patch changes 24 sec	0.7	1.3	1.9	-0.8	1.4
Patch foraging total patch changes 6 sec	0.1	0.1	0.2	0.2	0.5
Patch foraging time to switch 0 sec	0.6	1.2	2.4	0.3	-1.5
Patch foraging water rate 0 sec	0.4	0.8	1.3	-0.6	1.1
Patch foraging water rate 12 sec	0.3	0.6	1.1	-1.0	-0.0
Patch foraging water rate 18 sec	0.2	0.2	0.3	-0.4	-0.6
Patch foraging water rate 24 sec	0.3	0.4	0.8	-0.9	-0.1
Patch foraging water rate 6 sec	0.1	0.2	0.2	-0.3	-0.5
Seeking ratio, delayed vs. immediate footshock	0.2	0.3	0.3	-0.6	-0.5
Distance traveled before self-admin	0.8	1.0	2.0	1.4	0.3
Distance traveled after self-admin	0.2	0.3	0.5	0.2	-0.7
Extensor digitorum longus weight	2.2	8.8	12.4	-2.3	3.5
Bone: elastic displacement	0.1	0.1	0.2	-0.0	-0.4
Bone: elastic work	0.2	0.2	0.4	-0.6	-0.1
Bone: endosteal estimation	0.7	1.5	3.0	-1.7	-0.0
Bone: endosteal perimeter	1.2	2.6	3.1	-1.8	1.4
Epididymis fat weight	3.6	12.5	16.8	-4.1	2.9
Delta time in closed arm before/after self-admin	1.6	1.5	1.8	1.1	-1.4
Delta time in open arm before/after self-admin	0.6	0.6	0.6	-0.8	0.8
Diff in mean of infusions in LGA sessions	2.0	2.4	4.5	2.1	-0.6
Delay discount exponential model param	1.9	2.1	3.9	2.0	-0.7
Extinction: sum of active levers before priming	0.1	0.2	0.3	-0.2	0.5
Active lever presses in extinction session 6	0.7	0.7	1.3	-0.3	1.1
Bone: final force	0.1	0.1	0.2	-0.4	-0.1
Bone: final moment	0.2	0.3	0.5	-0.7	-0.0
Food consumed during 24 hour testing period	0.2	0.3	0.5	-0.7	-0.2
Glucose	2.3	3.6	6.4	-2.5	0.9
Heart weight	1.6	2.5	4.4	2.1	0.8
Delay discount hyperbolic model param	1.9	2.1	3.7	1.9	-0.7
Intermittent access intake day 1-15 change	0.7	1.5	2.6	-1.6	-0.6
Intermittent access intake escalation	0.7	1.5	2.8	-1.7	-0.5
Intermittent access intake escalation 2	1.7	1.9	3.7	-1.9	-0.4
Intermitt. access day 1 inactive lever presses	1.6	6.1	7.0	-2.6	2.3
Intermitt. access day 15 inactive lever presses	0.0	0.0	0.0	-0.1	-0.1
Intermitt. access escalation Index	0.3	0.4	0.7	-0.8	0.3
Intermittent access day 1 total infusions	0.5	0.8	0.8	-0.9	0.9
Intermittent access day 15 total infusions	0.9	1.4	2.4	-1.6	0.6
Intermittent access terminal intake (last 3 days)	1.4	1.8	3.6	-1.9	-0.0
Intermittent access total infusions	1.7	2.0	3.5	-1.9	0.6
Intermittent access day 1 locomotion	0.1	0.1	0.1	-0.4	-0.2
Intermittent access day 15 total locomotion	0.7	1.3	2.4	-1.5	0.5
Intermittent access total locomotion	0.6	0.8	1.1	-1.1	-0.6
Intermittent access standard deviation	0.7	1.4	2.6	-1.6	0.4
Left kidney weight	0.5	2.6	3.9	-1.1	-2.0
Right kidney weight	0.4	1.9	1.9	-1.4	-1.3
Cocaine induced anxiety	1.3	1.9	2.7	1.7	-1.0
Post-drug Anxiety	1.2	1.3	2.5	1.6	0.2
Baseline Anxiety	1.9	2.2	4.1	-0.7	2.0
Tail length	0.4	1.6	2.2	-1.5	1.0
Length with tail	1.2	5.4	7.5	-2.7	1.8
Length without tail	3.6	11.5	13.3	-3.6	3.1
Times rat made contact with spout	1.5	1.8	1.9	-1.3	1.4
Lifetime Intake	1.2	1.4	2.5	-1.6	0.6
Liver weight, left	0.8	1.3	2.0	-1.4	0.8
Liver weight, right	3.7	6.5	12.7	-3.6	0.5
Locomotor activity	0.1	0.2	0.3	0.6	-0.3
Locomotor testing distance	1.0	1.7	2.1	1.2	-1.5
Locomotor testing rearing	0.7	1.4	2.6	0.5	-1.6
Locomotion in novel chamber	2.0	2.6	2.8	1.7	-1.6
Locomotion in novel chamber post-restriction	0.4	0.7	1.0	0.7	-1.0
Fecal boli incidents, locomotor time 1	0.4	0.6	1.2	-1.1	0.1
Change in fecal boli incidents, locomotor task	0.3	0.3	0.5	0.7	0.3
Time >=10cm from walls, locomotor time 1	0.3	0.4	0.6	0.3	-0.8
Bouts of movement, locomotor time 1	0.9	1.0	1.9	-1.4	0.4
Total resting periods, locomotor time 1	1.4	1.6	2.8	-1.7	0.7
Rest time, locomotor task time 1	0.1	0.1	0.1	0.4	0.4
Distance moved, locomotor task time 1	0.8	1.2	2.1	-1.5	0.4
Vertical activity count, locomotor time 1	0.3	0.8	1.5	1.2	-0.2
Time >=10cm from walls, locomotor time 2	0.5	0.7	1.4	-0.0	1.2
Bouts of movement, locomotor time 2	0.1	0.2	0.4	-0.7	0.0
Total resting periods, locomotor time 2	0.2	0.3	0.6	-0.8	-0.2
Rest time, locomotor task time 2	0.7	0.9	1.8	0.0	-1.3
Distance moved, locomotor task time 2	0.3	0.4	0.7	0.2	0.8
Vertical activity count, locomotor time 2	1.1	1.5	1.9	1.0	1.4
Light reinforcement 1	0.4	1.0	2.0	1.4	0.0
Light reinforcement 2	0.3	0.4	0.5	0.7	0.6
Bone: marrow area	0.7	1.5	2.9	-1.7	-0.0
Bone: maximum diameter	1.7	3.2	5.2	-1.1	2.3
Bone: maximum force	0.1	0.1	0.2	-0.5	0.1
Bone: maximum moment	0.2	0.3	0.6	-0.8	0.2
Mean time between licks in bursts	0.1	0.3	0.7	0.1	-0.8
Mean num. licks in bursts	0.5	0.8	1.5	0.4	-1.2
Cd content in liver	5.9	6.6	6.8	2.5	-2.6
Co content in liver	3.8	4.4	5.3	2.3	-1.9
Cu content in liver	0.2	0.2	0.4	-0.6	0.2
Fe content in liver	0.8	1.0	1.9	1.4	-0.1
K content in liver	2.1	2.0	3.1	-1.8	0.9
Mg content in liver	1.8	1.8	2.3	-1.2	1.5
Mn content in liver	0.6	0.7	1.2	0.4	1.1
Na content in liver	0.5	0.5	1.1	0.0	1.0
Rb content in liver	0.4	0.5	0.7	0.9	-0.5
Se content in liver	0.9	1.1	1.3	0.9	-1.2
Sr content in liver	2.0	1.7	3.3	0.4	-1.8
Zn content in liver	0.1	0.1	0.2	-0.4	-0.1
Bone: minimum diameter	1.1	2.1	2.4	-1.3	1.6
Time in familiar zone, hab. session 1	2.8	2.7	4.9	0.7	-2.2
Time in novel zone, hab. session 1	4.5	4.5	6.9	-1.4	2.6
Total zone transitions, hab. session 1	0.6	0.8	1.5	0.1	1.2
Total locomotion distance, hab. session 1	0.4	0.6	1.1	-0.3	1.0
Locomotion velocity, hab. session 1	0.3	0.4	0.8	0.1	0.9
Time in familiar zone, hab. session 2	2.2	2.4	3.0	-1.7	1.3
Time in novel zone, hab. session 2	1.4	1.4	1.5	1.2	-1.1
Total zone transitions, hab. session 2	0.3	0.4	0.8	-0.2	0.9
Total locomotion distance, hab. session 2	0.7	0.9	1.6	-0.4	1.2
Locomotion velocity, hab. session 2	0.6	0.8	1.6	-0.3	1.3
Novel to familiar place preference ratio	0.1	0.1	0.3	-0.5	-0.0
Novelty place preference	0.5	0.6	1.1	-1.1	0.1
Time in novel zone, NPP test	0.9	1.0	1.8	-1.4	0.3
Total zone transitions, NPP test	1.8	2.5	4.8	-0.5	2.2
Total locomotion distance, NPP test	1.6	2.2	4.0	-0.7	2.0
Locomotion velocity, NPP test	0.8	1.2	2.3	-0.3	1.5
Intraocular pressure	0.6	0.8	1.2	-0.7	1.1
Delta distance traveled before/after self-admin	1.6	1.7	2.8	-0.8	-1.7
Delta ambulatory time before/after self-admin	1.3	1.6	1.8	-1.4	-1.2
Parametrial fat weight	3.0	7.1	10.4	-3.2	1.9
Pavlov. Cond. lever latency	0.1	0.2	0.3	-0.0	-0.6
Pavlov. Cond. magazine entry latency	0.8	1.0	1.1	-1.1	1.0
Pavlov. Cond. change in total contacts	0.4	0.5	0.6	-0.6	0.8
Pavlov. Cond. index score	0.8	1.0	1.2	-0.9	1.1
Pavlov. Cond. latency score	0.5	0.7	0.7	-0.8	0.9
Pavlov. Cond. lever contacts	0.1	0.1	0.2	-0.2	0.4
Pavlov. Cond. magazine entry number	1.2	1.5	2.3	1.5	-0.8
Pavlov. Cond. intertrial magazine entries	0.2	0.3	0.4	0.7	0.4
Pavlov. Cond. lever-magazine prob. diff.	0.9	1.1	1.5	-0.9	1.2
Pavlov. Cond. response bias	0.4	0.5	0.5	-0.7	0.7
Pavlov. Cond. lever latency	1.7	2.3	4.4	-0.4	-2.1
Pavlov. Cond. magazine entry latency	1.2	1.5	1.8	-1.4	1.1
Pavlov. Cond. change in total contacts	0.9	1.4	2.8	-0.3	1.7
Pavlov. Cond. index score	1.0	1.4	2.5	-0.5	1.6
Pavlov. Cond. latency score	1.3	1.8	2.7	-0.9	1.7
Pavlov. Cond. lever contacts	1.6	2.2	4.3	0.3	2.1
Pavlov. Cond. magazine entry number	1.5	1.8	2.0	1.4	-1.3
Pavlov. Cond. intertrial magazine entries	0.6	0.9	1.8	1.4	0.0
Pavlov. Cond. lever-magazine prob. diff.	1.2	1.6	2.7	-0.7	1.7
Pavlov. Cond. response bias	1.2	1.6	3.2	0.1	1.8
Time in closed arm before self-admin	0.2	0.3	0.5	-0.4	0.7
Time in closed arm after self-admin	0.9	0.9	1.1	1.1	-0.9
Time in open arm before self-admin	0.3	0.3	0.6	-0.1	0.8
Time in open arm after self-admin	0.9	1.0	1.3	-0.9	1.1
Bone: periosteal estimation	0.9	1.8	2.4	-1.5	1.1
Bone: periosteal perimeter	2.2	3.8	4.4	-1.8	2.1
Bone: post-yield work	0.4	0.6	1.0	-0.6	1.0
Progressive ratio test 1 active lever presses	0.6	0.8	1.3	-1.1	0.5
Progressive ratio test 1 breakpoint	0.6	0.7	1.2	-1.1	0.5
Progressive ratio test 1 inactive lever presses	2.9	4.2	4.4	-2.1	2.0
Progressive ratio test 2 active lever presses	1.8	2.1	4.1	-2.0	0.3
Progressive ratio test 2 breakpoint	1.8	2.1	4.1	-2.0	0.4
Progressive ratio test 2 inactive lever presses	2.2	3.5	6.3	-2.5	0.9
Incentive Sensitization - Responses	1.5	2.1	3.3	-1.8	1.0
Incentive Sensitization - Breakpoint	1.6	2.0	3.3	-1.8	0.9
Sum of active levers in priming session hrs 5-6	0.7	0.6	1.2	-0.2	1.1
Progressive ratio	0.4	0.7	1.3	1.1	0.4
Food seeking constrained by brief footshock	0.4	0.5	0.6	0.8	0.6
Seeking ratio, punishment vs. effort	0.6	0.9	1.2	-1.1	0.8
Retroperitoneal fat weight	5.0	21.1	35.6	-6.0	2.6
Reaction time number correct	0.7	1.3	2.3	-1.5	-0.6
Reaction time mean minus median	0.1	0.3	0.5	-0.2	-0.7
Reaction time mean minus median AUC	0.3	0.6	0.9	-0.6	-1.0
Reaction time num false alarms	1.0	1.4	2.8	-0.1	1.7
Reaction time num false alarms AUC	0.7	1.0	1.7	0.6	1.3
Reaction time trials correct on left	0.7	1.3	2.3	-1.5	-0.6
Reaction time trials on left	0.7	1.3	2.2	-1.5	-0.7
Reaction time mean	0.6	0.9	1.8	0.1	-1.4
Reaction time mean AUC	0.7	1.1	2.0	0.4	-1.4
Median of all reaction times	0.8	1.1	2.2	0.1	-1.5
Reaction time omissions	1.0	1.5	2.9	0.2	-1.7
Reaction time false alarm rate	1.4	1.9	2.6	1.1	1.6
Reaction time premature initiation rate	0.4	0.5	1.0	-0.0	1.0
Reaction time premature initiations	0.2	0.4	0.5	-0.7	0.5
Std. dev. reaction times	0.3	0.5	0.8	-0.4	-0.9
Reaction time trials completed	0.7	1.3	2.2	-1.5	-0.7
Reaction time trials AUC	0.7	1.3	2.3	-1.5	-0.5
Run reversals in cocaine runway, females	1.9	1.9	3.8	-0.2	-1.9
Run reversals in cocaine runway, males	0.2	0.2	0.3	0.6	-0.2
Latency to leave start box in cocaine runway	0.4	0.5	1.0	1.0	-0.0
Latency to leave start box in cocaine runway, F	2.7	3.0	5.6	2.4	-0.7
Latency to leave start box in cocaine runway, M	1.4	1.3	1.9	-1.4	0.9
Std. dev. time between licks in bursts	0.1	0.2	0.3	-0.3	0.5
Total sessions with >9 infusions	0.9	1.0	2.0	-1.4	-0.2
Short access day 1 total inactive lever presses	2.5	3.2	4.4	-2.1	1.4
Short access day 10 total inactive lever presses	0.8	2.0	2.7	-1.6	1.1
Short access day 1 total infusions	0.6	0.8	1.7	-1.3	0.0
Short access day 10 total infusions	0.5	0.6	1.0	-1.0	0.4
Short access total infusions	0.3	0.4	0.9	-0.9	0.2
Short access day 1 locomotion	1.6	2.0	3.9	-2.0	0.2
Short access day 10 total locomotion	0.9	1.8	3.1	-1.8	-0.6
Short access total locomotion	0.8	1.0	1.3	-1.2	-0.8
One hour access (0.3 mA shock)	5.6	6.4	11.4	-3.4	1.2
Compulsive drug intake	0.3	0.3	0.5	-0.5	0.7
One hour access (shock baseline)	1.1	1.7	3.4	-1.8	0.3
Social response proportion	3.7	4.2	5.8	-2.4	-1.6
Social responses	1.2	1.5	2.1	-1.5	-1.0
Social time	1.9	2.5	4.8	-0.5	-2.2
Soleus weight	1.6	4.8	9.0	-3.0	0.8
Bone: stiffness	0.0	0.0	0.0	0.2	-0.2
Tibialis anterior weight	0.7	2.2	3.8	-0.8	1.9
Time to tail flick, vehicle, before self-admin	0.3	0.3	0.5	-0.7	0.2
Time to tail flick, vehicle, after self-admin	0.0	0.0	0.1	-0.1	-0.3
Time to tail flick, test, before self-admin	0.2	0.2	0.4	-0.2	-0.6
Time to tail flick, test, after self-admin	0.4	0.4	0.4	0.6	0.6
Delta time to tail flick, vehicle, before/after SA	0.1	0.1	0.1	0.4	-0.3
Delta time to tail flick, test, before/after SA	0.5	0.5	0.7	0.8	0.6
Tibia length	0.0	0.1	0.2	0.2	-0.5
Ambulatory time before self-admin	0.7	1.0	1.7	1.3	0.6
Ambulatory time after self-admin	0.3	0.3	0.6	-0.8	-0.3
Bone: tissue strength	0.1	0.1	0.1	0.1	-0.3
Total heroin consumption	1.2	1.4	1.8	-1.4	1.0
Bone: trabecular number	1.0	1.7	3.3	-1.8	0.2
Bone: trabecular spacing	0.5	0.7	1.0	0.6	1.0
Bone: trabecular thickness	6.7	8.3	11.7	-3.4	2.2
Bone: trabecular tissue density	0.1	0.2	0.4	0.3	0.6
Water consumed over 24 hours	0.8	1.0	2.0	-1.4	-0.3
Number of responses in last shaping day	0.1	0.1	0.2	-0.3	-0.5