Hub : Genes

Spns2

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	Spns2	0.17	0.1	4.9e-11	0.08	0.07	0.07	0.07	7.4e-09	7.8e-08	4.0e-08	5.7e-08
2	Liver	gene expression	Spns2	0.02	0.02	6.0e-03	0	0.01	0	0	1.1e-01	2.0e-02	1.1e-01	1.0e-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 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	0.7	1.1	1.7	-0.7	-1.3
Area under the delay curve	0.1	0.1	0.1	0.4	0.3
BMI with tail	0.2	0.6	1.0	0.5	-1.0
BMI without tail	0.5	1.0	1.6	0.6	-1.3
Body weight	0.8	3.3	6.1	-0.6	-2.5
Weight adjusted by age	2.5	2.8	3.0	1.7	-1.6
Bone surface	0.8	1.5	2.5	0.6	-1.6
Bone volume	1.1	1.9	3.1	0.9	-1.8
Breakpoint value in progressive ratio session	0.6	0.7	1.3	-0.1	-1.2
Number of licking bursts	0.2	0.2	0.4	-0.3	0.6
Context. condit. distance diff. score	1.0	1.2	2.1	0.5	-1.5
Locomotion velocity, session 1	2.1	2.2	4.4	0.2	-2.1
Locomotion distance, session 1	0.8	1.0	1.1	0.9	-1.0
Locomotion velocity, session 2	0.4	0.5	1.0	-1.0	-0.2
Locomotion distance, session 2	0.3	0.4	0.7	-0.2	-0.8
Locomotion velocity, session 3	1.7	2.0	2.9	-1.0	1.7
Locomotion distance, session 3	0.1	0.1	0.1	-0.4	0.3
Stereotopy head waving bouts, day 3	0.0	0.0	0.0	-0.2	-0.1
Stereotopy head waving duration, day 3	0.6	0.8	1.2	1.1	0.6
Locomotion velocity, session 7	0.0	0.0	0.1	0.3	-0.1
Locomotion distance, session 7	0.0	0.0	0.0	-0.2	-0.0
Stereotopy head waving bouts, day 7	0.9	1.0	1.5	0.7	-1.2
Stereotopy head waving duration, day 7	1.1	1.3	2.0	0.8	-1.4
Locomotion velocity, session 8	0.8	1.0	1.3	0.8	-1.1
Locomotion distance, session 8	1.4	2.1	4.2	0.2	-2.0
Degree of sensitization distance	0.5	0.5	0.7	0.6	-0.8
Degree of sensitization stereotypy	1.1	1.2	2.4	0.3	-1.5
Conditioned locomotion	0.7	0.8	1.6	-0.3	1.3
Cocaine response after cond. corrected	0.6	0.7	1.4	-1.2	0.0
Cocaine response after cond. not corrected	0.4	0.4	0.7	-0.9	-0.2
Cocaine response before conditioning	0.6	0.8	0.8	0.9	-0.9
Saline control response	0.4	0.6	0.6	0.7	-0.8
Bone: connectivity density	0.9	1.4	2.7	-0.2	-1.7
Bone: cortical apparent density	0.9	1.2	1.9	-0.7	1.4
Bone: cortical area	0.3	0.4	0.6	0.5	0.8
Bone: cortical porosity	1.6	1.7	3.4	-1.8	0.3
Bone: cortical porosity	1.4	1.6	2.9	-1.7	0.5
Bone: cortical thickness	1.7	2.8	3.9	-1.3	2.0
Bone: cortical thickness	3.4	4.0	6.0	-2.4	1.4
Bone: cortical tissue density	0.8	1.0	1.5	-0.7	1.2
Condit. Reinf. active minus inactive responses	1.0	1.1	2.1	-1.4	0.4
Condit. Reinf. active-inactive response ratio	0.6	0.7	1.2	-1.1	0.3
Condit. Reinf. active responses	0.7	0.9	1.7	-1.3	0.2
Condit. Reinf. inactive responses	0.0	0.0	0.0	-0.2	0.2
Incentive salience index mean	1.4	1.7	3.4	-1.8	0.2
Condit. Reinf. lever presses	2.0	2.6	5.2	-2.3	-0.3
Condit. Reinf. active minus inactive responses	0.5	0.7	1.3	-1.2	0.1
Condit. Reinf. active-inactive response ratio	0.7	0.8	1.3	-1.2	0.4
Condit. Reinf. active responses	0.2	0.3	0.6	-0.8	0.0
Condit. Reinf. inactive responses	0.1	0.1	0.2	0.5	-0.0
Condit. Reinf. lever presses	0.3	0.4	0.9	0.0	0.9
Condit. Reinf. lever reinforcers received	0.2	0.2	0.4	-0.6	0.1
Conditioned reinforcement - actives	0.8	0.8	0.9	0.9	-1.0
Conditioned reinforcement - inactives	1.8	2.1	2.8	1.7	-1.2
Conditioned locomotion	0.7	0.9	1.8	1.3	0.1
Patch foraging indifference point 0 sec	1.4	2.2	3.6	-1.9	0.9
Patch foraging indifference point AUC	2.0	2.3	4.6	2.1	-0.0
Delay disc. indifference point, 0s delay	1.8	1.9	2.3	1.5	-1.2
Delay disc. indifference point, 16s delay	0.5	0.5	1.0	1.0	0.0
Delay disc. indifference point, 2s delay	0.2	0.2	0.3	-0.2	0.6
Delay disc. indifference point, 24s delay	0.7	0.7	0.7	-0.8	0.8
Delay disc. indifference point, 4s delay	0.4	0.4	0.6	0.8	-0.5
Delay disc. indifference point, 8s delay	0.0	0.0	0.0	0.1	0.1
Indifference point function ln k	5.1	7.1	12.5	-3.5	1.3
Indifference point function log k	5.1	7.1	12.5	-3.5	1.3
Patch foraging total patch changes 0 sec	0.9	1.4	2.4	-1.5	0.7
Patch foraging total patch changes 12 sec	0.9	1.2	2.0	1.4	-0.5
Patch foraging total patch changes 18 sec	0.4	0.6	1.0	1.0	-0.4
Patch foraging total patch changes 24 sec	0.5	0.6	1.2	1.1	0.2
Patch foraging total patch changes 6 sec	1.2	1.8	3.7	1.9	-0.1
Patch foraging time to switch 0 sec	1.2	1.9	1.9	1.4	-1.4
Patch foraging water rate 0 sec	0.6	0.9	1.2	-0.8	1.1
Patch foraging water rate 12 sec	0.3	0.5	1.0	0.1	-1.0
Patch foraging water rate 18 sec	0.9	1.2	2.1	-1.4	-0.5
Patch foraging water rate 24 sec	0.0	0.0	0.0	0.1	-0.2
Patch foraging water rate 6 sec	0.1	0.2	0.2	-0.5	0.5
Seeking ratio, delayed vs. immediate footshock	0.5	0.6	1.0	-0.4	1.0
Distance traveled before self-admin	0.7	0.8	1.3	1.2	0.4
Distance traveled after self-admin	5.5	6.1	9.2	3.0	-1.7
Extensor digitorum longus weight	3.0	11.9	12.0	3.4	-3.5
Bone: elastic displacement	0.3	0.4	0.8	0.2	0.9
Bone: elastic work	1.0	1.3	2.4	-0.5	1.6
Bone: endosteal estimation	2.6	5.7	9.5	3.1	-1.4
Bone: endosteal perimeter	2.7	5.6	9.0	3.0	-1.5
Epididymis fat weight	3.0	7.0	10.8	1.8	-3.3
Delta time in closed arm before/after self-admin	0.9	0.9	1.5	1.2	-0.5
Delta time in open arm before/after self-admin	0.6	0.6	0.8	0.6	-0.9
Diff in mean of infusions in LGA sessions	0.7	0.8	1.2	-1.1	-0.6
Delay discount exponential model param	0.1	0.1	0.1	-0.0	-0.4
Extinction: sum of active levers before priming	1.4	1.4	2.7	0.0	-1.7
Active lever presses in extinction session 6	1.1	1.1	1.6	0.7	-1.3
Bone: final force	0.5	0.8	1.0	1.0	-0.7
Bone: final moment	0.5	0.8	1.3	1.1	-0.6
Food consumed during 24 hour testing period	0.5	0.7	1.3	-1.1	0.2
Glucose	1.3	1.9	2.9	0.9	1.7
Heart weight	0.8	1.1	1.3	0.9	-1.1
Delay discount hyperbolic model param	0.1	0.1	0.1	-0.1	-0.3
Intermittent access intake day 1-15 change	1.6	1.6	3.1	1.8	0.3
Intermittent access intake escalation	1.6	1.5	2.8	1.7	0.5
Intermittent access intake escalation 2	1.1	1.1	1.3	0.9	1.1
Intermitt. access day 1 inactive lever presses	0.5	0.5	0.8	0.5	0.9
Intermitt. access day 15 inactive lever presses	0.1	0.2	0.3	-0.5	0.1
Intermitt. access escalation Index	1.1	1.0	1.8	-0.3	-1.4
Intermittent access day 1 total infusions	1.8	2.1	2.1	1.5	-1.4
Intermittent access day 15 total infusions	4.8	5.3	9.6	3.1	-1.1
Intermittent access terminal intake (last 3 days)	3.7	4.0	5.5	2.3	-1.6
Intermittent access total infusions	2.5	2.8	4.4	2.1	-1.1
Intermittent access day 1 locomotion	2.2	2.3	3.2	1.8	-1.2
Intermittent access day 15 total locomotion	1.6	1.7	3.3	1.8	-0.3
Intermittent access total locomotion	1.0	1.2	1.9	1.4	-0.7
Intermittent access standard deviation	4.4	4.7	9.3	3.0	-0.1
Left kidney weight	0.1	0.4	0.8	0.9	0.0
Right kidney weight	0.1	0.2	0.4	0.6	0.1
Cocaine induced anxiety	1.5	1.8	2.1	-1.2	1.4
Post-drug Anxiety	0.7	0.8	1.2	-1.1	0.6
Baseline Anxiety	0.5	0.6	0.8	0.6	-0.9
Tail length	1.5	4.6	8.8	-0.5	-3.0
Length with tail	0.8	3.1	5.0	-1.1	-2.2
Length without tail	0.7	1.5	2.7	-0.6	-1.6
Times rat made contact with spout	1.0	1.2	1.8	-1.3	0.8
Lifetime Intake	3.7	4.2	6.4	2.5	-1.4
Liver weight, left	0.4	0.6	0.7	-0.8	-0.7
Liver weight, right	0.7	1.2	2.2	0.3	-1.5
Locomotor activity	0.5	0.9	0.9	0.9	-0.9
Locomotor testing distance	2.7	4.4	6.0	2.5	-1.7
Locomotor testing rearing	3.2	4.9	7.8	2.8	-1.4
Locomotion in novel chamber	1.3	1.6	1.9	1.4	1.1
Locomotion in novel chamber post-restriction	0.3	0.4	0.5	-0.4	0.7
Fecal boli incidents, locomotor time 1	0.3	0.3	0.4	-0.6	0.5
Change in fecal boli incidents, locomotor task	0.5	0.5	0.6	-0.7	0.6
Time >=10cm from walls, locomotor time 1	0.3	0.3	0.5	-0.7	0.4
Bouts of movement, locomotor time 1	0.6	0.6	1.2	-1.1	0.3
Total resting periods, locomotor time 1	1.5	1.7	2.7	-1.6	0.8
Rest time, locomotor task time 1	0.5	0.6	0.9	-0.5	0.9
Distance moved, locomotor task time 1	0.9	1.0	1.1	1.1	-0.9
Vertical activity count, locomotor time 1	0.9	1.0	1.1	0.9	-1.0
Time >=10cm from walls, locomotor time 2	0.7	0.7	0.9	-0.9	0.7
Bouts of movement, locomotor time 2	1.0	1.1	1.5	-1.2	0.8
Total resting periods, locomotor time 2	0.7	0.7	1.2	-1.1	0.5
Rest time, locomotor task time 2	0.9	1.0	1.0	-1.0	1.0
Distance moved, locomotor task time 2	1.6	1.9	3.0	1.7	-0.8
Vertical activity count, locomotor time 2	0.6	0.6	0.8	0.9	-0.7
Light reinforcement 1	1.1	2.1	2.7	1.6	-1.2
Light reinforcement 2	0.1	0.2	0.4	0.6	0.0
Bone: marrow area	2.6	5.6	9.3	3.1	-1.3
Bone: maximum diameter	0.7	1.3	2.7	1.6	-0.1
Bone: maximum force	0.5	0.9	1.4	1.2	-0.7
Bone: maximum moment	0.7	1.1	1.9	1.4	-0.6
Mean time between licks in bursts	1.3	1.8	3.0	0.7	-1.7
Mean num. licks in bursts	0.1	0.1	0.2	-0.4	-0.2
Cd content in liver	1.0	1.1	1.3	0.9	-1.2
Co content in liver	0.2	0.2	0.3	0.3	-0.6
Cu content in liver	2.4	2.8	4.2	-2.0	1.2
Fe content in liver	0.4	0.5	0.6	-0.8	-0.6
K content in liver	0.4	0.4	0.4	-0.6	-0.6
Mg content in liver	0.0	0.0	0.0	0.2	0.2
Mn content in liver	1.3	1.5	2.6	-1.6	0.6
Na content in liver	0.2	0.2	0.3	0.5	0.3
Rb content in liver	0.6	0.8	1.1	1.0	-0.7
Se content in liver	0.9	1.1	1.6	-0.8	1.3
Sr content in liver	1.6	1.5	1.8	1.1	-1.3
Zn content in liver	0.1	0.2	0.3	-0.3	0.5
Bone: minimum diameter	1.7	3.1	4.8	2.2	-1.2
Time in familiar zone, hab. session 1	0.2	0.2	0.3	0.6	0.2
Time in novel zone, hab. session 1	0.4	0.3	0.7	-0.8	0.0
Total zone transitions, hab. session 1	4.0	5.6	7.9	2.8	-1.8
Total locomotion distance, hab. session 1	0.3	0.4	0.4	0.6	-0.6
Locomotion velocity, hab. session 1	0.3	0.5	0.6	0.8	-0.6
Time in familiar zone, hab. session 2	0.2	0.2	0.4	-0.6	-0.1
Time in novel zone, hab. session 2	0.3	0.3	0.6	-0.1	0.8
Total zone transitions, hab. session 2	2.0	2.6	2.7	1.6	-1.6
Total locomotion distance, hab. session 2	0.4	0.5	0.5	0.7	-0.7
Locomotion velocity, hab. session 2	0.4	0.5	0.6	0.8	-0.7
Novel to familiar place preference ratio	0.1	0.1	0.2	0.4	0.2
Novelty place preference	0.0	0.0	0.0	0.1	0.1
Time in novel zone, NPP test	0.0	0.0	0.0	-0.1	-0.1
Total zone transitions, NPP test	2.6	3.7	4.7	2.2	-1.7
Total locomotion distance, NPP test	0.3	0.4	0.9	0.9	0.0
Locomotion velocity, NPP test	0.4	0.6	0.9	1.0	0.5
Intraocular pressure	1.2	1.7	3.4	1.8	-0.0
Delta distance traveled before/after self-admin	3.4	3.7	4.9	1.6	-2.2
Delta ambulatory time before/after self-admin	2.2	2.4	3.3	1.2	-1.8
Parametrial fat weight	9.5	18.5	29.9	2.7	-5.5
Pavlov. Cond. lever latency	1.9	2.4	4.0	2.0	-0.9
Pavlov. Cond. magazine entry latency	3.0	3.9	7.2	-2.7	0.7
Pavlov. Cond. change in total contacts	2.0	2.1	2.3	-1.5	1.4
Pavlov. Cond. index score	2.1	2.7	5.1	-2.3	0.5
Pavlov. Cond. latency score	2.4	3.0	5.9	-2.4	0.4
Pavlov. Cond. lever contacts	1.4	1.7	3.0	-1.7	0.6
Pavlov. Cond. magazine entry number	1.6	1.9	3.3	1.8	-0.8
Pavlov. Cond. intertrial magazine entries	2.6	3.2	5.2	2.3	-1.1
Pavlov. Cond. lever-magazine prob. diff.	2.0	2.4	4.5	-2.1	0.6
Pavlov. Cond. response bias	1.8	2.2	4.0	-2.0	0.7
Pavlov. Cond. lever latency	1.5	2.0	3.6	0.6	-1.9
Pavlov. Cond. magazine entry latency	0.8	0.9	1.2	-0.8	1.1
Pavlov. Cond. change in total contacts	0.6	0.9	1.3	-0.7	1.1
Pavlov. Cond. index score	1.1	1.4	2.7	-0.1	1.6
Pavlov. Cond. latency score	1.3	1.6	3.2	-0.0	1.8
Pavlov. Cond. lever contacts	0.5	0.7	1.3	-0.2	1.1
Pavlov. Cond. magazine entry number	0.6	0.7	1.2	0.4	-1.1
Pavlov. Cond. intertrial magazine entries	0.8	1.0	1.6	0.7	-1.3
Pavlov. Cond. lever-magazine prob. diff.	1.1	1.4	2.7	-0.2	1.7
Pavlov. Cond. response bias	0.7	1.0	1.8	-0.5	1.3
Time in closed arm before self-admin	0.8	0.9	1.6	-1.3	-0.5
Time in closed arm after self-admin	0.0	0.0	0.0	0.0	0.1
Time in open arm before self-admin	1.1	1.2	2.4	0.1	1.5
Time in open arm after self-admin	0.8	0.9	1.6	1.3	0.3
Bone: periosteal estimation	1.3	2.6	4.9	2.2	-0.6
Bone: periosteal perimeter	0.8	1.4	2.6	1.6	-0.4
Bone: post-yield work	0.4	0.6	1.2	0.0	-1.1
Progressive ratio test 1 active lever presses	1.3	1.4	1.9	1.0	-1.4
Progressive ratio test 1 breakpoint	1.9	1.9	3.0	0.9	-1.7
Progressive ratio test 1 inactive lever presses	1.5	1.7	2.7	1.6	-0.8
Progressive ratio test 2 active lever presses	0.7	0.8	0.9	0.8	-0.9
Progressive ratio test 2 breakpoint	0.4	0.4	0.6	0.6	-0.8
Progressive ratio test 2 inactive lever presses	2.0	2.3	3.2	1.8	-1.2
Incentive Sensitization - Responses	0.1	0.1	0.2	0.2	-0.4
Incentive Sensitization - Breakpoint	0.1	0.1	0.1	0.2	-0.4
Sum of active levers in priming session hrs 5-6	1.2	1.2	1.5	-0.9	-1.2
Progressive ratio	0.6	0.6	1.2	1.1	-0.2
Food seeking constrained by brief footshock	0.1	0.2	0.2	-0.4	0.5
Seeking ratio, punishment vs. effort	0.9	1.1	1.9	-1.4	0.6
Retroperitoneal fat weight	0.2	0.6	1.1	1.1	-0.1
Reaction time number correct	0.1	0.2	0.3	-0.3	-0.5
Reaction time mean minus median	0.6	0.7	1.4	-0.3	1.2
Reaction time mean minus median AUC	0.1	0.2	0.4	-0.1	0.6
Reaction time num false alarms	1.0	1.3	1.7	-0.9	1.3
Reaction time num false alarms AUC	0.8	1.0	1.6	-0.7	1.2
Reaction time trials correct on left	0.1	0.2	0.3	-0.3	-0.5
Reaction time trials on left	0.1	0.2	0.2	-0.3	-0.5
Reaction time mean	0.2	0.3	0.5	-0.3	0.7
Reaction time mean AUC	0.5	0.7	1.3	-0.3	1.1
Median of all reaction times	0.1	0.1	0.2	-0.1	0.5
Reaction time omissions	0.3	0.4	0.6	0.8	-0.3
Reaction time false alarm rate	0.6	0.9	1.5	-0.5	1.2
Reaction time premature initiation rate	1.4	1.9	3.5	-1.9	0.5
Reaction time premature initiations	1.3	1.8	3.5	-1.9	0.2
Std. dev. reaction times	1.1	1.5	2.4	-0.8	1.5
Reaction time trials completed	0.1	0.2	0.2	-0.3	-0.5
Reaction time trials AUC	0.1	0.1	0.2	-0.3	-0.4
Run reversals in cocaine runway, females	0.1	0.1	0.1	-0.1	0.4
Run reversals in cocaine runway, males	1.6	1.6	3.1	1.8	-0.2
Latency to leave start box in cocaine runway	0.0	0.0	0.1	-0.3	0.1
Latency to leave start box in cocaine runway, F	0.2	0.2	0.3	-0.6	-0.2
Latency to leave start box in cocaine runway, M	0.2	0.2	0.3	0.5	-0.3
Std. dev. time between licks in bursts	0.4	0.5	0.8	0.5	-0.9
Total sessions with >9 infusions	2.8	3.0	3.8	2.0	-1.5
Short access day 1 total inactive lever presses	0.3	0.3	0.5	0.7	-0.4
Short access day 10 total inactive lever presses	0.1	0.1	0.2	-0.5	0.2
Short access day 1 total infusions	4.0	4.3	8.1	2.8	-0.7
Short access day 10 total infusions	1.5	1.6	2.1	1.4	-1.1
Short access total infusions	4.1	4.6	7.7	2.8	-1.2
Short access day 1 locomotion	1.3	1.4	2.8	1.7	-0.1
Short access day 10 total locomotion	0.8	0.9	1.9	1.4	-0.2
Short access total locomotion	1.0	1.0	2.0	1.4	-0.2
One hour access (0.3 mA shock)	1.5	1.7	2.3	1.5	-1.0
Compulsive drug intake	1.1	1.1	2.0	-1.4	0.3
One hour access (shock baseline)	2.3	2.6	4.0	2.0	-1.1
Social response proportion	2.5	2.7	4.4	-2.1	-1.0
Social responses	1.6	2.0	3.9	0.4	-2.0
Social time	1.1	1.5	3.0	0.0	-1.7
Soleus weight	2.3	6.7	13.3	0.4	-3.6
Bone: stiffness	1.7	2.6	4.8	0.7	-2.2
Tibialis anterior weight	3.1	10.5	15.9	2.3	-4.0
Time to tail flick, vehicle, before self-admin	0.7	0.8	0.9	-0.8	-1.0
Time to tail flick, vehicle, after self-admin	0.1	0.1	0.2	0.4	-0.3
Time to tail flick, test, before self-admin	3.3	3.2	5.6	-2.4	0.9
Time to tail flick, test, after self-admin	0.7	0.8	1.4	-1.2	0.3
Delta time to tail flick, vehicle, before/after SA	1.2	1.1	2.1	1.5	0.4
Delta time to tail flick, test, before/after SA	1.4	1.2	2.2	1.5	-0.5
Tibia length	0.7	2.0	3.9	-2.0	-0.5
Ambulatory time before self-admin	0.4	0.4	0.5	0.7	0.5
Ambulatory time after self-admin	2.7	2.9	2.9	1.7	-1.7
Bone: tissue strength	0.2	0.2	0.3	0.5	0.4
Total heroin consumption	1.7	2.0	2.6	-1.2	-1.6
Bone: trabecular number	0.5	0.9	1.1	-1.1	-0.8
Bone: trabecular spacing	0.3	0.4	0.7	0.8	0.4
Bone: trabecular thickness	0.2	0.2	0.4	-0.1	-0.6
Bone: trabecular tissue density	1.5	2.1	3.8	-0.6	2.0
Water consumed over 24 hours	3.2	3.8	6.6	-2.6	1.0
Number of responses in last shaping day	1.0	1.0	2.0	1.4	0.3