Hub : Genes

Vdr

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	ENSRNOG00000054420	0.42	0.18	0e+00	0.26	0.25	0.25	0.26	1.2e-28	2.6e-27	9.6e-28	2.6e-28

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
BMI with tail	5.0	16.2	16.2	-4.0
BMI without tail	0.1	0.1	0.1	-0.4
Body weight	7.6	32.0	32.0	-5.7
Epididymis fat weight	0.5	1.2	1.2	-1.1
Glucose	0.1	0.1	0.1	-0.3
Heart weight	0.0	0.0	0.0	-0.0
Left kidney weight	0.4	1.1	1.1	-1.0
Right kidney weight	3.1	8.7	8.7	-3.0
Tail length	0.0	0.1	0.1	0.3
Length with tail	2.3	8.4	8.4	-2.9
Length without tail	8.6	18.7	18.7	-4.3
Liver weight, left	1.7	2.8	2.8	-1.7
Liver weight, right	1.9	3.2	3.2	-1.8
Parametrial fat weight	1.0	1.9	1.9	1.4
Retroperitoneal fat weight	0.0	0.2	0.2	0.4
Intraocular pressure	11.4	16.1	16.1	4.0
Extensor digitorum longus weight	6.2	24.9	24.9	-5.0
Soleus weight	1.2	3.5	3.5	-1.9
Tibialis anterior weight	2.7	9.4	9.4	-3.1
Tibia length	5.8	16.4	16.4	-4.0
Number of licking bursts	0.2	0.2	0.2	0.5
Food consumed during 24 hour testing period	1.2	1.5	1.5	-1.2
Times rat made contact with spout	0.1	0.1	0.1	-0.3
Mean time between licks in bursts	0.5	0.7	0.7	0.9
Mean num. licks in bursts	0.0	0.0	0.0	-0.2
Std. dev. time between licks in bursts	1.2	1.4	1.4	1.2
Water consumed over 24 hours	0.2	0.2	0.2	-0.4
Indifference point 0 sec	1.3	2.1	2.1	1.4
Indifference point AUC	0.2	0.3	0.3	0.5
Indifference point function ln k	3.9	5.5	5.5	-2.4
Indifference point function log k	3.9	5.5	5.5	-2.4
Delay discounting total patch changes 0 sec	1.3	2.1	2.1	1.4
Delay discounting total patch changes 12 sec	1.5	2.0	2.0	1.4
Delay discounting total patch changes 18 sec	3.6	4.7	4.7	2.2
Delay discounting total patch changes 24 sec	1.2	1.6	1.6	1.2
Delay discounting total patch changes 6 sec	2.8	4.2	4.2	2.1
Delay discounting time to switch 0 sec	3.4	5.3	5.3	2.3
Delay discounting water rate 0 sec	4.9	7.8	7.8	-2.8
Delay discounting water rate 12 sec	3.8	5.6	5.6	-2.4
Delay discounting water rate 18 sec	0.8	1.1	1.1	-1.0
Delay discounting water rate 24 sec	3.5	4.9	4.9	-2.2
Delay discounting water rate 6 sec	5.0	7.2	7.2	-2.7
Locomotor activity	0.8	1.3	1.3	1.2
Locomotor testing distance	2.5	4.1	4.1	2.0
Locomotor testing rearing	2.6	4.1	4.1	2.0
Light reinforcement 1	3.1	5.7	5.7	2.4
Light reinforcement 2	1.0	1.4	1.4	1.2
Reaction time number correct	0.5	0.6	0.6	-0.8
Reaction time mean minus median	9.6	12.4	12.4	3.5
Reaction time mean minus median AUC	7.2	9.2	9.2	3.0
Reaction time num false alarms	1.5	2.1	2.1	1.4
Reaction time num false alarms AUC	2.6	3.7	3.7	1.9
Reaction time trials correct on left	0.5	0.6	0.6	-0.8
Reaction time trials on left	0.3	0.4	0.4	-0.6
Reaction time mean	1.0	1.3	1.3	1.2
Reaction time mean AUC	0.6	0.8	0.8	0.9
Median of all reaction times	0.0	0.0	0.0	0.2
Reaction time omissions	10.8	14.5	14.5	3.8
Reaction time false alarm rate	1.9	2.7	2.7	1.7
Reaction time premature initiation rate	4.9	6.6	6.6	2.6
Reaction time premature initiations	2.9	4.2	4.2	2.0
Std. dev. reaction times	7.3	10.1	10.1	3.2
Reaction time trials completed	0.3	0.4	0.4	-0.6
Reaction time trials AUC	0.7	1.0	1.0	-1.0
Social response proportion	0.9	0.9	0.9	1.0
Social responses	9.1	11.8	11.8	3.4
Social time	0.8	1.0	1.0	1.0
Conditioned locomotion	0.0	0.0	0.0	0.1
Cocaine response after cond. corrected	0.0	0.0	0.0	-0.2
Cocaine response after cond. not corrected	0.9	1.0	1.0	1.0
Cocaine response before conditioning	7.2	8.8	8.8	3.0
Saline control response	0.2	0.3	0.3	0.5
Condit. Reinf. active minus inactive responses	0.0	0.0	0.0	0.1
Condit. Reinf. active-inactive response ratio	0.2	0.2	0.2	0.5
Condit. Reinf. active responses	0.3	0.5	0.5	0.7
Condit. Reinf. inactive responses	1.2	1.5	1.5	1.2
Condit. Reinf. lever presses	0.0	0.1	0.1	0.2
Condit. Reinf. lever reinforcers received	0.7	0.9	0.9	1.0
Pavlov. Cond. lever latency	0.1	0.2	0.2	-0.4
Pavlov. Cond. magazine entry latency	0.2	0.2	0.2	-0.5
Pavlov. Cond. change in total contacts	0.5	0.6	0.6	-0.8
Pavlov. Cond. index score	0.0	0.0	0.0	-0.2
Pavlov. Cond. latency score	0.1	0.1	0.1	-0.3
Pavlov. Cond. lever contacts	0.4	0.6	0.6	0.8
Pavlov. Cond. magazine entry number	0.9	1.2	1.2	1.1
Pavlov. Cond. intertrial magazine entries	2.2	2.8	2.8	1.7
Pavlov. Cond. lever-magazine prob. diff.	0.1	0.2	0.2	-0.4
Pavlov. Cond. response bias	0.3	0.4	0.4	0.6
Conditioned reinforcement - actives	1.7	1.7	1.7	1.3
Conditioned reinforcement - inactives	1.2	1.4	1.4	1.2
Conditioned locomotion	0.3	0.4	0.4	0.6
Intermittent access intake day 1-15 change	1.1	1.1	1.1	1.0
Intermittent access intake escalation	0.7	0.7	0.7	0.8
Intermittent access intake escalation 2	1.1	1.1	1.1	1.1
Intermitt. access day 1 inactive lever presses	3.3	3.6	3.6	1.9
Intermitt. access day 15 inactive lever presses	0.9	1.0	1.0	1.0
Intermitt. access escalation Index	0.4	0.3	0.3	0.6
Intermittent access day 1 total infusions	1.3	1.5	1.5	1.2
Intermittent access day 15 total infusions	2.5	2.8	2.8	1.7
Intermittent access terminal intake (last 3 days)	2.6	2.8	2.8	1.7
Intermittent access total infusions	2.5	2.8	2.8	1.7
Intermittent access day 1 locomotion	1.0	1.0	1.0	1.0
Intermittent access day 15 total locomotion	0.9	1.0	1.0	1.0
Intermittent access total locomotion	2.6	2.9	2.9	1.7
Intermittent access standard deviation	0.5	0.5	0.5	0.7
Cocaine induced anxiety	0.9	1.0	1.0	-1.0
Post-drug Anxiety	4.1	4.5	4.5	-2.1
Baseline Anxiety	1.5	1.5	1.5	-1.2
Lifetime Intake	2.0	2.2	2.2	1.5
Incentive Sensitization - Responses	0.1	0.1	0.1	-0.3
Incentive Sensitization - Breakpoint	0.0	0.0	0.0	-0.1
Progressive ratio test 1 active lever presses	3.8	4.0	4.0	2.0
Progressive ratio test 1 breakpoint	3.4	3.5	3.5	1.9
Progressive ratio test 1 inactive lever presses	2.4	2.6	2.6	1.6
Progressive ratio test 2 active lever presses	1.8	2.0	2.0	1.4
Progressive ratio test 2 breakpoint	2.5	2.7	2.7	1.7
Progressive ratio test 2 inactive lever presses	2.8	3.2	3.2	1.8
Total sessions with >9 infusions	0.4	0.4	0.4	0.6
Short access day 1 total inactive lever presses	1.0	1.1	1.1	1.1
Short access day 10 total inactive lever presses	0.5	0.5	0.5	0.7
Short access day 1 total infusions	0.0	0.0	0.0	-0.2
Short access day 10 total infusions	0.6	0.6	0.6	0.8
Short access total infusions	0.2	0.2	0.2	0.4
Short access day 1 locomotion	0.0	0.0	0.0	-0.2
Short access day 10 total locomotion	0.1	0.1	0.1	0.3
Short access total locomotion	0.1	0.1	0.1	0.3
Compulsive drug intake	0.6	0.6	0.6	-0.8
One hour access (0.3 mA shock)	0.2	0.2	0.2	0.5
One hour access (shock baseline)	0.0	0.0	0.0	0.1
Number of responses in last shaping day	0.4	0.4	0.4	-0.6
Context. condit. distance diff. score	0.4	0.5	0.5	-0.7
Locomotion velocity, session 1	0.4	0.5	0.5	0.7
Locomotion distance, session 1	2.6	3.4	3.4	1.9
Locomotion velocity, session 2	0.2	0.2	0.2	0.5
Locomotion distance, session 2	2.1	3.1	3.1	1.7
Locomotion velocity, session 3	2.9	3.4	3.4	1.8
Locomotion distance, session 3	5.3	5.7	5.7	2.4
Stereotopy head waving bouts, day 3	0.8	0.9	0.9	-1.0
Stereotopy head waving duration, day 3	0.2	0.3	0.3	-0.5
Locomotion velocity, session 7	0.0	0.0	0.0	0.1
Locomotion distance, session 7	1.1	1.4	1.4	1.2
Stereotopy head waving bouts, day 7	1.0	1.1	1.1	-1.1
Stereotopy head waving duration, day 7	1.7	2.1	2.1	-1.4
Locomotion velocity, session 8	0.2	0.2	0.2	-0.5
Locomotion distance, session 8	0.9	1.3	1.3	1.1
Degree of sensitization distance	0.9	0.9	0.9	-1.0
Degree of sensitization stereotypy	0.6	0.7	0.7	-0.8
Condit. Reinf. active minus inactive responses	0.1	0.1	0.1	0.3
Condit. Reinf. active-inactive response ratio	0.1	0.1	0.1	-0.3
Condit. Reinf. active responses	0.6	0.7	0.7	0.8
Condit. Reinf. inactive responses	2.9	3.4	3.4	1.8
Incentive salience index mean	0.0	0.0	0.0	-0.1
Condit. Reinf. lever presses	0.1	0.2	0.2	-0.4
Time in familiar zone, hab. session 1	0.1	0.1	0.1	0.4
Time in novel zone, hab. session 1	0.0	0.0	0.0	-0.2
Total zone transitions, hab. session 1	0.3	0.4	0.4	0.6
Total locomotion distance, hab. session 1	0.0	0.1	0.1	0.3
Locomotion velocity, hab. session 1	0.0	0.0	0.0	0.2
Time in familiar zone, hab. session 2	0.0	0.0	0.0	-0.1
Time in novel zone, hab. session 2	0.0	0.0	0.0	0.1
Total zone transitions, hab. session 2	0.0	0.1	0.1	0.2
Total locomotion distance, hab. session 2	0.1	0.2	0.2	0.4
Locomotion velocity, hab. session 2	0.0	0.0	0.0	0.2
Novel to familiar place preference ratio	1.0	1.1	1.1	-1.0
Novelty place preference	0.5	0.6	0.6	-0.7
Time in novel zone, NPP test	0.3	0.4	0.4	-0.6
Total zone transitions, NPP test	0.9	1.3	1.3	1.2
Total locomotion distance, NPP test	2.5	3.5	3.5	1.9
Locomotion velocity, NPP test	1.3	1.9	1.9	1.4
Pavlov. Cond. lever latency	0.0	0.1	0.1	-0.2
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	0.1
Pavlov. Cond. change in total contacts	0.0	0.0	0.0	0.0
Pavlov. Cond. index score	0.0	0.1	0.1	-0.2
Pavlov. Cond. latency score	0.0	0.0	0.0	-0.1
Pavlov. Cond. lever contacts	0.4	0.5	0.5	0.7
Pavlov. Cond. magazine entry number	0.0	0.0	0.0	-0.1
Pavlov. Cond. intertrial magazine entries	0.4	0.5	0.5	0.7
Pavlov. Cond. lever-magazine prob. diff.	0.3	0.4	0.4	-0.6
Pavlov. Cond. response bias	0.1	0.1	0.1	0.3
Bone: apparent density	7.6	12.6	12.6	-3.5
Bone surface	10.3	18.1	18.1	-4.3
Bone volume	6.7	11.4	11.4	-3.4
Bone: connectivity density	5.7	8.9	8.9	-3.0
Bone: cortical apparent density	0.6	0.8	0.8	0.9
Bone: cortical area	10.2	15.5	15.5	-3.9
Bone: cortical porosity	2.3	2.5	2.5	1.6
Bone: cortical porosity	2.8	3.0	3.0	1.7
Bone: cortical thickness	4.2	6.9	6.9	-2.6
Bone: cortical thickness	0.3	0.4	0.4	-0.6
Bone: cortical tissue density	0.8	1.0	1.0	1.0
Bone: elastic displacement	5.2	5.9	5.9	2.4
Bone: elastic work	0.1	0.2	0.2	0.4
Bone: endosteal estimation	7.8	16.8	16.8	-4.1
Bone: endosteal perimeter	7.2	14.9	14.9	-3.9
Bone: final force	10.2	16.7	16.7	-4.1
Bone: final moment	10.2	16.8	16.8	-4.1
Bone: marrow area	7.9	17.0	17.0	-4.1
Bone: maximum diameter	5.3	9.6	9.6	-3.1
Bone: maximum force	12.8	22.2	22.2	-4.7
Bone: maximum moment	12.7	22.1	22.1	-4.7
Bone: minimum diameter	8.0	14.8	14.8	-3.9
Bone: periosteal estimation	12.4	25.3	25.3	-5.0
Bone: periosteal perimeter	11.4	18.8	18.8	-4.3
Bone: post-yield work	8.8	12.0	12.0	-3.5
Bone: stiffness	16.1	25.4	25.4	-5.0
Bone: tissue strength	0.2	0.2	0.2	-0.4
Bone: trabecular number	4.0	6.2	6.2	-2.5
Bone: trabecular spacing	1.1	1.4	1.4	1.2
Bone: trabecular thickness	0.3	0.4	0.4	0.6
Bone: trabecular tissue density	0.1	0.2	0.2	0.5
Breakpoint value in progressive ratio session	0.0	0.0	0.0	-0.2
Distance traveled before self-admin	1.0	1.1	1.1	1.0
Distance traveled after self-admin	0.1	0.1	0.1	0.3
Delta time in closed arm before/after self-admin	0.1	0.1	0.1	-0.3
Delta time in open arm before/after self-admin	4.0	3.8	3.8	2.0
Diff in mean of infusions in LGA sessions	1.0	1.1	1.1	-1.0
Extinction: sum of active levers before priming	0.4	0.4	0.4	-0.6
Active lever presses in extinction session 6	0.4	0.4	0.4	-0.6
Delta distance traveled before/after self-admin	0.1	0.1	0.1	-0.4
Delta ambulatory time before/after self-admin	0.0	0.0	0.0	-0.2
Time in closed arm before self-admin	1.0	1.1	1.1	-1.1
Time in closed arm after self-admin	0.3	0.3	0.3	-0.6
Time in open arm before self-admin	1.1	1.2	1.2	-1.1
Time in open arm after self-admin	0.2	0.2	0.2	0.5
Sum of active levers in priming session hrs 5-6	0.3	0.3	0.3	0.5
Time to tail flick, vehicle, before self-admin	1.5	1.5	1.5	1.2
Time to tail flick, vehicle, after self-admin	0.1	0.1	0.1	-0.2
Time to tail flick, test, before self-admin	0.7	0.7	0.7	0.8
Time to tail flick, test, after self-admin	0.1	0.1	0.1	-0.3
Delta time to tail flick, vehicle, before/after SA	0.4	0.4	0.4	-0.7
Delta time to tail flick, test, before/after SA	0.5	0.4	0.4	-0.7
Ambulatory time before self-admin	3.8	3.9	3.9	2.0
Ambulatory time after self-admin	1.5	1.6	1.6	1.3
Total heroin consumption	2.2	2.6	2.6	-1.6
Area under the delay curve	1.7	1.8	1.8	-1.3
Delay disc. indifference point, 0s delay	1.7	1.9	1.9	-1.4
Delay disc. indifference point, 16s delay	1.8	1.8	1.8	-1.3
Delay disc. indifference point, 2s delay	1.0	1.1	1.1	-1.1
Delay disc. indifference point, 24s delay	1.6	1.6	1.6	-1.3
Delay disc. indifference point, 4s delay	0.5	0.5	0.5	-0.7
Delay disc. indifference point, 8s delay	3.9	4.0	4.0	-2.0
Delay discount exponential model param	1.4	1.5	1.5	1.2
Delay discount hyperbolic model param	1.3	1.4	1.4	1.2
Fecal boli incidents, locomotor time 1	0.7	0.8	0.8	0.9
Change in fecal boli incidents, locomotor task	0.9	0.8	0.8	-0.9
Time >=10cm from walls, locomotor time 1	0.6	0.6	0.6	-0.8
Bouts of movement, locomotor time 1	0.2	0.2	0.2	-0.5
Total resting periods, locomotor time 1	0.0	0.0	0.0	0.1
Rest time, locomotor task time 1	0.0	0.0	0.0	0.2
Distance moved, locomotor task time 1	0.1	0.1	0.1	0.4
Vertical activity count, locomotor time 1	1.2	1.2	1.2	-1.1
Time >=10cm from walls, locomotor time 2	0.3	0.3	0.3	0.5
Bouts of movement, locomotor time 2	3.4	3.6	3.6	-1.9
Total resting periods, locomotor time 2	3.6	3.9	3.9	-2.0
Rest time, locomotor task time 2	0.2	0.3	0.3	-0.5
Distance moved, locomotor task time 2	0.4	0.5	0.5	0.7
Vertical activity count, locomotor time 2	0.2	0.2	0.2	-0.5
Weight adjusted by age	2.6	2.9	2.9	-1.7
Seeking ratio, delayed vs. immediate footshock	0.3	0.3	0.3	-0.6
Locomotion in novel chamber	0.9	1.1	1.1	-1.0
Locomotion in novel chamber post-restriction	0.6	0.7	0.7	-0.9
Progressive ratio	0.0	0.0	0.0	0.1
Food seeking constrained by brief footshock	0.0	0.0	0.0	0.0
Seeking ratio, punishment vs. effort	0.0	0.0	0.0	-0.1
Run reversals in cocaine runway, females	0.2	0.2	0.2	0.5
Run reversals in cocaine runway, males	1.6	1.5	1.5	1.2
Latency to leave start box in cocaine runway	0.0	0.0	0.0	0.1
Latency to leave start box in cocaine runway, F	2.0	2.2	2.2	1.5
Latency to leave start box in cocaine runway, M	3.0	2.9	2.9	-1.7
Cd content in liver	0.2	0.3	0.3	0.5
Co content in liver	0.2	0.3	0.3	0.5
Cu content in liver	1.5	1.8	1.8	-1.3
Fe content in liver	0.1	0.1	0.1	0.4
K content in liver	1.5	1.5	1.5	-1.2
Mg content in liver	0.0	0.0	0.0	-0.2
Mn content in liver	0.2	0.3	0.3	-0.5
Na content in liver	0.2	0.3	0.3	-0.5
Rb content in liver	0.0	0.0	0.0	0.1
Se content in liver	0.3	0.3	0.3	0.6
Sr content in liver	0.9	0.8	0.8	-0.9
Zn content in liver	0.4	0.4	0.4	0.6