Cfd

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	gene expression	Cfd	0.17	0.1	2.6e-15	0.12	0.12	0.12	0.12	1.0e-13	3.8e-13	1.5e-13	1.6e-13
2	Adipose	gene expression	Cfd	0.33	0.16	0.0e+00	0.13	0.16	0.16	0.16	1.2e-14	1.2e-17	1.5e-17	1.0e-17

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	0.5	0.9	1.0	-0.9	1.0
Area under the delay curve	2.5	2.7	2.8	1.7	-1.6
BMI with tail	7.0	22.8	23.1	4.7	-4.8
BMI without tail	3.9	8.0	9.0	2.7	-3.0
Body weight	1.4	5.7	6.1	2.3	-2.5
Weight adjusted by age	1.4	1.5	1.6	1.3	-1.2
Bone surface	2.1	3.6	3.8	-1.9	2.0
Bone volume	1.9	3.2	3.4	-1.7	1.9
Breakpoint value in progressive ratio session	4.0	4.4	4.5	-2.1	2.1
Number of licking bursts	0.5	0.6	0.7	0.8	-0.7
Context. condit. distance diff. score	0.3	0.4	0.6	0.3	-0.8
Locomotion velocity, session 1	1.4	1.5	1.6	-1.2	1.3
Locomotion distance, session 1	2.3	2.9	3.8	-1.9	1.4
Locomotion velocity, session 2	8.7	10.2	11.3	-3.4	3.0
Locomotion distance, session 2	4.7	6.6	6.8	-2.5	2.6
Locomotion velocity, session 3	5.9	6.9	7.5	-2.7	2.5
Locomotion distance, session 3	0.0	0.0	0.1	-0.1	-0.3
Stereotopy head waving bouts, day 3	6.9	8.2	8.8	-3.0	2.7
Stereotopy head waving duration, day 3	6.9	8.3	8.5	-2.9	2.8
Locomotion velocity, session 7	0.6	0.6	1.1	-1.0	0.4
Locomotion distance, session 7	0.6	0.7	1.0	0.7	-1.0
Stereotopy head waving bouts, day 7	0.5	0.6	0.8	-0.9	0.6
Stereotopy head waving duration, day 7	1.0	1.2	1.3	-1.2	1.0
Locomotion velocity, session 8	2.7	3.2	4.0	-2.0	1.6
Locomotion distance, session 8	0.8	1.1	1.6	-1.3	0.8
Degree of sensitization distance	0.3	0.3	0.4	0.5	-0.6
Degree of sensitization stereotypy	0.8	0.9	1.0	0.9	-1.0
Conditioned locomotion	2.7	3.2	3.5	1.7	-1.9
Cocaine response after cond. corrected	10.2	11.5	11.7	3.4	-3.4
Cocaine response after cond. not corrected	10.7	11.8	11.8	3.4	-3.4
Cocaine response before conditioning	0.8	0.9	1.2	-1.1	0.8
Saline control response	0.1	0.1	0.1	0.3	-0.3
Bone: connectivity density	0.1	0.1	0.1	-0.4	0.3
Bone: cortical apparent density	1.1	1.5	2.2	1.5	-0.9
Bone: cortical area	0.1	0.2	0.3	0.4	-0.5
Bone: cortical porosity	1.1	1.2	1.2	-1.1	1.0
Bone: cortical porosity	0.6	0.6	0.8	-0.9	0.7
Bone: cortical thickness	0.6	1.0	1.1	1.0	-1.0
Bone: cortical thickness	0.4	0.5	0.6	0.8	-0.6
Bone: cortical tissue density	0.9	1.1	1.8	1.3	-0.7
Condit. Reinf. active minus inactive responses	4.7	5.3	5.8	-2.4	2.2
Condit. Reinf. active-inactive response ratio	1.0	1.1	1.3	-1.0	1.1
Condit. Reinf. active responses	6.3	7.7	8.4	-2.9	2.7
Condit. Reinf. inactive responses	3.1	3.7	4.2	-2.0	1.8
Incentive salience index mean	4.1	5.0	5.8	-2.4	2.0
Condit. Reinf. lever presses	1.2	1.6	2.0	-1.4	1.1
Condit. Reinf. active minus inactive responses	0.7	0.9	1.2	-0.8	1.1
Condit. Reinf. active-inactive response ratio	0.4	0.4	0.6	0.8	-0.3
Condit. Reinf. active responses	1.0	1.3	1.6	-1.0	1.3
Condit. Reinf. inactive responses	0.8	1.0	1.0	-1.0	1.0
Condit. Reinf. lever presses	1.0	1.4	1.5	-1.2	1.2
Condit. Reinf. lever reinforcers received	0.4	0.6	0.7	-0.6	0.9
Conditioned reinforcement - actives	2.2	2.2	2.5	-1.6	1.4
Conditioned reinforcement - inactives	0.8	0.9	1.1	0.8	-1.1
Conditioned locomotion	6.9	8.3	9.0	-3.0	2.8
Patch foraging indifference point 0 sec	0.1	0.1	0.1	0.3	-0.3
Patch foraging indifference point AUC	0.5	0.6	0.7	-0.7	0.8
Delay disc. indifference point, 0s delay	2.7	2.9	3.0	1.7	-1.7
Delay disc. indifference point, 16s delay	0.2	0.2	0.3	0.5	-0.3
Delay disc. indifference point, 2s delay	4.0	4.4	4.5	2.1	-2.1
Delay disc. indifference point, 24s delay	1.5	1.4	1.6	1.3	-1.1
Delay disc. indifference point, 4s delay	0.6	0.7	0.7	0.8	-0.8
Delay disc. indifference point, 8s delay	2.5	2.5	2.6	1.6	-1.6
Indifference point function ln k	0.4	0.6	0.7	0.8	-0.8
Indifference point function log k	0.4	0.6	0.7	0.8	-0.8
Patch foraging total patch changes 0 sec	0.1	0.1	0.1	0.3	-0.3
Patch foraging total patch changes 12 sec	0.6	0.8	0.9	0.8	-0.9
Patch foraging total patch changes 18 sec	1.0	1.3	1.4	-1.1	1.2
Patch foraging total patch changes 24 sec	0.1	0.1	0.1	-0.2	0.4
Patch foraging total patch changes 6 sec	0.2	0.3	0.5	-0.4	0.7
Patch foraging time to switch 0 sec	0.0	0.0	0.1	-0.1	-0.2
Patch foraging water rate 0 sec	0.8	1.3	1.3	1.1	-1.1
Patch foraging water rate 12 sec	3.4	5.2	5.7	2.4	-2.2
Patch foraging water rate 18 sec	1.4	1.8	2.0	1.4	-1.3
Patch foraging water rate 24 sec	3.0	4.1	4.3	2.1	-2.0
Patch foraging water rate 6 sec	0.2	0.4	0.5	0.7	-0.5
Seeking ratio, delayed vs. immediate footshock	4.6	5.3	5.8	-2.2	2.4
Distance traveled before self-admin	0.3	0.4	0.5	0.7	-0.5
Distance traveled after self-admin	0.7	0.7	0.8	-0.8	0.9
Extensor digitorum longus weight	5.6	22.2	24.1	4.5	-4.9
Bone: elastic displacement	0.2	0.2	0.4	-0.2	0.6
Bone: elastic work	0.3	0.4	0.5	0.7	-0.5
Bone: endosteal estimation	0.1	0.2	0.2	0.4	-0.4
Bone: endosteal perimeter	0.5	1.0	1.2	-1.1	0.9
Epididymis fat weight	0.2	0.4	0.5	-0.7	0.6
Delta time in closed arm before/after self-admin	3.5	3.4	3.5	1.9	-1.8
Delta time in open arm before/after self-admin	0.7	0.6	0.7	0.8	-0.8
Diff in mean of infusions in LGA sessions	2.0	2.2	2.3	-1.5	1.5
Delay discount exponential model param	2.5	2.6	2.7	-1.6	1.6
Extinction: sum of active levers before priming	0.5	0.5	0.7	-0.8	0.6
Active lever presses in extinction session 6	2.6	2.5	2.7	-1.5	1.6
Bone: final force	0.8	1.2	1.4	1.1	-1.2
Bone: final moment	0.6	1.0	1.0	1.0	-1.0
Food consumed during 24 hour testing period	1.3	1.6	2.0	1.4	-1.1
Glucose	1.9	2.9	3.2	1.8	-1.6
Heart weight	0.0	0.0	0.0	0.0	0.2
Delay discount hyperbolic model param	3.2	3.4	3.4	-1.8	1.8
Intermittent access intake day 1-15 change	5.3	5.2	5.6	-2.4	2.2
Intermittent access intake escalation	3.3	3.3	3.6	-1.9	1.7
Intermittent access intake escalation 2	4.3	4.3	4.7	-2.2	2.0
Intermitt. access day 1 inactive lever presses	0.0	0.1	0.1	0.2	-0.3
Intermitt. access day 15 inactive lever presses	0.2	0.3	0.3	-0.6	0.5
Intermitt. access escalation Index	0.0	0.0	0.0	0.0	0.1
Intermittent access day 1 total infusions	0.0	0.0	0.0	0.1	-0.2
Intermittent access day 15 total infusions	1.1	1.3	1.5	-1.2	1.0
Intermittent access terminal intake (last 3 days)	0.8	0.8	1.1	-1.1	0.8
Intermittent access total infusions	0.1	0.1	0.2	-0.4	0.2
Intermittent access day 1 locomotion	0.3	0.3	0.3	-0.6	0.5
Intermittent access day 15 total locomotion	3.3	3.5	3.7	-1.9	1.8
Intermittent access total locomotion	1.0	1.2	1.3	-1.1	1.0
Intermittent access standard deviation	1.4	1.5	1.7	-1.3	1.2
Left kidney weight	0.1	0.2	0.3	-0.3	0.5
Right kidney weight	1.2	3.5	3.8	-1.8	2.0
Cocaine induced anxiety	1.4	1.6	1.6	-1.3	1.3
Post-drug Anxiety	1.4	1.6	1.6	-1.3	1.3
Baseline Anxiety	0.0	0.0	0.0	0.0	-0.0
Tail length	2.3	7.1	7.9	-2.8	2.5
Length with tail	2.0	7.3	7.6	-2.7	2.7
Length without tail	0.4	0.9	0.9	-0.9	0.9
Times rat made contact with spout	0.9	1.0	1.2	1.1	-0.9
Lifetime Intake	0.1	0.1	0.1	-0.3	0.1
Liver weight, left	2.3	3.8	4.0	1.9	-2.0
Liver weight, right	1.0	1.7	2.0	1.2	-1.4
Locomotor activity	4.5	7.2	7.3	-2.6	2.7
Locomotor testing distance	2.4	4.0	4.1	-2.0	2.0
Locomotor testing rearing	0.1	0.1	0.1	0.3	-0.3
Locomotion in novel chamber	0.0	0.0	0.1	0.1	0.3
Locomotion in novel chamber post-restriction	0.5	0.6	0.6	-0.8	0.7
Fecal boli incidents, locomotor time 1	2.1	2.3	2.5	1.4	-1.6
Change in fecal boli incidents, locomotor task	0.2	0.2	0.2	-0.4	0.4
Time >=10cm from walls, locomotor time 1	0.2	0.2	0.2	0.5	-0.4
Bouts of movement, locomotor time 1	0.1	0.1	0.1	-0.3	0.2
Total resting periods, locomotor time 1	0.2	0.2	0.3	-0.5	0.4
Rest time, locomotor task time 1	0.7	0.7	1.0	-1.0	0.7
Distance moved, locomotor task time 1	0.2	0.2	0.3	0.6	-0.3
Vertical activity count, locomotor time 1	1.1	1.1	1.5	1.2	-0.9
Time >=10cm from walls, locomotor time 2	2.6	2.8	2.8	1.6	-1.7
Bouts of movement, locomotor time 2	1.5	1.6	1.7	-1.2	1.3
Total resting periods, locomotor time 2	1.4	1.5	1.6	-1.2	1.3
Rest time, locomotor task time 2	1.0	1.1	1.2	-1.0	1.1
Distance moved, locomotor task time 2	1.0	1.1	1.2	1.0	-1.1
Vertical activity count, locomotor time 2	1.7	1.9	2.1	1.3	-1.5
Light reinforcement 1	7.6	13.9	13.9	-3.7	3.7
Light reinforcement 2	3.1	4.1	4.2	-2.1	2.0
Bone: marrow area	0.1	0.2	0.2	0.4	-0.5
Bone: maximum diameter	1.3	2.4	2.5	-1.6	1.5
Bone: maximum force	1.0	1.7	1.9	1.3	-1.4
Bone: maximum moment	0.8	1.4	1.5	1.2	-1.2
Mean time between licks in bursts	3.4	4.7	4.7	-2.2	2.2
Mean num. licks in bursts	0.0	0.0	0.0	0.1	-0.0
Cd content in liver	0.1	0.2	0.2	0.5	-0.3
Co content in liver	0.5	0.6	0.8	-0.9	0.7
Cu content in liver	0.1	0.1	0.1	-0.3	0.2
Fe content in liver	0.1	0.2	0.3	-0.6	-0.1
K content in liver	0.8	0.8	1.2	-1.1	0.6
Mg content in liver	0.5	0.6	0.8	-0.9	0.6
Mn content in liver	3.9	4.5	5.5	-2.3	1.9
Na content in liver	0.1	0.1	0.2	-0.4	-0.3
Rb content in liver	0.0	0.0	0.0	-0.1	0.0
Se content in liver	0.6	0.7	1.1	-1.1	0.6
Sr content in liver	0.2	0.2	0.2	0.4	-0.4
Zn content in liver	0.2	0.2	0.3	-0.3	0.5
Bone: minimum diameter	0.0	0.1	0.2	-0.4	0.1
Time in familiar zone, hab. session 1	1.2	1.1	1.2	-1.0	1.1
Time in novel zone, hab. session 1	0.4	0.3	0.4	0.6	-0.6
Total zone transitions, hab. session 1	2.8	3.9	4.0	-2.0	1.9
Total locomotion distance, hab. session 1	4.0	5.7	6.6	-2.6	2.2
Locomotion velocity, hab. session 1	4.8	6.8	7.7	-2.8	2.4
Time in familiar zone, hab. session 2	3.2	3.3	3.8	-1.7	1.9
Time in novel zone, hab. session 2	3.1	3.1	3.4	1.9	-1.7
Total zone transitions, hab. session 2	0.6	0.8	1.0	-0.8	1.0
Total locomotion distance, hab. session 2	2.9	3.8	4.2	-1.9	2.0
Locomotion velocity, hab. session 2	3.3	4.4	4.9	-2.0	2.2
Novel to familiar place preference ratio	2.1	2.1	2.2	1.4	-1.5
Novelty place preference	1.1	1.1	1.2	1.0	-1.1
Time in novel zone, NPP test	1.5	1.5	1.6	1.2	-1.3
Total zone transitions, NPP test	0.7	0.9	1.0	-0.9	1.0
Total locomotion distance, NPP test	0.7	0.9	1.1	-1.1	0.8
Locomotion velocity, NPP test	1.0	1.4	1.5	-1.2	1.1
Intraocular pressure	0.6	0.9	1.2	1.1	-0.7
Delta distance traveled before/after self-admin	2.1	2.2	2.5	-1.6	1.4
Delta ambulatory time before/after self-admin	2.5	2.7	3.0	-1.7	1.6
Parametrial fat weight	0.1	0.2	0.3	-0.5	0.4
Pavlov. Cond. lever latency	0.6	0.8	1.3	1.1	-0.6
Pavlov. Cond. magazine entry latency	3.6	4.7	5.7	-2.4	1.9
Pavlov. Cond. change in total contacts	0.5	0.5	0.8	-0.9	0.4
Pavlov. Cond. index score	1.7	2.1	3.0	-1.7	1.1
Pavlov. Cond. latency score	2.0	2.6	3.7	-1.9	1.2
Pavlov. Cond. lever contacts	1.1	1.3	1.9	-1.4	0.8
Pavlov. Cond. magazine entry number	1.3	1.7	2.3	1.5	-1.0
Pavlov. Cond. intertrial magazine entries	0.0	0.0	0.1	0.3	-0.0
Pavlov. Cond. lever-magazine prob. diff.	2.2	2.7	3.7	-1.9	1.3
Pavlov. Cond. response bias	2.0	2.4	3.2	-1.8	1.3
Pavlov. Cond. lever latency	0.3	0.4	0.4	0.6	-0.6
Pavlov. Cond. magazine entry latency	0.3	0.4	0.5	-0.7	0.5
Pavlov. Cond. change in total contacts	0.2	0.3	0.4	-0.4	0.6
Pavlov. Cond. index score	0.3	0.4	0.4	-0.7	0.6
Pavlov. Cond. latency score	0.4	0.5	0.5	-0.7	0.7
Pavlov. Cond. lever contacts	0.1	0.2	0.2	-0.4	0.4
Pavlov. Cond. magazine entry number	0.6	0.7	0.9	1.0	-0.7
Pavlov. Cond. intertrial magazine entries	0.7	1.0	1.0	1.0	-0.9
Pavlov. Cond. lever-magazine prob. diff.	0.4	0.6	0.6	-0.8	0.7
Pavlov. Cond. response bias	0.6	0.8	0.9	-0.9	0.9
Time in closed arm before self-admin	0.0	0.0	0.0	-0.1	-0.0
Time in closed arm after self-admin	0.0	0.0	0.0	-0.0	0.0
Time in open arm before self-admin	0.3	0.3	0.3	-0.6	0.6
Time in open arm after self-admin	0.9	1.0	1.1	1.1	-1.0
Bone: periosteal estimation	0.0	0.1	0.1	0.3	-0.3
Bone: periosteal perimeter	0.3	0.4	0.6	-0.8	0.5
Bone: post-yield work	0.6	0.8	1.1	0.7	-1.1
Progressive ratio test 1 active lever presses	0.2	0.3	0.3	0.5	-0.5
Progressive ratio test 1 breakpoint	0.3	0.3	0.4	0.6	-0.6
Progressive ratio test 1 inactive lever presses	0.0	0.0	0.0	-0.2	0.2
Progressive ratio test 2 active lever presses	0.0	0.0	0.0	-0.0	-0.1
Progressive ratio test 2 breakpoint	0.1	0.1	0.1	-0.3	0.2
Progressive ratio test 2 inactive lever presses	0.1	0.1	0.2	-0.4	0.2
Incentive Sensitization - Responses	0.0	0.0	0.0	0.0	-0.2
Incentive Sensitization - Breakpoint	0.0	0.0	0.0	-0.1	-0.1
Sum of active levers in priming session hrs 5-6	0.0	0.0	0.0	-0.1	0.1
Progressive ratio	0.1	0.1	0.2	0.2	-0.4
Food seeking constrained by brief footshock	0.8	1.0	1.2	-1.1	0.9
Seeking ratio, punishment vs. effort	0.5	0.6	0.6	-0.8	0.8
Retroperitoneal fat weight	0.3	1.0	1.0	1.0	-1.0
Reaction time number correct	2.0	2.9	3.0	1.7	-1.6
Reaction time mean minus median	0.2	0.3	0.3	-0.6	0.5
Reaction time mean minus median AUC	0.1	0.1	0.1	-0.3	0.3
Reaction time num false alarms	0.6	0.9	1.2	0.7	-1.1
Reaction time num false alarms AUC	0.9	1.2	1.6	0.9	-1.3
Reaction time trials correct on left	2.0	2.9	3.0	1.7	-1.6
Reaction time trials on left	1.9	2.8	3.0	1.7	-1.6
Reaction time mean	0.0	0.0	0.0	0.1	0.1
Reaction time mean AUC	0.0	0.0	0.1	0.2	0.0
Median of all reaction times	0.1	0.2	0.2	0.5	-0.3
Reaction time omissions	0.3	0.4	0.7	-0.4	0.8
Reaction time false alarm rate	0.1	0.1	0.1	-0.0	-0.4
Reaction time premature initiation rate	0.3	0.4	0.6	-0.5	0.8
Reaction time premature initiations	0.0	0.1	0.1	0.4	-0.0
Std. dev. reaction times	0.1	0.1	0.1	-0.2	0.3
Reaction time trials completed	1.9	2.8	3.0	1.7	-1.6
Reaction time trials AUC	2.1	3.1	3.3	1.8	-1.7
Run reversals in cocaine runway, females	0.5	0.5	0.5	-0.7	0.7
Run reversals in cocaine runway, males	2.1	2.1	2.2	-1.4	1.5
Latency to leave start box in cocaine runway	1.6	1.7	2.0	-1.2	1.4
Latency to leave start box in cocaine runway, F	0.3	0.3	0.4	-0.4	0.7
Latency to leave start box in cocaine runway, M	1.2	1.1	1.2	-1.1	1.0
Std. dev. time between licks in bursts	0.8	1.0	1.0	-1.0	1.0
Total sessions with >9 infusions	0.0	0.0	0.0	-0.1	-0.0
Short access day 1 total inactive lever presses	0.1	0.1	0.2	-0.4	0.3
Short access day 10 total inactive lever presses	0.0	0.0	0.0	0.2	-0.2
Short access day 1 total infusions	0.7	0.7	0.9	-0.9	0.8
Short access day 10 total infusions	0.0	0.0	0.0	0.0	-0.2
Short access total infusions	0.0	0.0	0.0	-0.2	0.0
Short access day 1 locomotion	1.5	1.6	1.7	-1.3	1.2
Short access day 10 total locomotion	2.7	3.0	3.1	-1.8	1.7
Short access total locomotion	0.9	0.9	1.1	-1.0	0.9
One hour access (0.3 mA shock)	0.1	0.2	0.2	0.3	-0.5
Compulsive drug intake	0.6	0.6	0.7	0.8	-0.8
One hour access (shock baseline)	0.0	0.0	0.0	-0.0	-0.2
Social response proportion	1.5	1.7	2.0	-1.2	1.4
Social responses	8.1	10.4	10.5	-3.2	3.2
Social time	0.3	0.4	0.4	0.6	-0.6
Soleus weight	9.3	27.1	27.4	5.2	-5.2
Bone: stiffness	2.2	3.4	4.3	1.6	-2.1
Tibialis anterior weight	1.1	3.8	4.6	1.7	-2.1
Time to tail flick, vehicle, before self-admin	1.1	1.1	1.1	-1.0	1.0
Time to tail flick, vehicle, after self-admin	0.0	0.0	0.0	-0.1	-0.2
Time to tail flick, test, before self-admin	0.7	0.7	0.8	-0.8	0.9
Time to tail flick, test, after self-admin	0.6	0.6	0.6	-0.8	0.8
Delta time to tail flick, vehicle, before/after SA	1.3	1.3	1.5	1.0	-1.2
Delta time to tail flick, test, before/after SA	0.0	0.0	0.0	-0.1	-0.0
Tibia length	0.7	1.9	2.1	-1.3	1.4
Ambulatory time before self-admin	0.3	0.3	0.4	0.6	-0.5
Ambulatory time after self-admin	0.4	0.4	0.5	-0.6	0.7
Bone: tissue strength	1.1	1.1	1.2	1.1	-1.0
Total heroin consumption	2.0	2.4	2.4	-1.5	1.6
Bone: trabecular number	1.7	2.7	3.0	-1.7	1.6
Bone: trabecular spacing	2.7	3.5	3.7	1.9	-1.8
Bone: trabecular thickness	1.4	1.7	1.9	-1.2	1.4
Bone: trabecular tissue density	1.8	2.5	2.5	1.6	-1.6
Water consumed over 24 hours	0.3	0.4	0.5	0.7	-0.5
Number of responses in last shaping day	0.1	0.1	0.2	-0.4	0.2