Chmp4c

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 mRNA stability Chmp4c 0.04 0.03 5.6e-04 0 0.02 0.02 0.01 7.7e-02 1.5e-03 5.2e-03 7.9e-03
2 Liver gene expression Chmp4c 0.04 0.03 3.4e-03 0.02 0.02 0 0.01 1.8e-03 4.7e-03 1.0e-01 2.0e-02
3 Brain gene expression Chmp4c 0.07 0.05 8.1e-05 0.01 0.04 0.03 0.02 4.2e-02 2.4e-04 1.2e-03 2.7e-03
4 LHb gene expression Chmp4c 0.45 0.18 5.9e-05 0.09 0.05 0.08 0.1 4.5e-03 2.9e-02 5.7e-03 2.6e-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 3 4
Bone: apparent density0.81.42.80.31.7-0.2-1.6
Area under the delay curve0.50.61.2-0.2-1.10.11.0
BMI with tail0.31.11.5-1.2-1.1-0.90.9
BMI without tail0.51.42.6-1.6-0.9-1.30.7
Body weight0.62.86.0-2.5-0.4-2.20.2
Weight adjusted by age0.20.30.7-0.80.3-0.8-0.3
Bone surface2.64.89.1-0.23.0-0.9-3.0
Bone volume2.64.68.6-0.32.9-1.1-2.9
Breakpoint value in progressive ratio session0.40.51.1-1.10.0-1.0-0.1
Number of licking bursts0.20.30.60.20.80.0-0.7
Context. condit. distance diff. score0.20.20.30.3-0.50.50.6
Locomotion velocity, session 11.01.12.0-1.4-0.8-1.10.7
Locomotion distance, session 10.91.22.5-1.60.0-1.5-0.2
Locomotion velocity, session 20.91.12.0-1.4-0.8-1.10.6
Locomotion distance, session 21.62.34.4-2.10.3-2.1-0.5
Locomotion velocity, session 30.10.10.20.1-0.40.20.4
Locomotion distance, session 30.30.30.6-0.10.8-0.3-0.8
Stereotopy head waving bouts, day 30.91.11.4-1.01.0-1.2-1.0
Stereotopy head waving duration, day 30.20.30.6-0.8-0.1-0.7-0.0
Locomotion velocity, session 75.25.711.0-0.13.3-0.9-3.3
Locomotion distance, session 72.32.95.21.22.30.6-2.2
Stereotopy head waving bouts, day 70.50.51.1-1.1-0.3-1.00.2
Stereotopy head waving duration, day 70.60.70.8-0.9-0.9-0.60.8
Locomotion velocity, session 81.51.82.3-1.5-1.5-1.01.4
Locomotion distance, session 80.50.71.6-1.3-0.4-1.00.3
Degree of sensitization distance0.20.20.30.40.60.3-0.5
Degree of sensitization stereotypy0.80.91.4-1.2-0.9-0.90.8
Conditioned locomotion0.10.10.2-0.4-0.2-0.30.1
Cocaine response after cond. corrected0.30.40.80.90.40.8-0.3
Cocaine response after cond. not corrected0.60.71.31.20.60.9-0.5
Cocaine response before conditioning0.30.30.60.00.8-0.2-0.8
Saline control response1.11.42.4-0.61.5-0.9-1.5
Bone: connectivity density0.81.22.20.71.50.2-1.4
Bone: cortical apparent density0.60.81.5-0.5-1.2-0.21.1
Bone: cortical area0.91.41.9-1.21.0-1.4-1.1
Bone: cortical porosity0.20.30.4-0.30.6-0.5-0.6
Bone: cortical porosity0.30.30.5-0.60.5-0.7-0.5
Bone: cortical thickness1.01.62.8-1.60.6-1.7-0.8
Bone: cortical thickness1.61.93.7-1.9-1.0-1.60.8
Bone: cortical tissue density0.60.81.6-0.5-1.3-0.11.2
Condit. Reinf. active minus inactive responses5.05.510.9-3.30.5-3.2-0.8
Condit. Reinf. active-inactive response ratio5.96.312.6-3.60.5-3.4-0.7
Condit. Reinf. active responses4.75.910.8-3.30.9-3.3-1.1
Condit. Reinf. inactive responses0.10.10.2-0.40.2-0.5-0.3
Incentive salience index mean5.16.312.4-3.50.5-3.5-0.8
Condit. Reinf. lever presses1.82.65.5-2.3-0.1-2.2-0.1
Condit. Reinf. active minus inactive responses3.44.58.1-0.52.8-1.2-2.8
Condit. Reinf. active-inactive response ratio2.73.15.3-0.72.3-1.2-2.3
Condit. Reinf. active responses3.95.410.1-0.43.2-1.2-3.2
Condit. Reinf. inactive responses0.20.30.5-0.20.7-0.4-0.7
Condit. Reinf. lever presses2.02.75.0-0.32.2-0.9-2.2
Condit. Reinf. lever reinforcers received3.85.310.0-0.33.2-1.1-3.2
Conditioned reinforcement - actives1.93.26.30.92.50.1-2.4
Conditioned reinforcement - inactives0.40.51.0-0.11.0-0.3-1.0
Conditioned locomotion1.01.32.50.51.6-0.1-1.6
Patch foraging indifference point 0 sec0.50.92.01.40.11.30.1
Patch foraging indifference point AUC0.20.20.5-0.1-0.70.10.7
Delay disc. indifference point, 0s delay0.20.20.30.5-0.40.50.5
Delay disc. indifference point, 16s delay0.20.20.4-0.2-0.60.10.6
Delay disc. indifference point, 2s delay1.31.42.6-1.60.5-1.6-0.6
Delay disc. indifference point, 24s delay0.10.10.10.1-0.30.20.3
Delay disc. indifference point, 4s delay1.21.22.4-0.5-1.5-0.11.5
Delay disc. indifference point, 8s delay0.60.70.90.6-1.00.81.0
Indifference point function ln k0.00.00.10.1-0.20.20.2
Indifference point function log k0.00.00.10.1-0.20.20.2
Patch foraging total patch changes 0 sec0.50.91.81.3-0.21.30.3
Patch foraging total patch changes 12 sec0.60.71.11.0-0.61.00.7
Patch foraging total patch changes 18 sec0.20.20.5-0.2-0.70.00.7
Patch foraging total patch changes 24 sec0.40.70.90.7-0.90.90.9
Patch foraging total patch changes 6 sec0.30.40.50.5-0.70.70.7
Patch foraging time to switch 0 sec1.53.15.4-2.30.8-2.3-1.0
Patch foraging water rate 0 sec0.61.31.91.2-0.91.41.0
Patch foraging water rate 12 sec0.61.22.41.50.71.3-0.6
Patch foraging water rate 18 sec0.10.20.30.60.40.4-0.3
Patch foraging water rate 24 sec0.91.21.71.1-0.91.31.0
Patch foraging water rate 6 sec0.91.42.41.50.91.2-0.8
Seeking ratio, delayed vs. immediate footshock3.03.66.92.61.42.0-1.2
Distance traveled before self-admin0.30.50.8-0.5-0.9-0.30.8
Distance traveled after self-admin0.10.10.20.40.00.40.0
Extensor digitorum longus weight4.216.731.7-5.6-3.0-4.42.6
Bone: elastic displacement1.31.51.7-1.11.2-1.3-1.2
Bone: elastic work1.31.71.9-1.11.3-1.4-1.4
Bone: endosteal estimation1.43.25.3-0.72.3-1.2-2.3
Bone: endosteal perimeter0.40.91.90.21.4-0.1-1.3
Epididymis fat weight0.31.02.0-0.5-1.4-0.11.4
Delta time in closed arm before/after self-admin0.90.81.10.7-1.00.81.1
Delta time in open arm before/after self-admin0.30.30.50.10.7-0.0-0.7
Diff in mean of infusions in LGA sessions1.82.23.7-1.90.9-1.9-0.9
Delay discount exponential model param0.50.51.00.11.0-0.2-1.0
Extinction: sum of active levers before priming0.30.30.5-0.60.3-0.7-0.3
Active lever presses in extinction session 60.30.30.50.7-0.30.70.4
Bone: final force1.01.52.3-1.31.0-1.5-1.1
Bone: final moment0.91.51.7-1.01.2-1.3-1.3
Food consumed during 24 hour testing period0.81.12.5-1.6-0.3-1.40.2
Glucose0.50.71.5-1.2-0.5-1.00.4
Heart weight0.40.61.20.0-1.10.31.0
Delay discount hyperbolic model param0.40.50.80.50.90.2-0.9
Intermittent access intake day 1-15 change0.81.72.91.71.21.3-0.9
Intermittent access intake escalation1.02.14.22.10.91.7-0.7
Intermittent access intake escalation 22.42.74.32.11.61.5-1.3
Intermitt. access day 1 inactive lever presses0.51.83.5-0.1-1.90.41.9
Intermitt. access day 15 inactive lever presses1.02.13.01.0-1.61.41.7
Intermitt. access escalation Index0.81.12.00.4-1.30.81.4
Intermittent access day 1 total infusions1.42.24.30.72.10.1-2.0
Intermittent access day 15 total infusions2.84.25.22.32.31.6-2.0
Intermittent access terminal intake (last 3 days)3.64.76.22.32.51.5-2.2
Intermittent access total infusions2.32.73.81.72.01.0-1.8
Intermittent access day 1 locomotion0.70.81.60.51.30.3-1.2
Intermittent access day 15 total locomotion0.51.02.00.31.4-0.1-1.4
Intermittent access total locomotion1.11.32.20.91.50.5-1.4
Intermittent access standard deviation1.42.96.32.50.72.1-0.5
Left kidney weight0.20.71.21.0-0.61.10.6
Right kidney weight0.00.20.4-0.0-0.60.20.6
Cocaine induced anxiety0.20.30.6-0.1-0.80.20.7
Post-drug Anxiety0.80.81.4-1.2-0.8-0.90.6
Baseline Anxiety0.50.61.1-1.00.3-1.0-0.3
Tail length0.31.02.3-1.5-0.1-1.30.0
Length with tail0.41.73.3-1.80.4-1.8-0.5
Length without tail0.20.71.0-0.60.9-0.8-1.0
Times rat made contact with spout0.00.00.10.30.10.2-0.0
Lifetime Intake1.82.13.61.91.31.4-1.1
Liver weight, left0.40.71.3-1.10.2-1.1-0.3
Liver weight, right0.61.11.70.6-1.20.81.3
Locomotor activity0.00.00.0-0.10.0-0.1-0.0
Locomotor testing distance0.10.20.2-0.40.4-0.4-0.4
Locomotor testing rearing0.20.50.91.00.50.7-0.4
Locomotion in novel chamber0.70.91.8-1.30.0-1.3-0.1
Locomotion in novel chamber post-restriction0.20.30.60.3-0.80.50.6
Fecal boli incidents, locomotor time 10.00.10.1-0.4-0.1-0.30.1
Change in fecal boli incidents, locomotor task0.80.81.61.30.70.9-0.5
Time >=10cm from walls, locomotor time 10.40.40.80.40.90.1-0.8
Bouts of movement, locomotor time 14.34.85.81.8-2.32.22.4
Total resting periods, locomotor time 13.13.44.11.6-1.91.92.0
Rest time, locomotor task time 10.91.11.50.9-1.11.01.2
Distance moved, locomotor task time 10.10.20.2-0.30.5-0.3-0.5
Vertical activity count, locomotor time 10.71.72.2-1.11.4-1.3-1.5
Time >=10cm from walls, locomotor time 20.60.91.8-0.31.3-0.6-1.2
Bouts of movement, locomotor time 22.43.96.11.1-2.51.52.5
Total resting periods, locomotor time 22.54.46.81.1-2.61.62.6
Rest time, locomotor task time 20.81.01.80.4-1.30.71.3
Distance moved, locomotor task time 20.00.00.10.20.10.2-0.0
Vertical activity count, locomotor time 20.81.12.2-1.50.3-1.4-0.5
Light reinforcement 10.61.53.1-0.1-1.80.31.7
Light reinforcement 20.81.31.8-1.2-1.3-0.71.2
Bone: marrow area1.43.25.1-0.82.2-1.3-2.3
Bone: maximum diameter0.10.10.2-0.00.4-0.1-0.4
Bone: maximum force1.11.92.7-1.41.2-1.6-1.3
Bone: maximum moment1.11.92.4-1.01.5-1.4-1.5
Mean time between licks in bursts0.71.83.1-1.70.7-1.8-0.9
Mean num. licks in bursts0.20.30.50.0-0.70.20.7
Cd content in liver1.01.22.20.3-1.50.61.4
Co content in liver1.72.02.61.0-1.61.31.6
Cu content in liver1.51.84.02.00.21.8-0.0
Fe content in liver0.40.40.80.00.9-0.3-0.9
K content in liver0.50.51.01.0-0.01.00.1
Mg content in liver0.30.30.50.70.40.6-0.3
Mn content in liver0.00.00.00.1-0.10.20.1
Na content in liver0.70.71.51.20.31.1-0.2
Rb content in liver0.20.20.30.5-0.40.50.5
Se content in liver0.20.30.50.5-0.40.70.4
Sr content in liver0.50.50.6-0.70.6-0.7-0.7
Zn content in liver1.71.83.92.00.51.8-0.3
Bone: minimum diameter4.27.79.5-2.62.6-3.1-2.8
Time in familiar zone, hab. session 11.41.42.11.3-0.91.40.9
Time in novel zone, hab. session 10.20.20.2-0.40.5-0.4-0.5
Total zone transitions, hab. session 10.81.12.4-1.6-0.3-1.40.1
Total locomotion distance, hab. session 11.11.52.5-1.50.8-1.6-0.9
Locomotion velocity, hab. session 11.31.93.5-1.80.6-1.9-0.7
Time in familiar zone, hab. session 23.13.35.22.2-1.12.31.3
Time in novel zone, hab. session 22.12.12.7-1.51.3-1.6-1.4
Total zone transitions, hab. session 20.40.51.1-0.3-1.1-0.01.0
Total locomotion distance, hab. session 20.20.30.5-0.70.1-0.7-0.1
Locomotion velocity, hab. session 20.10.20.3-0.6-0.0-0.6-0.1
Novel to familiar place preference ratio0.40.40.6-0.50.7-0.6-0.8
Novelty place preference0.20.20.4-0.20.6-0.2-0.6
Time in novel zone, NPP test0.10.10.1-0.00.4-0.0-0.3
Total zone transitions, NPP test0.60.81.3-0.8-1.2-0.51.0
Total locomotion distance, NPP test0.50.71.4-1.20.1-1.2-0.2
Locomotion velocity, NPP test0.50.71.4-1.10.4-1.2-0.5
Intraocular pressure1.42.14.3-2.1-0.5-1.90.3
Delta distance traveled before/after self-admin2.02.13.61.11.90.7-1.7
Delta ambulatory time before/after self-admin1.72.13.41.21.80.8-1.7
Parametrial fat weight0.10.30.5-0.70.2-0.7-0.2
Pavlov. Cond. lever latency0.50.61.31.1-0.11.10.2
Pavlov. Cond. magazine entry latency0.40.51.0-1.00.2-1.0-0.3
Pavlov. Cond. change in total contacts1.71.84.0-2.0-0.1-1.8-0.1
Pavlov. Cond. index score0.50.61.2-1.1-0.3-1.00.2
Pavlov. Cond. latency score0.40.51.0-1.0-0.4-0.90.3
Pavlov. Cond. lever contacts1.01.22.3-1.50.5-1.5-0.6
Pavlov. Cond. magazine entry number0.40.51.11.00.40.9-0.4
Pavlov. Cond. intertrial magazine entries0.20.20.40.30.60.1-0.6
Pavlov. Cond. lever-magazine prob. diff.0.40.51.1-1.1-0.3-1.00.2
Pavlov. Cond. response bias0.91.12.1-1.50.2-1.4-0.3
Pavlov. Cond. lever latency0.60.91.4-0.8-1.2-0.51.1
Pavlov. Cond. magazine entry latency0.00.00.0-0.10.1-0.1-0.1
Pavlov. Cond. change in total contacts1.82.94.2-1.22.0-1.5-2.0
Pavlov. Cond. index score0.81.11.8-0.51.3-0.8-1.3
Pavlov. Cond. latency score0.60.81.5-0.21.2-0.5-1.2
Pavlov. Cond. lever contacts0.50.71.30.41.20.1-1.1
Pavlov. Cond. magazine entry number0.20.20.30.4-0.40.50.4
Pavlov. Cond. intertrial magazine entries0.30.50.9-0.90.4-1.0-0.4
Pavlov. Cond. lever-magazine prob. diff.0.70.91.6-0.41.2-0.7-1.2
Pavlov. Cond. response bias0.81.01.9-0.31.4-0.6-1.4
Time in closed arm before self-admin0.60.71.41.20.41.1-0.3
Time in closed arm after self-admin1.61.82.51.4-1.11.61.2
Time in open arm before self-admin0.50.60.8-0.70.7-0.9-0.7
Time in open arm after self-admin0.40.50.9-0.90.2-0.9-0.3
Bone: periosteal estimation2.24.75.8-1.72.3-2.2-2.4
Bone: periosteal perimeter0.40.71.3-0.31.1-0.5-1.1
Bone: post-yield work1.31.92.91.71.31.2-1.2
Progressive ratio test 1 active lever presses0.91.12.21.50.61.3-0.4
Progressive ratio test 1 breakpoint0.91.12.11.40.71.2-0.5
Progressive ratio test 1 inactive lever presses0.00.00.00.00.10.0-0.0
Progressive ratio test 2 active lever presses1.92.23.81.22.00.5-1.8
Progressive ratio test 2 breakpoint1.92.13.71.21.90.5-1.8
Progressive ratio test 2 inactive lever presses0.50.81.10.91.00.6-1.0
Incentive Sensitization - Responses2.12.95.6-0.02.4-0.7-2.4
Incentive Sensitization - Breakpoint2.12.75.30.12.3-0.6-2.3
Sum of active levers in priming session hrs 5-61.21.12.2-0.21.4-0.5-1.5
Progressive ratio1.62.53.71.8-1.21.91.3
Food seeking constrained by brief footshock2.43.06.2-2.50.2-2.4-0.4
Seeking ratio, punishment vs. effort2.94.27.6-2.80.9-2.7-1.0
Retroperitoneal fat weight0.10.40.6-0.8-0.7-0.60.6
Reaction time number correct0.81.52.6-0.41.6-0.8-1.6
Reaction time mean minus median0.82.03.9-0.8-2.0-0.31.9
Reaction time mean minus median AUC0.71.82.9-1.2-1.7-0.71.5
Reaction time num false alarms1.82.54.7-0.22.2-0.7-2.2
Reaction time num false alarms AUC1.42.14.1-0.02.0-0.6-2.0
Reaction time trials correct on left0.81.52.6-0.41.6-0.8-1.6
Reaction time trials on left0.81.52.5-0.51.6-0.9-1.6
Reaction time mean0.71.11.9-1.4-0.9-1.10.8
Reaction time mean AUC0.81.22.3-1.5-0.8-1.30.6
Median of all reaction times0.81.12.4-1.6-0.3-1.40.1
Reaction time omissions1.62.33.4-1.8-1.5-1.31.4
Reaction time false alarm rate0.10.10.20.40.50.2-0.4
Reaction time premature initiation rate1.21.73.41.8-0.41.80.5
Reaction time premature initiations0.51.02.21.50.31.2-0.2
Std. dev. reaction times0.61.12.1-0.6-1.4-0.21.4
Reaction time trials completed0.81.52.5-0.51.6-0.9-1.6
Reaction time trials AUC0.81.62.6-0.61.6-1.0-1.6
Run reversals in cocaine runway, females0.20.20.3-0.5-0.3-0.40.3
Run reversals in cocaine runway, males1.41.43.1-1.8-0.1-1.60.0
Latency to leave start box in cocaine runway0.30.30.60.80.40.6-0.4
Latency to leave start box in cocaine runway, F1.11.22.11.51.01.1-0.8
Latency to leave start box in cocaine runway, M1.00.91.4-1.2-1.0-0.90.8
Std. dev. time between licks in bursts0.40.50.6-0.60.8-0.7-0.8
Total sessions with >9 infusions1.21.43.11.80.31.6-0.1
Short access day 1 total inactive lever presses1.62.13.71.9-0.71.90.8
Short access day 10 total inactive lever presses0.51.32.20.4-1.50.71.5
Short access day 1 total infusions1.41.83.92.0-0.11.80.2
Short access day 10 total infusions1.11.42.31.51.01.2-0.8
Short access total infusions0.91.12.41.60.51.3-0.4
Short access day 1 locomotion0.40.50.90.9-0.31.00.3
Short access day 10 total locomotion0.10.20.4-0.1-0.60.10.6
Short access total locomotion0.30.30.60.80.40.7-0.3
One hour access (0.3 mA shock)2.63.05.51.22.40.5-2.2
Compulsive drug intake0.30.30.6-0.5-0.8-0.20.7
One hour access (shock baseline)3.55.49.61.73.10.7-2.9
Social response proportion0.30.30.60.0-0.80.20.8
Social responses0.60.81.6-0.0-1.30.31.3
Social time0.00.00.1-0.20.2-0.2-0.2
Soleus weight0.41.12.4-1.5-0.5-1.30.4
Bone: stiffness0.30.50.9-0.90.5-0.9-0.6
Tibialis anterior weight4.013.428.8-5.4-1.7-4.51.2
Time to tail flick, vehicle, before self-admin0.40.40.8-0.00.9-0.3-0.9
Time to tail flick, vehicle, after self-admin0.91.21.81.31.11.0-0.9
Time to tail flick, test, before self-admin0.60.60.70.7-0.80.90.8
Time to tail flick, test, after self-admin0.80.91.91.40.31.2-0.2
Delta time to tail flick, vehicle, before/after SA1.01.01.81.40.81.0-0.6
Delta time to tail flick, test, before/after SA0.10.10.10.2-0.20.30.3
Tibia length0.61.53.21.80.61.6-0.4
Ambulatory time before self-admin0.50.81.1-0.9-1.0-0.61.0
Ambulatory time after self-admin0.40.40.90.10.9-0.1-0.9
Bone: tissue strength1.41.43.11.70.41.5-0.3
Total heroin consumption0.91.01.7-0.61.2-0.8-1.3
Bone: trabecular number0.20.30.60.40.80.1-0.8
Bone: trabecular spacing0.81.12.1-0.3-1.50.11.4
Bone: trabecular thickness1.82.24.30.02.1-0.5-2.1
Bone: trabecular tissue density1.31.93.5-1.0-1.9-0.51.8
Water consumed over 24 hours0.10.10.1-0.4-0.2-0.30.2
Number of responses in last shaping day0.30.40.80.90.20.8-0.2