Chkb

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 Chkb 0.2 0.09 2.6e-14 0.1 0.09 0.08 0.09 3.5e-11 1.2e-09 1.4e-09 8.6e-10
2 NAcc gene expression Chkb 0.03 0.02 4.3e-03 0.02 0.02 0.01 0.01 5.7e-04 6.4e-04 1.8e-03 1.7e-03
3 Adipose alternative TSS XM_006242181.5 0.05 0.03 4.5e-06 0.03 0.04 0.04 0.04 6.6e-04 1.3e-05 7.4e-05 5.0e-05
4 Brain gene expression Chkb 0.03 0.02 7.9e-03 0.02 0.01 0 0.01 1.1e-02 1.9e-02 2.6e-01 7.3e-02

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 density0.71.32.5-1.6-0.1-1.4-0.7
Area under the delay curve1.31.52.4-1.1-1.0-1.2-1.6
BMI with tail2.27.515.33.9-2.52.61.2
BMI without tail1.44.37.12.7-0.72.51.9
Body weight0.93.87.52.7-1.71.91.1
Weight adjusted by age1.01.63.01.7-1.70.6-0.2
Bone surface1.52.84.2-1.7-1.1-2.1-1.7
Bone volume1.42.54.2-1.9-0.6-2.0-1.4
Breakpoint value in progressive ratio session0.20.20.80.3-0.9-0.1-0.3
Number of licking bursts0.00.10.1-0.10.30.20.3
Context. condit. distance diff. score1.61.93.11.7-0.11.81.3
Locomotion velocity, session 10.20.20.30.5-0.50.50.2
Locomotion distance, session 11.31.63.3-1.80.2-1.3-1.2
Locomotion velocity, session 20.50.61.11.1-0.90.60.3
Locomotion distance, session 20.60.81.7-1.30.2-1.0-0.7
Locomotion velocity, session 31.82.03.40.51.41.61.8
Locomotion distance, session 30.20.20.3-0.40.50.20.4
Stereotopy head waving bouts, day 31.71.93.4-1.5-0.1-1.9-1.4
Stereotopy head waving duration, day 30.30.40.7-0.80.5-0.8-0.4
Locomotion velocity, session 71.11.22.40.70.91.11.6
Locomotion distance, session 70.30.40.70.30.40.80.7
Stereotopy head waving bouts, day 70.40.50.9-0.90.1-1.0-0.5
Stereotopy head waving duration, day 70.40.40.7-0.90.8-0.60.2
Locomotion velocity, session 81.11.32.21.5-0.11.21.3
Locomotion distance, session 80.40.60.90.9-0.90.70.2
Degree of sensitization distance0.80.81.71.3-1.20.5-0.1
Degree of sensitization stereotypy0.20.20.3-0.10.60.10.6
Conditioned locomotion0.50.51.31.10.10.80.5
Cocaine response after cond. corrected0.70.81.21.1-0.51.10.8
Cocaine response after cond. not corrected1.82.23.31.8-0.61.81.3
Cocaine response before conditioning0.70.91.61.2-0.51.10.8
Saline control response0.91.23.70.7-1.9-0.1-0.9
Bone: connectivity density0.40.71.7-1.30.1-0.9-0.3
Bone: cortical apparent density1.11.53.1-1.81.3-1.2-0.3
Bone: cortical area0.71.12.90.3-1.7-0.7-0.8
Bone: cortical porosity1.11.23.30.3-1.8-0.4-1.1
Bone: cortical porosity1.61.75.30.6-2.3-0.2-1.1
Bone: cortical thickness0.10.20.3-0.4-0.4-0.6-0.3
Bone: cortical thickness0.50.60.90.50.90.80.9
Bone: cortical tissue density1.01.32.6-1.61.2-1.1-0.2
Condit. Reinf. active minus inactive responses0.91.12.41.3-1.50.3-0.1
Condit. Reinf. active-inactive response ratio0.10.10.30.5-0.50.20.0
Condit. Reinf. active responses1.41.73.61.9-1.70.70.1
Condit. Reinf. inactive responses0.91.12.31.5-1.20.70.2
Incentive salience index mean1.61.94.31.8-2.10.2-0.4
Condit. Reinf. lever presses1.21.73.61.7-1.90.3-0.4
Condit. Reinf. active minus inactive responses1.51.92.9-0.7-1.2-1.7-1.7
Condit. Reinf. active-inactive response ratio0.40.50.7-0.7-0.4-0.8-0.7
Condit. Reinf. active responses1.31.83.00.1-1.7-1.2-1.6
Condit. Reinf. inactive responses0.50.71.40.9-1.20.1-0.7
Condit. Reinf. lever presses0.91.23.61.0-1.9-0.2-0.5
Condit. Reinf. lever reinforcers received1.52.03.2-0.0-1.7-1.4-1.8
Conditioned reinforcement - actives0.40.61.80.7-1.3-0.1-0.5
Conditioned reinforcement - inactives0.10.10.30.5-0.10.30.3
Conditioned locomotion1.21.63.11.8-1.21.30.6
Patch foraging indifference point 0 sec0.10.20.40.6-0.70.3-0.1
Patch foraging indifference point AUC2.73.96.5-0.9-2.0-2.1-2.6
Delay disc. indifference point, 0s delay2.02.16.00.6-2.5-0.9-1.2
Delay disc. indifference point, 16s delay0.60.61.3-0.4-0.7-0.8-1.1
Delay disc. indifference point, 2s delay5.96.610.4-1.9-2.3-2.7-3.2
Delay disc. indifference point, 24s delay0.20.30.50.6-0.30.70.3
Delay disc. indifference point, 4s delay1.41.52.5-1.1-0.9-1.3-1.6
Delay disc. indifference point, 8s delay0.50.61.6-1.30.1-0.6-0.7
Indifference point function ln k1.42.53.61.70.21.91.8
Indifference point function log k1.42.53.61.70.21.91.8
Patch foraging total patch changes 0 sec0.00.10.20.4-0.40.2-0.1
Patch foraging total patch changes 12 sec1.41.83.1-0.0-1.7-1.1-1.8
Patch foraging total patch changes 18 sec2.03.05.2-1.5-0.8-2.0-2.3
Patch foraging total patch changes 24 sec0.61.01.7-0.4-0.6-1.2-1.3
Patch foraging total patch changes 6 sec1.01.52.6-0.2-1.5-1.0-1.6
Patch foraging time to switch 0 sec0.10.20.6-0.50.8-0.3-0.1
Patch foraging water rate 0 sec0.30.71.11.0-0.11.00.8
Patch foraging water rate 12 sec0.71.42.41.6-0.61.41.0
Patch foraging water rate 18 sec2.33.55.31.90.12.32.3
Patch foraging water rate 24 sec1.21.72.91.10.41.71.5
Patch foraging water rate 6 sec0.50.71.10.8-0.11.11.0
Seeking ratio, delayed vs. immediate footshock0.20.30.5-0.70.5-0.60.0
Distance traveled before self-admin0.60.81.7-1.30.4-1.0-0.6
Distance traveled after self-admin0.20.20.5-0.00.70.40.5
Extensor digitorum longus weight0.20.81.31.1-0.11.10.8
Bone: elastic displacement0.30.30.9-1.0-0.2-0.2-0.4
Bone: elastic work0.10.20.6-0.0-0.80.1-0.2
Bone: endosteal estimation0.30.72.30.4-1.5-0.3-0.7
Bone: endosteal perimeter2.45.212.90.6-3.6-1.6-2.2
Epididymis fat weight1.03.56.92.6-2.60.5-0.2
Delta time in closed arm before/after self-admin0.20.20.5-0.2-0.4-0.1-0.7
Delta time in open arm before/after self-admin0.00.00.20.10.1-0.20.4
Diff in mean of infusions in LGA sessions1.21.44.01.1-2.0-0.2-0.7
Delay discount exponential model param0.91.01.71.00.70.91.3
Extinction: sum of active levers before priming0.60.71.2-0.5-0.8-0.8-1.1
Active lever presses in extinction session 61.31.32.61.6-0.81.20.7
Bone: final force0.20.40.5-0.6-0.4-0.7-0.7
Bone: final moment0.20.40.6-0.8-0.3-0.7-0.6
Food consumed during 24 hour testing period0.91.32.11.5-0.61.40.9
Glucose0.40.60.9-0.6-0.9-0.8-0.9
Heart weight0.61.01.80.80.61.01.3
Delay discount hyperbolic model param1.31.52.41.20.81.21.5
Intermittent access intake day 1-15 change0.20.51.01.0-0.90.4-0.1
Intermittent access intake escalation0.20.51.01.0-0.90.3-0.1
Intermittent access intake escalation 21.41.63.91.3-2.0-0.3-0.7
Intermitt. access day 1 inactive lever presses0.20.61.50.8-1.20.1-0.3
Intermitt. access day 15 inactive lever presses1.42.84.22.10.32.01.7
Intermitt. access escalation Index0.30.41.0-0.51.00.00.4
Intermittent access day 1 total infusions0.10.20.40.10.40.60.5
Intermittent access day 15 total infusions0.10.10.20.5-0.20.40.2
Intermittent access terminal intake (last 3 days)0.60.81.41.2-1.20.5-0.0
Intermittent access total infusions0.10.10.20.4-0.40.40.1
Intermittent access day 1 locomotion0.00.00.1-0.1-0.3-0.0-0.2
Intermittent access day 15 total locomotion0.40.71.41.0-1.20.6-0.1
Intermittent access total locomotion0.40.50.90.9-0.50.90.3
Intermittent access standard deviation0.30.61.00.70.50.81.0
Left kidney weight2.411.323.04.8-3.33.01.6
Right kidney weight3.817.435.15.9-3.44.12.5
Cocaine induced anxiety0.60.81.31.20.21.10.9
Post-drug Anxiety1.21.31.91.30.41.41.2
Baseline Anxiety0.20.20.4-0.60.6-0.3-0.1
Tail length0.20.81.7-1.30.7-1.0-0.3
Length with tail0.10.20.5-0.3-0.4-0.7-0.5
Length without tail0.31.13.00.5-1.7-0.5-0.9
Times rat made contact with spout3.03.44.80.91.82.22.2
Lifetime Intake0.20.20.40.5-0.30.60.3
Liver weight, left0.50.82.20.3-1.5-0.5-0.7
Liver weight, right0.20.40.7-0.4-0.6-0.6-0.8
Locomotor activity0.91.33.60.5-1.9-0.6-1.1
Locomotor testing distance0.20.40.7-0.80.2-0.7-0.6
Locomotor testing rearing2.04.06.9-0.6-2.3-1.9-2.6
Locomotion in novel chamber2.43.14.51.51.22.12.1
Locomotion in novel chamber post-restriction0.50.81.7-0.3-0.9-0.8-1.3
Fecal boli incidents, locomotor time 10.20.30.7-0.80.5-0.2-0.2
Change in fecal boli incidents, locomotor task0.10.10.20.5-0.30.10.1
Time >=10cm from walls, locomotor time 10.30.30.70.6-0.8-0.3-0.4
Bouts of movement, locomotor time 10.40.40.50.70.40.70.7
Total resting periods, locomotor time 10.20.20.40.30.60.50.5
Rest time, locomotor task time 10.81.02.6-0.01.61.00.7
Distance moved, locomotor task time 10.40.61.80.4-1.3-0.5-0.2
Vertical activity count, locomotor time 10.61.34.20.9-2.1-0.4-0.2
Time >=10cm from walls, locomotor time 20.71.12.01.4-1.40.40.3
Bouts of movement, locomotor time 20.10.20.3-0.60.4-0.4-0.2
Total resting periods, locomotor time 20.10.20.4-0.60.2-0.5-0.5
Rest time, locomotor task time 20.81.03.2-0.81.80.20.5
Distance moved, locomotor task time 21.31.54.31.3-2.10.3-0.2
Vertical activity count, locomotor time 21.31.74.71.4-2.20.2-0.4
Light reinforcement 10.40.92.60.8-1.6-0.0-0.5
Light reinforcement 21.62.47.31.4-2.70.1-0.6
Bone: marrow area0.30.72.00.3-1.4-0.4-0.7
Bone: maximum diameter0.81.53.71.5-1.90.1-0.4
Bone: maximum force0.10.20.3-0.6-0.4-0.4-0.4
Bone: maximum moment0.10.20.5-0.7-0.3-0.4-0.3
Mean time between licks in bursts0.71.73.6-1.71.9-0.60.1
Mean num. licks in bursts0.30.50.60.30.80.80.8
Cd content in liver0.50.61.0-0.8-0.1-0.8-1.0
Co content in liver0.50.51.80.2-1.3-0.1-0.5
Cu content in liver2.32.77.1-0.42.71.01.6
Fe content in liver0.50.61.2-0.7-0.6-0.7-1.1
K content in liver0.00.00.10.00.2-0.4-0.0
Mg content in liver0.70.81.3-0.7-0.5-1.1-1.0
Mn content in liver0.10.10.30.1-0.5-0.4-0.2
Na content in liver3.94.27.4-2.2-0.0-2.7-2.1
Rb content in liver0.40.51.0-0.1-0.9-0.6-1.0
Se content in liver0.40.40.70.90.20.80.6
Sr content in liver1.00.92.2-1.11.5-0.20.3
Zn content in liver0.70.82.2-0.41.50.60.7
Bone: minimum diameter0.40.82.20.3-1.5-0.5-0.7
Time in familiar zone, hab. session 11.11.01.70.60.71.31.3
Time in novel zone, hab. session 11.31.31.9-1.0-0.6-1.3-1.4
Total zone transitions, hab. session 11.52.23.6-1.90.5-1.7-1.4
Total locomotion distance, hab. session 10.50.71.3-0.5-0.8-0.7-1.2
Locomotion velocity, hab. session 10.71.01.8-0.6-0.9-1.0-1.4
Time in familiar zone, hab. session 21.81.92.91.40.41.71.6
Time in novel zone, hab. session 21.31.32.2-1.50.0-1.4-1.1
Total zone transitions, hab. session 20.20.20.50.30.30.70.4
Total locomotion distance, hab. session 20.50.71.01.0-0.91.00.1
Locomotion velocity, hab. session 20.40.60.90.9-1.00.8-0.0
Novel to familiar place preference ratio0.50.61.4-0.11.20.40.9
Novelty place preference0.60.71.20.01.10.71.0
Time in novel zone, NPP test0.91.01.8-0.01.40.81.2
Total zone transitions, NPP test0.30.40.9-1.00.6-0.6-0.3
Total locomotion distance, NPP test0.30.40.8-0.0-0.9-0.3-0.8
Locomotion velocity, NPP test0.20.30.80.1-0.9-0.2-0.7
Intraocular pressure0.71.02.0-0.0-1.4-0.6-1.3
Delta distance traveled before/after self-admin3.03.24.82.10.32.21.8
Delta ambulatory time before/after self-admin1.72.13.61.70.41.91.4
Parametrial fat weight0.10.20.60.6-0.80.2-0.1
Pavlov. Cond. lever latency1.01.22.5-1.61.5-0.40.3
Pavlov. Cond. magazine entry latency0.10.10.30.00.1-0.5-0.5
Pavlov. Cond. change in total contacts0.50.50.80.3-0.9-0.7-0.9
Pavlov. Cond. index score0.10.20.30.5-0.4-0.3-0.5
Pavlov. Cond. latency score0.20.30.60.7-0.6-0.2-0.4
Pavlov. Cond. lever contacts0.91.12.41.5-1.40.4-0.3
Pavlov. Cond. magazine entry number0.20.30.60.30.00.70.8
Pavlov. Cond. intertrial magazine entries0.81.02.21.2-1.50.4-0.1
Pavlov. Cond. lever-magazine prob. diff.0.20.20.40.4-0.3-0.4-0.6
Pavlov. Cond. response bias0.20.30.50.7-0.70.0-0.4
Pavlov. Cond. lever latency0.71.01.9-1.40.7-0.9-0.9
Pavlov. Cond. magazine entry latency0.30.30.80.9-0.30.30.5
Pavlov. Cond. change in total contacts0.40.71.2-0.1-1.1-0.9-0.9
Pavlov. Cond. index score0.30.51.01.0-0.70.30.5
Pavlov. Cond. latency score0.60.81.71.3-0.80.60.7
Pavlov. Cond. lever contacts0.81.02.01.4-0.80.90.8
Pavlov. Cond. magazine entry number0.40.51.3-1.10.6-0.4-0.5
Pavlov. Cond. intertrial magazine entries0.20.30.6-0.10.60.70.5
Pavlov. Cond. lever-magazine prob. diff.0.40.51.11.1-0.70.40.5
Pavlov. Cond. response bias0.20.30.60.8-0.60.20.4
Time in closed arm before self-admin2.12.74.4-1.0-1.5-2.1-1.8
Time in closed arm after self-admin2.52.74.2-0.5-2.0-1.5-2.0
Time in open arm before self-admin0.40.51.4-0.11.20.60.4
Time in open arm after self-admin0.10.10.20.10.40.20.4
Bone: periosteal estimation0.71.43.90.4-2.0-0.7-1.0
Bone: periosteal perimeter1.73.08.40.8-2.9-1.0-1.4
Bone: post-yield work0.60.81.9-1.11.4-0.20.2
Progressive ratio test 1 active lever presses0.70.81.20.11.10.91.1
Progressive ratio test 1 breakpoint0.60.71.20.11.10.81.0
Progressive ratio test 1 inactive lever presses0.00.10.10.3-0.4-0.0-0.1
Progressive ratio test 2 active lever presses0.50.51.01.0-0.60.80.4
Progressive ratio test 2 breakpoint0.40.40.70.8-0.50.70.3
Progressive ratio test 2 inactive lever presses0.40.61.11.0-1.00.50.0
Incentive Sensitization - Responses0.81.12.81.1-1.70.2-0.4
Incentive Sensitization - Breakpoint0.81.02.61.1-1.60.2-0.4
Sum of active levers in priming session hrs 5-60.10.10.20.3-0.50.0-0.3
Progressive ratio0.20.30.50.7-0.10.70.5
Food seeking constrained by brief footshock1.61.93.51.9-1.41.50.3
Seeking ratio, punishment vs. effort0.30.40.8-0.0-0.9-0.5-0.8
Retroperitoneal fat weight1.25.310.93.3-2.71.70.2
Reaction time number correct0.20.40.8-0.90.4-0.3-0.7
Reaction time mean minus median0.10.10.50.1-0.7-0.0-0.1
Reaction time mean minus median AUC0.10.10.20.4-0.40.30.2
Reaction time num false alarms0.00.10.2-0.2-0.1-0.4-0.2
Reaction time num false alarms AUC0.00.10.1-0.10.30.20.3
Reaction time trials correct on left0.20.40.8-0.90.4-0.3-0.7
Reaction time trials on left0.20.40.9-0.90.5-0.3-0.7
Reaction time mean0.50.81.7-0.31.30.51.1
Reaction time mean AUC0.40.71.5-0.41.20.31.0
Median of all reaction times1.21.73.7-0.31.90.81.6
Reaction time omissions0.20.30.6-0.60.80.10.4
Reaction time false alarm rate0.00.00.10.2-0.00.00.3
Reaction time premature initiation rate2.63.510.01.8-3.2-0.2-0.9
Reaction time premature initiations1.11.95.51.0-2.3-0.3-1.1
Std. dev. reaction times0.10.20.50.20.20.50.7
Reaction time trials completed0.20.40.9-0.90.5-0.3-0.7
Reaction time trials AUC0.10.30.6-0.80.4-0.1-0.5
Run reversals in cocaine runway, females0.40.40.70.30.70.70.9
Run reversals in cocaine runway, males0.90.91.5-1.0-0.6-0.8-1.2
Latency to leave start box in cocaine runway1.72.03.61.60.11.91.3
Latency to leave start box in cocaine runway, F4.35.07.12.31.12.72.5
Latency to leave start box in cocaine runway, M0.80.71.4-0.2-1.2-0.4-1.1
Std. dev. time between licks in bursts0.81.13.10.9-1.70.1-0.6
Total sessions with >9 infusions0.60.71.50.50.41.20.9
Short access day 1 total inactive lever presses2.73.56.02.4-0.42.31.6
Short access day 10 total inactive lever presses1.63.88.22.9-2.41.10.3
Short access day 1 total infusions1.11.52.81.10.31.71.3
Short access day 10 total infusions0.70.91.71.1-0.21.30.9
Short access total infusions0.70.81.70.9-0.11.30.8
Short access day 1 locomotion1.01.32.11.20.31.51.2
Short access day 10 total locomotion0.40.81.31.1-0.41.20.7
Short access total locomotion0.50.61.10.8-0.31.00.6
One hour access (0.3 mA shock)0.70.82.30.9-1.5-0.0-0.4
Compulsive drug intake0.00.00.0-0.1-0.20.0-0.0
One hour access (shock baseline)0.30.51.30.6-1.1-0.1-0.4
Social response proportion0.40.50.7-0.5-0.4-0.8-0.8
Social responses0.30.40.6-0.1-0.7-0.8-0.8
Social time0.81.12.00.80.81.41.1
Soleus weight0.72.03.51.9-0.31.61.4
Bone: stiffness0.10.20.6-0.80.3-0.5-0.0
Tibialis anterior weight0.00.10.10.20.10.40.2
Time to tail flick, vehicle, before self-admin0.91.02.11.4-1.40.2-0.1
Time to tail flick, vehicle, after self-admin0.30.40.80.9-0.80.10.0
Time to tail flick, test, before self-admin0.20.20.50.7-0.60.00.3
Time to tail flick, test, after self-admin2.52.64.22.1-0.01.71.7
Delta time to tail flick, vehicle, before/after SA0.40.40.7-0.80.8-0.3-0.1
Delta time to tail flick, test, before/after SA0.50.51.00.60.41.00.7
Tibia length1.02.96.1-2.51.2-1.7-0.9
Ambulatory time before self-admin0.20.30.7-0.60.8-0.00.3
Ambulatory time after self-admin0.50.60.80.50.80.90.8
Bone: tissue strength0.80.82.1-1.51.0-0.10.0
Total heroin consumption0.20.20.70.3-0.80.0-0.3
Bone: trabecular number0.50.92.3-1.5-0.1-1.0-0.5
Bone: trabecular spacing1.21.63.61.9-0.51.50.7
Bone: trabecular thickness0.70.81.2-0.4-1.1-1.0-0.9
Bone: trabecular tissue density1.11.62.9-1.71.0-1.3-0.8
Water consumed over 24 hours0.10.10.20.0-0.20.40.3
Number of responses in last shaping day0.30.30.8-0.40.90.40.4