Chka

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 PL mRNA stability Chka 0.04 0.03 1.1e-03 0.03 0.03 0.02 0.02 4.6e-04 6.1e-04 1.1e-03 1.3e-03
2 NAcc intron excision ratio chr1_201104111_201113038 0.02 0.02 3.8e-03 0.02 0.01 0.01 0.02 9.6e-04 8.4e-03 7.0e-03 4.0e-03
3 Brain isoform ratio NM_001398586.1 0.03 0.02 4.0e-03 0.03 0.01 0.01 0.01 9.3e-04 1.6e-02 1.3e-02 1.3e-02
4 Liver isoform ratio NM_017127.3 0.02 0.02 3.7e-03 0.01 0.01 0.01 0.01 3.7e-02 2.1e-02 8.2e-03 2.7e-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 density2.74.56.60.52.62.5-2.2
Area under the delay curve0.60.60.9-0.10.91.0-0.7
BMI with tail3.09.712.52.53.33.5-3.0
BMI without tail1.83.64.51.52.12.1-1.9
Body weight1.77.115.23.92.22.3-1.8
Weight adjusted by age0.80.92.91.70.40.7-0.2
Bone surface3.56.28.71.93.02.9-2.0
Bone volume2.13.65.60.82.42.3-1.7
Breakpoint value in progressive ratio session1.01.13.11.80.90.7-0.3
Number of licking bursts0.10.10.20.10.40.4-0.1
Context. condit. distance diff. score0.30.31.3-1.2-0.1-0.00.2
Locomotion velocity, session 10.00.00.00.10.10.10.1
Locomotion distance, session 11.62.03.10.81.71.7-1.1
Locomotion velocity, session 21.01.23.81.90.60.7-0.4
Locomotion distance, session 20.91.21.71.31.21.2-0.5
Locomotion velocity, session 31.41.72.40.01.51.5-1.4
Locomotion distance, session 30.10.10.20.10.40.4-0.3
Stereotopy head waving bouts, day 31.11.31.7-0.71.21.2-1.3
Stereotopy head waving duration, day 30.60.71.7-1.30.60.5-0.7
Locomotion velocity, session 71.11.22.0-0.01.21.2-1.4
Locomotion distance, session 70.40.50.70.70.60.6-0.9
Stereotopy head waving bouts, day 70.80.91.0-1.01.00.9-0.9
Stereotopy head waving duration, day 71.82.23.40.51.81.7-1.5
Locomotion velocity, session 80.60.72.11.40.60.7-0.1
Locomotion distance, session 80.10.10.3-0.30.50.50.1
Degree of sensitization distance0.60.61.00.50.70.7-1.0
Degree of sensitization stereotypy0.60.71.20.11.11.0-0.7
Conditioned locomotion1.61.92.91.7-1.0-1.01.6
Cocaine response after cond. corrected0.10.10.2-0.40.10.1-0.2
Cocaine response after cond. not corrected0.30.30.4-0.50.50.5-0.6
Cocaine response before conditioning0.20.20.30.20.50.5-0.4
Saline control response1.21.64.42.10.90.9-0.6
Bone: connectivity density4.16.59.01.83.02.9-2.3
Bone: cortical apparent density0.10.20.80.9-0.0-0.0-0.0
Bone: cortical area0.40.61.00.8-0.5-0.61.0
Bone: cortical porosity0.10.10.1-0.20.30.20.4
Bone: cortical porosity0.10.10.20.40.30.20.3
Bone: cortical thickness1.93.27.22.7-0.9-1.01.9
Bone: cortical thickness0.60.82.61.6-0.2-0.30.5
Bone: cortical tissue density0.20.20.91.0-0.1-0.0-0.0
Condit. Reinf. active minus inactive responses0.40.40.70.30.80.8-0.5
Condit. Reinf. active-inactive response ratio0.20.20.2-0.10.50.5-0.4
Condit. Reinf. active responses0.00.00.10.10.20.3-0.2
Condit. Reinf. inactive responses0.00.10.1-0.2-0.3-0.30.0
Incentive salience index mean0.30.30.50.50.70.7-0.1
Condit. Reinf. lever presses0.10.20.50.4-0.2-0.20.7
Condit. Reinf. active minus inactive responses0.91.11.2-1.01.01.1-1.1
Condit. Reinf. active-inactive response ratio0.70.72.5-1.60.30.3-0.3
Condit. Reinf. active responses1.42.02.7-0.31.61.6-1.7
Condit. Reinf. inactive responses1.51.92.20.91.51.5-1.4
Condit. Reinf. lever presses1.11.52.11.01.41.4-1.0
Condit. Reinf. lever reinforcers received1.62.23.0-0.11.71.7-1.7
Conditioned reinforcement - actives0.50.50.9-0.4-0.9-0.70.7
Conditioned reinforcement - inactives2.02.36.8-2.6-1.2-0.9-0.3
Conditioned locomotion5.97.111.0-3.3-2.6-2.42.1
Patch foraging indifference point 0 sec0.30.51.2-1.1-0.1-0.2-1.0
Patch foraging indifference point AUC0.81.02.31.5-0.2-0.11.2
Delay disc. indifference point, 0s delay1.21.32.1-0.21.51.2-1.3
Delay disc. indifference point, 16s delay0.40.41.6-1.3-0.2-0.10.3
Delay disc. indifference point, 2s delay0.20.30.4-0.60.60.5-0.3
Delay disc. indifference point, 24s delay0.20.20.50.3-0.4-0.50.7
Delay disc. indifference point, 4s delay0.20.20.4-0.00.60.6-0.1
Delay disc. indifference point, 8s delay0.50.50.80.30.70.7-0.9
Indifference point function ln k1.72.47.2-2.7-1.1-1.1-0.2
Indifference point function log k1.72.47.2-2.7-1.1-1.1-0.2
Patch foraging total patch changes 0 sec0.20.30.5-0.7-0.4-0.5-0.5
Patch foraging total patch changes 12 sec0.70.92.81.70.60.6-0.2
Patch foraging total patch changes 18 sec0.20.20.30.60.50.4-0.5
Patch foraging total patch changes 24 sec0.30.30.91.0-0.3-0.20.6
Patch foraging total patch changes 6 sec1.01.52.60.81.11.1-1.6
Patch foraging time to switch 0 sec3.24.96.31.52.52.5-2.2
Patch foraging water rate 0 sec5.69.010.7-2.6-3.3-3.32.8
Patch foraging water rate 12 sec7.010.812.1-3.0-3.4-3.53.3
Patch foraging water rate 18 sec1.31.72.2-1.5-1.2-1.21.2
Patch foraging water rate 24 sec3.95.56.3-1.8-2.5-2.52.5
Patch foraging water rate 6 sec2.73.95.2-1.2-2.3-2.22.0
Seeking ratio, delayed vs. immediate footshock0.60.61.20.11.11.0-0.6
Distance traveled before self-admin0.10.10.20.30.40.3-0.1
Distance traveled after self-admin0.10.10.4-0.10.30.2-0.6
Extensor digitorum longus weight2.28.831.75.61.21.3-0.0
Bone: elastic displacement3.03.44.6-0.4-2.1-2.12.1
Bone: elastic work1.11.42.41.4-0.8-0.91.5
Bone: endosteal estimation0.71.63.1-1.80.80.8-1.4
Bone: endosteal perimeter1.43.06.9-2.61.11.1-1.6
Epididymis fat weight1.22.89.0-3.0-1.0-0.90.3
Delta time in closed arm before/after self-admin0.50.41.21.1-0.3-0.20.7
Delta time in open arm before/after self-admin0.10.10.2-0.50.10.1-0.4
Diff in mean of infusions in LGA sessions0.20.30.60.8-0.0-0.20.6
Delay discount exponential model param0.40.40.70.0-0.8-0.80.5
Extinction: sum of active levers before priming2.22.24.82.21.51.3-0.1
Active lever presses in extinction session 60.60.61.21.1-0.6-0.50.7
Bone: final force0.91.53.31.81.11.1-0.5
Bone: final moment0.81.22.71.71.01.0-0.4
Food consumed during 24 hour testing period0.40.50.6-0.5-0.7-0.80.7
Glucose0.81.22.1-1.40.90.9-1.1
Heart weight0.60.82.7-1.7-0.3-0.2-0.6
Delay discount hyperbolic model param0.40.40.70.0-0.8-0.90.5
Intermittent access intake day 1-15 change1.31.31.6-1.2-1.1-1.11.1
Intermittent access intake escalation0.80.71.4-1.2-0.8-0.70.7
Intermittent access intake escalation 20.50.50.7-0.8-0.8-0.70.6
Intermitt. access day 1 inactive lever presses0.60.62.3-1.5-0.4-0.3-0.0
Intermitt. access day 15 inactive lever presses0.70.72.6-1.6-0.1-0.0-0.6
Intermitt. access escalation Index1.81.62.5-1.6-1.1-1.21.0
Intermittent access day 1 total infusions3.54.19.0-1.91.31.4-3.0
Intermittent access day 15 total infusions2.42.69.1-3.0-0.4-0.2-1.1
Intermittent access terminal intake (last 3 days)2.02.26.3-2.50.10.2-1.6
Intermittent access total infusions1.51.73.6-1.90.50.6-1.6
Intermittent access day 1 locomotion2.42.55.3-1.01.21.4-2.3
Intermittent access day 15 total locomotion1.21.24.7-2.2-0.4-0.2-0.3
Intermittent access total locomotion1.92.25.9-2.40.50.6-1.5
Intermittent access standard deviation0.30.30.9-1.0-0.6-0.40.2
Left kidney weight0.92.43.6-1.9-1.6-1.61.1
Right kidney weight1.13.14.0-1.6-2.0-1.91.4
Cocaine induced anxiety0.00.00.0-0.1-0.1-0.2-0.1
Post-drug Anxiety0.30.31.01.0-0.2-0.30.1
Baseline Anxiety0.60.62.21.5-0.0-0.00.5
Tail length0.30.91.81.4-0.9-0.90.5
Length with tail0.62.39.23.0-0.1-0.10.2
Length without tail0.71.66.02.40.50.5-0.2
Times rat made contact with spout0.70.81.30.61.11.1-0.5
Lifetime Intake1.61.83.7-1.70.50.7-1.9
Liver weight, left0.10.10.2-0.4-0.2-0.30.3
Liver weight, right0.40.71.1-0.3-0.9-0.81.1
Locomotor activity0.81.21.5-1.2-1.1-1.11.0
Locomotor testing distance0.91.51.9-1.4-1.2-1.11.2
Locomotor testing rearing0.20.41.3-1.10.10.20.3
Locomotion in novel chamber1.92.38.1-2.8-0.7-0.7-0.4
Locomotion in novel chamber post-restriction1.61.95.2-2.3-0.9-1.10.7
Fecal boli incidents, locomotor time 10.00.00.1-0.2-0.20.10.1
Change in fecal boli incidents, locomotor task0.40.40.50.60.50.6-0.7
Time >=10cm from walls, locomotor time 12.02.04.5-1.01.01.2-2.1
Bouts of movement, locomotor time 10.60.61.01.0-0.5-0.60.9
Total resting periods, locomotor time 10.50.50.90.7-0.6-0.71.0
Rest time, locomotor task time 11.92.12.8-1.3-1.7-1.51.3
Distance moved, locomotor task time 11.51.63.30.21.21.3-1.8
Vertical activity count, locomotor time 10.80.81.7-1.20.30.2-1.3
Time >=10cm from walls, locomotor time 20.30.30.7-0.2-0.7-0.40.8
Bouts of movement, locomotor time 20.20.20.70.8-0.00.00.2
Total resting periods, locomotor time 20.10.10.30.50.10.10.1
Rest time, locomotor task time 21.01.22.7-1.60.20.1-1.4
Distance moved, locomotor task time 20.30.30.70.8-0.4-0.40.5
Vertical activity count, locomotor time 21.82.03.00.2-1.5-1.61.7
Light reinforcement 10.71.22.1-1.0-0.9-1.01.5
Light reinforcement 21.82.54.0-2.0-1.2-1.31.6
Bone: marrow area0.81.63.1-1.80.80.8-1.5
Bone: maximum diameter0.10.20.4-0.4-0.5-0.50.6
Bone: maximum force2.44.25.71.62.42.4-1.7
Bone: maximum moment2.03.44.71.42.22.2-1.5
Mean time between licks in bursts0.30.41.21.10.30.3-0.5
Mean num. licks in bursts0.10.10.1-0.00.40.3-0.3
Cd content in liver1.01.12.0-1.4-1.0-1.00.6
Co content in liver1.51.73.2-0.4-1.3-1.41.8
Cu content in liver0.10.10.20.5-0.1-0.1-0.1
Fe content in liver0.00.00.10.30.2-0.00.1
K content in liver1.81.82.91.11.71.6-0.5
Mg content in liver2.22.23.7-0.21.91.9-1.2
Mn content in liver0.70.82.21.50.70.6-0.1
Na content in liver0.60.61.50.1-0.6-0.71.2
Rb content in liver1.51.92.3-1.51.21.3-1.5
Se content in liver0.50.71.1-0.40.80.8-1.0
Sr content in liver0.90.82.71.7-0.4-0.40.3
Zn content in liver0.30.31.01.00.20.20.0
Bone: minimum diameter1.12.12.4-1.41.41.4-1.5
Time in familiar zone, hab. session 10.20.20.3-0.60.30.3-0.5
Time in novel zone, hab. session 10.00.00.00.1-0.2-0.20.1
Total zone transitions, hab. session 10.30.40.91.00.70.6-0.0
Total locomotion distance, hab. session 10.10.10.4-0.60.00.00.2
Locomotion velocity, hab. session 10.00.10.2-0.20.0-0.00.5
Time in familiar zone, hab. session 20.50.50.80.9-0.5-0.60.8
Time in novel zone, hab. session 21.21.22.1-0.41.11.1-1.5
Total zone transitions, hab. session 23.95.17.61.22.82.7-2.0
Total locomotion distance, hab. session 21.01.32.10.11.51.5-1.0
Locomotion velocity, hab. session 20.81.01.6-0.21.31.3-0.9
Novel to familiar place preference ratio0.80.81.70.30.90.9-1.3
Novelty place preference0.80.81.9-0.00.80.8-1.4
Time in novel zone, NPP test0.80.81.8-0.00.80.8-1.3
Total zone transitions, NPP test1.31.92.61.41.61.6-0.7
Total locomotion distance, NPP test0.20.30.50.20.70.7-0.2
Locomotion velocity, NPP test0.10.10.30.20.50.5-0.0
Intraocular pressure1.31.82.3-0.7-1.5-1.51.5
Delta distance traveled before/after self-admin0.00.00.1-0.2-0.10.0-0.3
Delta ambulatory time before/after self-admin0.00.00.10.0-0.10.0-0.4
Parametrial fat weight0.51.03.7-1.90.30.4-0.2
Pavlov. Cond. lever latency0.20.30.3-0.6-0.5-0.5-0.5
Pavlov. Cond. magazine entry latency0.81.01.6-0.31.31.2-1.0
Pavlov. Cond. change in total contacts0.20.20.5-0.70.50.4-0.1
Pavlov. Cond. index score0.10.10.5-0.10.10.00.7
Pavlov. Cond. latency score0.10.10.2-0.00.30.30.5
Pavlov. Cond. lever contacts0.20.20.50.30.30.30.7
Pavlov. Cond. magazine entry number0.10.10.30.20.20.2-0.6
Pavlov. Cond. intertrial magazine entries0.70.81.2-0.4-1.1-1.00.9
Pavlov. Cond. lever-magazine prob. diff.0.10.10.30.10.20.10.5
Pavlov. Cond. response bias0.10.10.2-0.20.1-0.00.5
Pavlov. Cond. lever latency0.00.00.1-0.2-0.3-0.2-0.1
Pavlov. Cond. magazine entry latency2.73.14.01.82.01.9-1.1
Pavlov. Cond. change in total contacts0.70.91.50.41.21.2-0.8
Pavlov. Cond. index score0.81.11.51.01.21.2-0.5
Pavlov. Cond. latency score0.60.81.20.91.11.0-0.4
Pavlov. Cond. lever contacts0.10.10.30.2-0.2-0.20.6
Pavlov. Cond. magazine entry number3.54.35.1-2.1-2.3-2.21.7
Pavlov. Cond. intertrial magazine entries0.81.02.0-1.4-1.0-1.00.0
Pavlov. Cond. lever-magazine prob. diff.1.11.31.81.21.31.3-0.6
Pavlov. Cond. response bias0.50.60.90.90.90.8-0.3
Time in closed arm before self-admin0.20.20.4-0.60.30.1-0.6
Time in closed arm after self-admin0.10.10.10.2-0.3-0.30.1
Time in open arm before self-admin0.30.30.60.8-0.1-0.10.7
Time in open arm after self-admin0.00.00.00.1-0.2-0.20.1
Bone: periosteal estimation0.00.10.2-0.50.10.1-0.2
Bone: periosteal perimeter0.20.40.5-0.40.60.6-0.7
Bone: post-yield work6.18.411.4-0.83.43.4-3.2
Progressive ratio test 1 active lever presses0.70.71.8-1.3-0.7-0.6-0.6
Progressive ratio test 1 breakpoint0.70.81.7-1.3-0.8-0.7-0.3
Progressive ratio test 1 inactive lever presses0.20.20.5-0.7-0.20.0-0.7
Progressive ratio test 2 active lever presses1.11.23.5-1.9-0.7-0.5-0.8
Progressive ratio test 2 breakpoint1.61.84.6-2.1-1.2-1.0-0.2
Progressive ratio test 2 inactive lever presses2.32.69.2-3.0-0.6-0.4-0.9
Incentive Sensitization - Responses0.20.20.6-0.5-0.00.1-0.8
Incentive Sensitization - Breakpoint0.20.20.5-0.7-0.20.0-0.6
Sum of active levers in priming session hrs 5-61.91.93.00.4-1.7-1.61.3
Progressive ratio4.45.17.51.22.72.5-2.2
Food seeking constrained by brief footshock0.20.20.30.50.40.4-0.5
Seeking ratio, punishment vs. effort2.73.34.9-0.9-2.2-2.01.8
Retroperitoneal fat weight2.06.421.0-4.6-1.5-1.50.5
Reaction time number correct0.50.71.11.0-0.6-0.71.1
Reaction time mean minus median1.31.72.41.61.21.3-1.1
Reaction time mean minus median AUC0.60.72.41.50.40.6-0.1
Reaction time num false alarms0.60.81.20.0-1.0-1.10.9
Reaction time num false alarms AUC0.30.40.60.8-0.5-0.60.6
Reaction time trials correct on left0.50.71.11.0-0.6-0.71.1
Reaction time trials on left0.60.81.31.1-0.6-0.71.1
Reaction time mean0.40.61.5-0.00.60.7-1.2
Reaction time mean AUC0.50.61.5-0.20.60.7-1.2
Median of all reaction times0.60.82.1-0.30.60.7-1.5
Reaction time omissions0.70.92.91.70.50.5-0.5
Reaction time false alarm rate0.10.20.30.0-0.5-0.50.3
Reaction time premature initiation rate1.11.44.42.10.70.7-0.6
Reaction time premature initiations1.41.97.62.80.30.20.1
Std. dev. reaction times0.50.71.20.70.70.8-1.1
Reaction time trials completed0.60.81.31.1-0.6-0.71.1
Reaction time trials AUC0.40.61.01.0-0.5-0.60.9
Run reversals in cocaine runway, females2.52.43.11.11.71.8-1.5
Run reversals in cocaine runway, males0.50.40.80.3-0.9-0.80.6
Latency to leave start box in cocaine runway0.91.01.7-0.21.11.1-1.3
Latency to leave start box in cocaine runway, F0.70.81.3-0.01.00.9-1.1
Latency to leave start box in cocaine runway, M0.00.00.00.00.10.2-0.1
Std. dev. time between licks in bursts0.80.91.00.9-1.0-1.00.9
Total sessions with >9 infusions0.30.40.7-0.80.10.3-0.8
Short access day 1 total inactive lever presses1.21.33.5-1.9-0.4-0.3-1.2
Short access day 10 total inactive lever presses0.40.41.6-1.3-0.2-0.2-0.2
Short access day 1 total infusions1.51.63.3-1.50.40.6-1.8
Short access day 10 total infusions3.53.98.9-0.71.71.8-3.0
Short access total infusions1.82.05.5-0.70.91.1-2.3
Short access day 1 locomotion0.70.81.5-1.20.50.7-0.9
Short access day 10 total locomotion0.60.71.3-0.70.60.8-1.2
Short access total locomotion0.60.61.2-0.60.60.8-1.1
One hour access (0.3 mA shock)2.63.09.9-3.2-1.0-0.8-0.7
Compulsive drug intake1.11.14.22.0-0.1-0.20.6
One hour access (shock baseline)3.13.612.1-3.5-1.2-1.0-0.1
Social response proportion1.21.31.90.91.11.1-1.4
Social responses0.20.31.01.0-0.2-0.10.2
Social time0.30.41.21.10.40.60.1
Soleus weight2.67.512.9-3.6-2.8-2.61.7
Bone: stiffness2.54.05.61.22.32.4-1.9
Tibialis anterior weight2.79.333.35.8-0.6-0.51.8
Time to tail flick, vehicle, before self-admin2.12.13.40.51.81.6-1.5
Time to tail flick, vehicle, after self-admin1.41.52.81.71.21.2-0.6
Time to tail flick, test, before self-admin1.71.72.8-0.01.41.4-1.7
Time to tail flick, test, after self-admin0.00.00.00.10.0-0.00.1
Delta time to tail flick, vehicle, before/after SA0.40.41.31.10.10.30.2
Delta time to tail flick, test, before/after SA2.11.92.80.6-1.5-1.51.7
Tibia length0.61.62.40.3-1.3-1.41.6
Ambulatory time before self-admin0.10.10.40.20.60.30.3
Ambulatory time after self-admin0.80.81.3-0.80.90.7-1.2
Bone: tissue strength0.20.20.4-0.30.30.30.7
Total heroin consumption1.51.85.82.40.80.7-0.4
Bone: trabecular number2.33.65.50.62.32.2-1.9
Bone: trabecular spacing0.91.22.0-0.2-1.2-1.11.4
Bone: trabecular thickness1.41.62.4-1.01.31.3-1.5
Bone: trabecular tissue density3.95.68.6-2.9-2.3-2.31.8
Water consumed over 24 hours0.60.70.90.80.90.9-0.5
Number of responses in last shaping day0.20.20.4-0.6-0.6-0.50.2