Zkscan2

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 gene expression Zkscan2 0.04 0.02 3.0e-04 0.04 0.03 0.03 0.03 8.2e-05 1.9e-04 5.7e-04 2.1e-04
2 Brain gene expression Zkscan2 0.09 0.05 6.2e-08 0.08 0.07 0.06 0.07 9.9e-08 3.3e-07 1.8e-06 8.1e-07
3 Brain isoform ratio XM_039101194.1 0.07 0.04 3.8e-05 0.01 0.05 0.04 0.04 9.0e-02 2.1e-05 6.8e-05 2.6e-04

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
Bone: apparent density0.40.61.01.00.90.1
Area under the delay curve0.20.20.60.1-0.00.8
BMI with tail1.85.87.72.82.81.5
BMI without tail5.912.318.04.24.21.0
Body weight2.39.614.33.83.7-0.8
Weight adjusted by age1.21.41.41.21.11.2
Bone surface1.01.72.61.61.50.6
Bone volume1.32.33.41.81.80.6
Breakpoint value in progressive ratio session0.00.00.00.10.1-0.1
Number of licking bursts7.48.79.1-2.9-2.93.0
Context. condit. distance diff. score0.50.71.5-0.5-0.51.2
Locomotion velocity, session 10.10.10.10.30.40.4
Locomotion distance, session 10.10.20.30.50.40.3
Locomotion velocity, session 20.40.51.20.50.41.1
Locomotion distance, session 20.30.40.60.80.60.4
Locomotion velocity, session 30.40.50.70.80.90.2
Locomotion distance, session 30.20.20.3-0.3-0.30.6
Stereotopy head waving bouts, day 30.60.71.90.20.2-1.4
Stereotopy head waving duration, day 30.30.30.70.40.3-0.8
Locomotion velocity, session 70.80.91.70.70.7-1.3
Locomotion distance, session 70.30.30.8-0.3-0.30.9
Stereotopy head waving bouts, day 70.40.41.20.20.2-1.1
Stereotopy head waving duration, day 70.40.50.50.70.7-0.6
Locomotion velocity, session 80.00.00.10.20.30.2
Locomotion distance, session 80.50.72.00.0-0.01.4
Degree of sensitization distance0.10.10.1-0.2-0.20.3
Degree of sensitization stereotypy0.10.10.10.20.1-0.4
Conditioned locomotion0.10.10.2-0.3-0.2-0.5
Cocaine response after cond. corrected0.80.91.2-1.1-1.10.5
Cocaine response after cond. not corrected0.10.10.10.30.2-0.3
Cocaine response before conditioning4.55.47.62.72.8-1.1
Saline control response0.30.51.1-0.4-0.31.1
Bone: connectivity density0.10.10.10.30.20.4
Bone: cortical apparent density0.81.01.2-1.0-1.10.9
Bone: cortical area4.06.07.52.72.71.8
Bone: cortical porosity1.41.62.01.21.4-1.1
Bone: cortical porosity1.51.62.21.11.2-1.5
Bone: cortical thickness1.72.94.21.51.52.0
Bone: cortical thickness0.81.02.70.30.31.6
Bone: cortical tissue density0.81.01.3-1.1-1.10.8
Condit. Reinf. active minus inactive responses0.10.10.2-0.3-0.40.2
Condit. Reinf. active-inactive response ratio0.40.41.30.1-0.0-1.1
Condit. Reinf. active responses0.81.02.4-0.4-0.61.5
Condit. Reinf. inactive responses2.22.67.2-0.5-0.62.7
Incentive salience index mean0.20.20.40.40.30.6
Condit. Reinf. lever presses1.21.52.41.11.01.5
Condit. Reinf. active minus inactive responses0.60.82.30.20.21.5
Condit. Reinf. active-inactive response ratio2.93.08.5-0.5-0.62.9
Condit. Reinf. active responses0.30.41.2-0.1-0.11.1
Condit. Reinf. inactive responses0.50.71.50.40.6-1.2
Condit. Reinf. lever presses1.01.41.51.21.21.1
Condit. Reinf. lever reinforcers received0.40.61.5-0.4-0.31.2
Conditioned reinforcement - actives0.20.20.4-0.3-0.3-0.6
Conditioned reinforcement - inactives0.10.10.2-0.4-0.4-0.0
Conditioned locomotion0.81.01.1-1.0-1.0-0.9
Patch foraging indifference point 0 sec1.22.03.11.81.70.2
Patch foraging indifference point AUC0.30.30.40.60.70.3
Delay disc. indifference point, 0s delay0.30.30.50.70.70.1
Delay disc. indifference point, 16s delay1.51.51.9-1.3-1.41.0
Delay disc. indifference point, 2s delay2.93.24.72.22.20.4
Delay disc. indifference point, 24s delay0.60.60.9-0.9-0.90.2
Delay disc. indifference point, 4s delay0.40.41.30.00.01.1
Delay disc. indifference point, 8s delay0.00.00.10.0-0.10.3
Indifference point function ln k1.52.02.71.61.61.0
Indifference point function log k1.52.02.71.61.61.0
Patch foraging total patch changes 0 sec1.21.92.91.71.60.5
Patch foraging total patch changes 12 sec0.00.00.00.10.0-0.1
Patch foraging total patch changes 18 sec0.00.10.1-0.2-0.40.0
Patch foraging total patch changes 24 sec0.20.20.40.40.20.6
Patch foraging total patch changes 6 sec0.10.20.20.40.50.5
Patch foraging time to switch 0 sec1.92.94.1-2.0-2.0-0.8
Patch foraging water rate 0 sec0.81.31.61.21.30.8
Patch foraging water rate 12 sec1.01.63.90.60.62.0
Patch foraging water rate 18 sec0.81.11.41.21.10.7
Patch foraging water rate 24 sec1.31.83.11.11.11.7
Patch foraging water rate 6 sec0.71.02.80.30.31.7
Seeking ratio, delayed vs. immediate footshock0.20.30.4-0.6-0.7-0.2
Distance traveled before self-admin0.50.50.7-0.8-0.80.4
Distance traveled after self-admin0.50.50.7-0.9-0.9-0.3
Extensor digitorum longus weight4.015.723.44.84.8-0.7
Bone: elastic displacement1.11.23.2-0.5-0.5-1.8
Bone: elastic work0.00.10.10.20.1-0.3
Bone: endosteal estimation1.53.34.92.22.20.4
Bone: endosteal perimeter1.12.23.41.81.8-0.1
Epididymis fat weight0.61.41.91.41.40.7
Delta time in closed arm before/after self-admin0.90.91.3-1.1-1.1-0.1
Delta time in open arm before/after self-admin3.43.34.52.12.10.9
Diff in mean of infusions in LGA sessions1.21.33.6-0.5-0.51.9
Delay discount exponential model param0.10.10.40.00.1-0.6
Extinction: sum of active levers before priming0.30.30.4-0.6-0.6-0.3
Active lever presses in extinction session 60.90.91.31.21.20.1
Bone: final force4.47.110.13.23.11.3
Bone: final moment3.96.39.03.02.91.3
Food consumed during 24 hour testing period0.81.01.11.01.00.9
Glucose0.20.20.40.60.5-0.2
Heart weight0.10.20.4-0.1-0.30.6
Delay discount hyperbolic model param0.10.20.4-0.2-0.1-0.6
Intermittent access intake day 1-15 change0.20.20.5-0.1-0.10.7
Intermittent access intake escalation0.30.30.7-0.2-0.20.9
Intermittent access intake escalation 20.50.51.2-0.4-0.41.1
Intermitt. access day 1 inactive lever presses0.90.91.1-1.1-1.10.7
Intermitt. access day 15 inactive lever presses0.20.30.40.60.60.3
Intermitt. access escalation Index0.10.10.10.30.3-0.1
Intermittent access day 1 total infusions0.10.10.20.40.4-0.1
Intermittent access day 15 total infusions0.20.20.6-0.1-0.10.7
Intermittent access terminal intake (last 3 days)0.10.10.30.10.10.5
Intermittent access total infusions0.50.60.80.90.90.4
Intermittent access day 1 locomotion0.70.71.70.40.41.3
Intermittent access day 15 total locomotion1.51.64.9-0.1-0.12.2
Intermittent access total locomotion2.02.24.21.11.12.1
Intermittent access standard deviation0.30.30.80.20.20.9
Left kidney weight4.412.418.74.34.3-0.2
Right kidney weight4.412.318.44.34.3-0.7
Cocaine induced anxiety0.30.41.0-0.2-0.21.0
Post-drug Anxiety0.10.10.10.30.3-0.2
Baseline Anxiety1.51.63.30.90.9-1.8
Tail length3.19.313.33.63.6-1.3
Length with tail1.34.85.02.22.2-2.1
Length without tail0.30.71.3-0.6-0.6-1.1
Times rat made contact with spout0.60.71.3-0.6-0.61.1
Lifetime Intake0.30.30.50.70.7-0.1
Liver weight, left1.42.22.71.61.6-1.2
Liver weight, right1.21.92.51.51.6-1.0
Locomotor activity1.01.74.70.30.3-2.2
Locomotor testing distance0.20.30.50.40.6-0.7
Locomotor testing rearing0.71.11.8-1.3-1.2-0.2
Locomotion in novel chamber0.60.71.70.50.51.3
Locomotion in novel chamber post-restriction2.63.13.5-1.9-1.71.8
Fecal boli incidents, locomotor time 11.41.62.7-1.0-1.0-1.6
Change in fecal boli incidents, locomotor task1.31.21.61.31.30.6
Time >=10cm from walls, locomotor time 10.30.30.3-0.5-0.5-0.6
Bouts of movement, locomotor time 10.10.10.2-0.2-0.2-0.4
Total resting periods, locomotor time 10.00.00.1-0.1-0.1-0.3
Rest time, locomotor task time 10.70.80.9-1.0-1.0-0.7
Distance moved, locomotor task time 11.51.63.50.80.81.9
Vertical activity count, locomotor time 10.80.80.80.90.90.9
Time >=10cm from walls, locomotor time 20.30.30.60.30.3-0.8
Bouts of movement, locomotor time 20.90.91.7-0.7-0.71.3
Total resting periods, locomotor time 20.50.51.3-0.4-0.41.1
Rest time, locomotor task time 20.40.50.90.50.5-0.9
Distance moved, locomotor task time 21.21.43.8-0.5-0.51.9
Vertical activity count, locomotor time 20.50.50.7-0.8-0.80.4
Light reinforcement 11.22.23.7-1.2-1.2-1.9
Light reinforcement 20.20.20.30.50.6-0.3
Bone: marrow area1.43.14.72.22.10.4
Bone: maximum diameter2.44.56.42.52.50.9
Bone: maximum force4.06.99.83.13.11.2
Bone: maximum moment3.56.08.52.92.81.1
Mean time between licks in bursts1.92.63.5-1.5-1.5-1.9
Mean num. licks in bursts3.84.55.22.02.1-2.3
Cd content in liver2.93.14.7-2.1-2.2-0.3
Co content in liver0.80.91.41.21.10.3
Cu content in liver0.91.13.20.40.41.8
Fe content in liver1.31.51.8-1.3-1.31.0
K content in liver1.21.21.91.41.30.2
Mg content in liver0.50.50.60.70.7-0.8
Mn content in liver0.60.71.01.01.0-0.4
Na content in liver3.74.05.52.32.3-1.0
Rb content in liver0.00.00.0-0.0-0.00.1
Se content in liver0.40.41.30.10.11.1
Sr content in liver0.10.10.20.10.10.4
Zn content in liver0.80.91.31.21.1-0.4
Bone: minimum diameter1.73.14.42.12.10.8
Time in familiar zone, hab. session 11.41.33.90.20.22.0
Time in novel zone, hab. session 12.92.88.4-0.2-0.2-2.9
Total zone transitions, hab. session 10.91.31.91.41.40.2
Total locomotion distance, hab. session 12.23.24.72.22.1-0.5
Locomotion velocity, hab. session 11.52.13.21.81.7-0.4
Time in familiar zone, hab. session 21.71.74.20.70.72.1
Time in novel zone, hab. session 21.11.12.5-0.7-0.7-1.6
Total zone transitions, hab. session 20.60.70.80.90.9-0.8
Total locomotion distance, hab. session 20.70.91.31.11.0-0.7
Locomotion velocity, hab. session 20.91.31.81.31.2-0.7
Novel to familiar place preference ratio1.81.82.5-1.6-1.6-0.7
Novelty place preference1.71.72.5-1.6-1.6-0.4
Time in novel zone, NPP test1.91.92.8-1.7-1.7-0.3
Total zone transitions, NPP test1.21.72.81.71.60.1
Total locomotion distance, NPP test1.01.42.21.51.4-0.2
Locomotion velocity, NPP test1.31.92.91.71.6-0.4
Intraocular pressure1.52.13.0-1.7-1.7-0.6
Delta distance traveled before/after self-admin0.20.30.4-0.6-0.6-0.1
Delta ambulatory time before/after self-admin0.20.20.3-0.6-0.6-0.0
Parametrial fat weight4.79.213.33.63.51.3
Pavlov. Cond. lever latency1.41.72.9-1.7-1.50.1
Pavlov. Cond. magazine entry latency1.01.31.61.11.1-1.2
Pavlov. Cond. change in total contacts0.30.30.60.50.4-0.8
Pavlov. Cond. index score0.60.81.11.11.0-0.4
Pavlov. Cond. latency score1.21.52.31.51.4-0.4
Pavlov. Cond. lever contacts1.01.21.91.41.3-0.4
Pavlov. Cond. magazine entry number0.40.51.3-0.4-0.31.2
Pavlov. Cond. intertrial magazine entries0.60.71.6-0.6-0.51.2
Pavlov. Cond. lever-magazine prob. diff.0.60.81.11.01.0-0.5
Pavlov. Cond. response bias0.40.51.00.50.4-1.0
Pavlov. Cond. lever latency0.81.11.6-0.9-1.0-1.3
Pavlov. Cond. magazine entry latency1.31.52.1-1.5-1.4-0.8
Pavlov. Cond. change in total contacts0.10.20.50.10.20.7
Pavlov. Cond. index score0.10.10.3-0.3-0.20.6
Pavlov. Cond. latency score0.00.10.2-0.00.10.4
Pavlov. Cond. lever contacts0.91.21.51.11.20.9
Pavlov. Cond. magazine entry number1.72.13.11.81.7-0.4
Pavlov. Cond. intertrial magazine entries3.24.26.22.52.5-0.5
Pavlov. Cond. lever-magazine prob. diff.0.10.10.2-0.4-0.30.3
Pavlov. Cond. response bias0.40.51.2-0.4-0.31.1
Time in closed arm before self-admin0.30.30.3-0.6-0.60.5
Time in closed arm after self-admin2.22.33.2-1.8-1.80.6
Time in open arm before self-admin0.40.41.20.00.0-1.1
Time in open arm after self-admin2.83.04.42.12.10.6
Bone: periosteal estimation3.98.110.83.33.21.7
Bone: periosteal perimeter1.83.04.52.12.10.0
Bone: post-yield work4.25.88.42.92.90.7
Progressive ratio test 1 active lever presses0.10.10.10.30.3-0.1
Progressive ratio test 1 breakpoint0.10.10.10.40.4-0.0
Progressive ratio test 1 inactive lever presses0.10.10.20.50.50.1
Progressive ratio test 2 active lever presses0.20.30.4-0.6-0.60.1
Progressive ratio test 2 breakpoint0.10.10.1-0.3-0.30.3
Progressive ratio test 2 inactive lever presses0.00.00.10.20.2-0.2
Incentive Sensitization - Responses0.20.20.2-0.4-0.4-0.4
Incentive Sensitization - Breakpoint0.10.10.1-0.1-0.1-0.4
Sum of active levers in priming session hrs 5-61.61.61.71.21.2-1.3
Progressive ratio0.60.71.90.30.3-1.4
Food seeking constrained by brief footshock0.20.30.8-0.10.0-0.9
Seeking ratio, punishment vs. effort0.00.00.10.00.10.2
Retroperitoneal fat weight0.30.91.41.11.2-0.4
Reaction time number correct1.42.03.0-1.6-1.7-0.5
Reaction time mean minus median0.10.10.10.20.4-0.1
Reaction time mean minus median AUC0.10.10.2-0.4-0.3-0.2
Reaction time num false alarms0.10.10.2-0.2-0.30.4
Reaction time num false alarms AUC0.00.00.10.30.20.2
Reaction time trials correct on left1.42.03.0-1.6-1.7-0.5
Reaction time trials on left1.31.92.9-1.6-1.7-0.5
Reaction time mean0.81.12.80.40.5-1.7
Reaction time mean AUC0.81.13.10.30.4-1.8
Median of all reaction times0.91.33.20.50.6-1.8
Reaction time omissions0.70.92.8-0.00.1-1.7
Reaction time false alarm rate0.30.50.60.80.70.5
Reaction time premature initiation rate0.71.02.9-0.2-0.1-1.7
Reaction time premature initiations1.52.14.0-1.1-1.0-2.0
Std. dev. reaction times0.30.40.80.40.6-0.9
Reaction time trials completed1.31.92.9-1.6-1.7-0.5
Reaction time trials AUC1.11.62.4-1.4-1.5-0.5
Run reversals in cocaine runway, females2.62.53.71.91.8-0.6
Run reversals in cocaine runway, males0.10.10.1-0.3-0.10.3
Latency to leave start box in cocaine runway1.01.12.10.80.71.4
Latency to leave start box in cocaine runway, F0.50.51.5-0.3-0.31.2
Latency to leave start box in cocaine runway, M0.70.71.11.10.90.4
Std. dev. time between licks in bursts0.10.10.2-0.1-0.1-0.5
Total sessions with >9 infusions0.00.00.10.20.2-0.2
Short access day 1 total inactive lever presses0.30.30.90.20.2-0.9
Short access day 10 total inactive lever presses0.70.80.9-0.9-0.90.9
Short access day 1 total infusions1.01.12.1-0.8-0.8-1.5
Short access day 10 total infusions0.20.20.2-0.5-0.50.3
Short access total infusions0.30.40.60.50.5-0.8
Short access day 1 locomotion1.81.92.8-1.7-1.70.4
Short access day 10 total locomotion1.61.85.40.10.12.3
Short access total locomotion1.01.02.00.70.71.4
One hour access (0.3 mA shock)0.50.50.60.80.80.7
Compulsive drug intake0.40.40.50.60.6-0.7
One hour access (shock baseline)0.20.30.7-0.3-0.30.8
Social response proportion0.40.50.6-0.8-0.7-0.6
Social responses0.20.30.3-0.5-0.5-0.6
Social time0.91.11.3-1.1-1.1-1.0
Soleus weight3.410.114.53.83.81.2
Bone: stiffness6.610.413.83.73.62.1
Tibialis anterior weight6.221.432.15.65.7-0.2
Time to tail flick, vehicle, before self-admin0.20.20.20.50.5-0.4
Time to tail flick, vehicle, after self-admin0.20.20.20.50.5-0.3
Time to tail flick, test, before self-admin0.90.81.11.01.0-0.6
Time to tail flick, test, after self-admin1.11.12.7-0.6-0.61.6
Delta time to tail flick, vehicle, before/after SA0.20.20.40.40.40.6
Delta time to tail flick, test, before/after SA0.80.81.8-0.5-0.51.3
Tibia length0.00.00.10.20.20.0
Ambulatory time before self-admin1.01.01.0-1.0-1.01.0
Ambulatory time after self-admin0.91.01.5-1.2-1.2-0.1
Bone: tissue strength0.10.10.3-0.1-0.1-0.5
Total heroin consumption0.50.61.70.10.1-1.3
Bone: trabecular number0.40.60.80.90.90.6
Bone: trabecular spacing1.01.32.6-0.8-0.7-1.6
Bone: trabecular thickness1.61.92.61.61.60.8
Bone: trabecular tissue density0.91.31.81.31.3-0.7
Water consumed over 24 hours1.82.23.1-1.7-1.80.6
Number of responses in last shaping day0.50.51.60.00.0-1.3