Arhgef39

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 Adipose gene expression ENSRNOG00000021433 0.05 0.04 3.5e-04 0.03 0.03 0.04 0.03 1.3e-04 1.1e-04 4.6e-05 2.7e-04
2 BLA gene expression ENSRNOG00000021433 0.1 0.07 5.5e-05 0.03 0.05 0.01 0.04 6.2e-03 9.8e-04 5.5e-02 5.8e-03
3 NAcc gene expression ENSRNOG00000021433 0.06 0.05 1.6e-04 0.04 0.05 0.04 0.05 3.1e-04 1.7e-04 1.2e-03 2.1e-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 strong Z-scores (below -2 or above 2): lower negative Z-scores are darker blue, higher positive Z-scores are darker red.

Trait Avg chi2 ratio Avg chi2 Max chi2 1 2 3
BMI with tail2.37.510.21.93.23.0
BMI without tail4.59.414.50.73.73.8
Body weight2.711.516.81.04.14.1
Epididymis fat weight0.30.71.3-0.10.91.2
Glucose0.91.32.00.11.41.4
Heart weight0.50.71.0-0.30.91.0
Left kidney weight0.31.01.2-0.91.01.1
Right kidney weight0.10.30.8-0.9-0.10.1
Tail length1.95.79.60.02.73.1
Length with tail0.62.03.2-0.71.51.8
Length without tail0.40.91.1-0.7-1.0-1.1
Liver weight, left0.30.50.90.30.61.0
Liver weight, right0.10.20.3-0.5-0.5-0.3
Parametrial fat weight0.10.20.3-0.40.40.6
Retroperitoneal fat weight0.10.20.20.4-0.5-0.5
Intraocular pressure1.52.13.3-0.41.71.8
Extensor digitorum longus weight3.514.221.21.04.54.6
Soleus weight1.02.87.6-2.8-0.9-0.4
Tibialis anterior weight4.816.626.40.34.85.1
Tibia length0.41.33.4-1.9-0.6-0.1
Number of licking bursts4.24.96.51.32.62.6
Food consumed during 24 hour testing period0.50.61.1-0.30.91.0
Times rat made contact with spout0.50.60.70.90.80.6
Mean time between licks in bursts0.30.40.8-0.0-0.9-0.7
Mean num. licks in bursts1.82.13.3-0.5-1.7-1.8
Std. dev. time between licks in bursts0.30.30.5-0.0-0.7-0.6
Water consumed over 24 hours0.60.71.10.41.11.0
Indifference point 0 sec1.22.05.8-2.40.30.3
Indifference point AUC6.57.611.60.63.33.4
Indifference point function ln k2.23.24.6-0.7-2.1-2.1
Indifference point function log k2.23.24.6-0.7-2.1-2.1
Delay discounting total patch changes 0 sec1.11.84.4-2.10.70.7
Delay discounting total patch changes 12 sec1.82.43.80.41.91.8
Delay discounting total patch changes 18 sec0.50.71.0-0.31.01.0
Delay discounting total patch changes 24 sec1.82.33.4-0.41.81.8
Delay discounting total patch changes 6 sec1.92.93.9-1.12.02.0
Delay discounting time to switch 0 sec2.13.24.90.3-2.1-2.2
Delay discounting water rate 0 sec1.21.92.7-0.81.61.6
Delay discounting water rate 12 sec0.10.20.5-0.7-0.00.0
Delay discounting water rate 18 sec0.40.50.70.70.90.6
Delay discounting water rate 24 sec0.40.61.71.30.30.1
Delay discounting water rate 6 sec0.40.50.80.10.80.9
Locomotor activity0.00.00.0-0.00.10.1
Locomotor testing distance0.30.51.4-1.2-0.4-0.2
Locomotor testing rearing0.40.61.0-0.40.81.0
Light reinforcement 11.42.66.9-2.60.40.9
Light reinforcement 22.43.29.5-3.1-0.30.2
Reaction time number correct0.10.20.4-0.70.20.2
Reaction time mean minus median2.53.37.32.71.21.0
Reaction time mean minus median AUC2.53.14.92.21.61.5
Reaction time num false alarms0.20.20.60.80.30.2
Reaction time num false alarms AUC0.30.40.60.40.70.7
Reaction time trials correct on left0.10.20.4-0.70.20.2
Reaction time trials on left0.10.20.4-0.70.10.1
Reaction time mean1.11.63.01.7-0.9-1.0
Reaction time mean AUC1.31.73.11.8-1.0-1.1
Median of all reaction times1.72.43.20.8-1.8-1.8
Reaction time omissions1.01.32.00.2-1.4-1.4
Reaction time false alarm rate0.10.10.40.60.10.0
Reaction time premature initiation rate1.52.03.30.5-1.5-1.8
Reaction time premature initiations0.91.32.30.2-1.2-1.5
Std. dev. reaction times1.52.05.92.40.30.2
Reaction time trials completed0.10.20.4-0.70.10.1
Reaction time trials AUC0.10.10.4-0.60.10.1
Social response proportion1.51.62.40.5-1.5-1.5
Social responses0.50.71.00.40.91.0
Social time0.10.20.4-0.2-0.6-0.2
Conditioned locomotion0.60.71.9-1.4-0.4-0.4
Cocaine response after cond. corrected3.33.75.3-2.3-1.8-1.6
Cocaine response after cond. not corrected3.23.65.9-2.4-1.7-1.4
Cocaine response before conditioning0.70.91.30.61.01.1
Saline control response0.70.91.5-1.20.70.9
Condit. Reinf. active minus inactive responses0.70.81.10.51.11.0
Condit. Reinf. active-inactive response ratio0.30.30.40.60.50.4
Condit. Reinf. active responses1.92.73.90.61.92.0
Condit. Reinf. inactive responses2.83.54.61.22.12.1
Condit. Reinf. lever presses2.83.94.41.82.12.0
Condit. Reinf. lever reinforcers received2.33.24.60.82.12.1
Pavlov. Cond. lever latency3.24.44.9-1.9-2.2-2.2
Pavlov. Cond. magazine entry latency0.30.30.50.3-0.7-0.6
Pavlov. Cond. change in total contacts1.92.75.02.21.31.2
Pavlov. Cond. index score0.71.02.11.40.70.6
Pavlov. Cond. latency score1.01.32.61.60.80.8
Pavlov. Cond. lever contacts1.62.32.61.31.61.6
Pavlov. Cond. magazine entry number0.70.92.4-1.6-0.3-0.2
Pavlov. Cond. intertrial magazine entries0.30.40.6-0.20.80.7
Pavlov. Cond. lever-magazine prob. diff.0.81.02.31.50.60.6
Pavlov. Cond. response bias0.91.31.71.31.01.0
Conditioned reinforcement - actives0.20.20.30.30.50.3
Conditioned reinforcement - inactives0.10.10.2-0.4-0.3-0.4
Conditioned locomotion0.20.20.4-0.10.70.5
Intermittent access intake day 1-15 change1.41.42.31.51.00.9
Intermittent access intake escalation1.71.72.01.41.31.2
Intermittent access intake escalation 22.42.43.81.91.41.2
Intermitt. access day 1 inactive lever presses0.50.50.80.10.90.9
Intermitt. access day 15 inactive lever presses0.20.20.5-0.7-0.0-0.0
Intermitt. access escalation Index0.70.61.0-0.50.81.0
Intermittent access day 1 total infusions1.11.22.4-1.6-0.8-0.9
Intermittent access day 15 total infusions0.30.40.70.10.80.6
Intermittent access terminal intake (last 3 days)0.40.40.8-0.00.90.7
Intermittent access total infusions0.40.50.9-0.30.90.7
Intermittent access day 1 locomotion1.31.31.9-1.4-0.9-1.1
Intermittent access day 15 total locomotion0.70.71.1-0.7-0.8-1.0
Intermittent access total locomotion0.20.30.6-0.1-0.4-0.8
Intermittent access standard deviation0.40.40.50.70.70.6
Cocaine induced anxiety1.11.31.8-0.6-1.4-1.3
Post-drug Anxiety0.20.20.4-0.10.40.6
Baseline Anxiety1.92.02.41.21.51.6
Lifetime Intake0.60.71.4-1.20.70.6
Incentive Sensitization - Responses0.30.30.7-0.8-0.3-0.3
Incentive Sensitization - Breakpoint0.30.40.7-0.8-0.4-0.4
Progressive ratio test 1 active lever presses0.60.61.8-1.30.2-0.0
Progressive ratio test 1 breakpoint0.50.61.5-1.20.40.2
Progressive ratio test 1 inactive lever presses1.21.33.9-2.00.20.2
Progressive ratio test 2 active lever presses0.80.92.5-1.6-0.3-0.4
Progressive ratio test 2 breakpoint0.91.12.6-1.6-0.5-0.6
Progressive ratio test 2 inactive lever presses0.10.10.2-0.50.40.3
Total sessions with >9 infusions1.41.64.4-2.1-0.4-0.4
Short access day 1 total inactive lever presses1.11.21.7-0.61.31.2
Short access day 10 total inactive lever presses0.10.20.20.20.40.5
Short access day 1 total infusions1.31.43.4-1.90.60.6
Short access day 10 total infusions0.80.92.3-1.50.40.4
Short access total infusions1.21.44.1-2.0-0.0-0.0
Short access day 1 locomotion0.80.81.8-1.4-0.5-0.6
Short access day 10 total locomotion0.30.40.60.4-0.6-0.8
Short access total locomotion0.40.41.1-1.1-0.0-0.1
Compulsive drug intake0.30.30.50.10.60.7
One hour access (0.3 mA shock)0.40.40.5-0.70.70.6
One hour access (shock baseline)0.40.51.1-1.10.40.3
Number of responses in last shaping day1.91.95.5-2.4-0.3-0.1
Context. condit. distance diff. score0.10.10.10.2-0.2-0.3
Locomotion velocity, session 12.83.08.8-3.0-0.10.3
Locomotion distance, session 10.70.92.5-1.60.20.4
Locomotion velocity, session 22.63.03.71.31.91.9
Locomotion distance, session 21.21.83.0-0.71.41.7
Locomotion velocity, session 30.70.82.3-1.5-0.2-0.0
Locomotion distance, session 31.51.72.3-0.61.51.5
Stereotopy head waving bouts, day 30.91.12.5-1.6-0.7-0.5
Stereotopy head waving duration, day 30.70.81.1-1.0-0.9-0.7
Locomotion velocity, session 70.00.00.1-0.0-0.2-0.3
Locomotion distance, session 70.10.20.2-0.30.50.5
Stereotopy head waving bouts, day 71.51.72.6-0.01.61.6
Stereotopy head waving duration, day 70.30.40.6-0.40.70.8
Locomotion velocity, session 80.40.51.4-1.2-0.30.0
Locomotion distance, session 80.20.40.9-0.90.20.4
Degree of sensitization distance0.80.81.30.1-1.1-1.0
Degree of sensitization stereotypy1.01.11.70.21.31.2
Condit. Reinf. active minus inactive responses0.60.60.80.60.90.9
Condit. Reinf. active-inactive response ratio0.40.40.70.2-0.8-0.8
Condit. Reinf. active responses2.93.54.61.22.12.1
Condit. Reinf. inactive responses3.84.45.51.62.32.3
Incentive salience index mean3.64.36.50.72.52.6
Condit. Reinf. lever presses7.710.316.20.33.84.0
Time in familiar zone, hab. session 11.91.85.22.30.1-0.3
Time in novel zone, hab. session 14.34.27.2-2.7-1.9-1.4
Total zone transitions, hab. session 10.00.00.00.20.10.2
Total locomotion distance, hab. session 11.11.62.91.71.00.9
Locomotion velocity, hab. session 12.13.13.21.71.81.8
Time in familiar zone, hab. session 20.80.92.01.4-0.5-0.6
Time in novel zone, hab. session 22.92.94.7-2.2-1.5-1.3
Total zone transitions, hab. session 20.40.50.7-0.60.60.8
Total locomotion distance, hab. session 20.70.91.30.51.11.1
Locomotion velocity, hab. session 21.01.31.80.61.31.3
Novel to familiar place preference ratio4.34.55.0-2.0-2.2-2.1
Novelty place preference5.25.46.4-2.0-2.5-2.4
Time in novel zone, NPP test6.36.67.9-2.1-2.8-2.7
Total zone transitions, NPP test0.50.70.9-0.90.70.9
Total locomotion distance, NPP test1.21.72.7-0.51.51.6
Locomotion velocity, NPP test1.72.43.8-0.11.92.0
Pavlov. Cond. lever latency5.67.111.0-0.4-3.2-3.3
Pavlov. Cond. magazine entry latency0.40.50.70.50.80.8
Pavlov. Cond. change in total contacts2.02.13.30.21.71.8
Pavlov. Cond. index score2.73.55.10.82.22.3
Pavlov. Cond. latency score2.53.24.70.72.12.2
Pavlov. Cond. lever contacts4.35.17.60.62.72.8
Pavlov. Cond. magazine entry number0.70.91.2-0.6-1.1-1.1
Pavlov. Cond. intertrial magazine entries0.30.30.40.40.60.6
Pavlov. Cond. lever-magazine prob. diff.2.83.54.71.12.12.2
Pavlov. Cond. response bias2.63.24.70.62.12.2
Bone: apparent density1.11.92.60.91.61.5
Bone surface0.50.91.3-0.11.11.1
Bone volume0.50.91.30.31.21.1
Bone: connectivity density0.71.11.50.91.21.1
Bone: cortical apparent density0.70.92.81.70.1-0.1
Bone: cortical area2.33.54.31.42.12.0
Bone: cortical porosity0.30.30.5-0.1-0.7-0.7
Bone: cortical porosity0.00.00.0-0.00.0-0.0
Bone: cortical thickness1.32.13.01.71.41.2
Bone: cortical thickness0.10.10.30.5-0.3-0.3
Bone: cortical tissue density0.60.82.31.5-0.0-0.2
Bone: elastic displacement3.03.45.60.4-2.1-2.4
Bone: elastic work1.72.23.81.9-1.0-1.4
Bone: endosteal estimation0.71.42.4-0.61.31.5
Bone: endosteal perimeter0.71.52.2-0.91.21.5
Bone: final force1.01.62.50.51.41.6
Bone: final moment0.81.31.90.71.21.4
Bone: marrow area0.71.62.6-0.31.41.6
Bone: maximum diameter1.93.55.20.92.22.3
Bone: maximum force2.44.26.11.02.32.5
Bone: maximum moment2.03.44.71.22.12.2
Bone: minimum diameter0.00.10.20.4-0.0-0.0
Bone: periosteal estimation1.22.43.80.31.81.9
Bone: periosteal perimeter0.40.60.8-0.60.70.9
Bone: post-yield work1.01.32.2-0.41.21.5
Bone: stiffness3.25.17.81.02.52.8
Bone: tissue strength0.20.20.20.50.30.5
Bone: trabecular number1.42.12.61.21.61.5
Bone: trabecular spacing0.20.20.70.80.10.0
Bone: trabecular thickness0.00.00.10.2-0.2-0.3
Bone: trabecular tissue density1.92.64.40.51.82.1
Breakpoint value in progressive ratio session1.51.73.8-2.0-0.8-0.7
Distance traveled before self-admin2.83.04.9-0.42.02.2
Distance traveled after self-admin0.70.80.90.90.80.9
Delta time in closed arm before/after self-admin3.53.43.71.81.91.9
Delta time in open arm before/after self-admin0.80.81.1-1.0-0.9-0.8
Diff in mean of infusions in LGA sessions0.00.00.10.3-0.1-0.1
Extinction: sum of active levers before priming1.61.62.3-0.6-1.5-1.5
Active lever presses in extinction session 60.40.40.4-0.6-0.6-0.7
Delta distance traveled before/after self-admin0.50.50.80.3-0.9-0.8
Delta ambulatory time before/after self-admin1.21.32.00.3-1.4-1.3
Time in closed arm before self-admin2.02.33.6-0.6-1.7-1.9
Time in closed arm after self-admin0.20.20.50.7-0.1-0.3
Time in open arm before self-admin1.51.62.7-0.61.41.6
Time in open arm after self-admin0.90.91.2-0.81.01.1
Sum of active levers in priming session hrs 5-63.53.54.0-1.6-2.0-2.0
Time to tail flick, vehicle, before self-admin0.90.91.5-0.1-1.1-1.2
Time to tail flick, vehicle, after self-admin0.00.00.1-0.3-0.1-0.1
Time to tail flick, test, before self-admin0.40.40.40.60.70.6
Time to tail flick, test, after self-admin1.21.31.61.31.10.9
Delta time to tail flick, vehicle, before/after SA0.10.10.20.10.40.5
Delta time to tail flick, test, before/after SA0.00.00.10.2-0.1-0.2
Ambulatory time before self-admin2.12.23.3-0.81.61.8
Ambulatory time after self-admin0.10.10.2-0.10.30.4
Total heroin consumption1.11.42.4-1.6-0.9-0.9
Area under the delay curve0.80.81.1-1.1-0.8-0.8
Delay disc. indifference point, 0s delay1.61.72.0-1.2-1.4-1.3
Delay disc. indifference point, 16s delay2.32.33.6-1.9-1.4-1.3
Delay disc. indifference point, 2s delay0.10.10.30.60.20.1
Delay disc. indifference point, 24s delay0.10.10.2-0.1-0.4-0.3
Delay disc. indifference point, 4s delay0.10.10.1-0.2-0.3-0.3
Delay disc. indifference point, 8s delay0.00.00.0-0.20.10.1
Delay discount exponential model param0.60.71.01.00.70.7
Delay discount hyperbolic model param0.50.60.90.90.70.6
Fecal boli incidents, locomotor time 10.40.40.70.3-0.7-0.8
Change in fecal boli incidents, locomotor task0.60.60.7-0.70.70.9
Time >=10cm from walls, locomotor time 10.30.31.0-1.0-0.2-0.1
Bouts of movement, locomotor time 11.31.42.2-0.2-1.5-1.5
Total resting periods, locomotor time 11.51.72.50.2-1.5-1.6
Rest time, locomotor task time 11.71.94.12.0-0.8-1.0
Distance moved, locomotor task time 11.51.61.9-1.41.11.3
Vertical activity count, locomotor time 11.51.53.6-1.90.50.8
Time >=10cm from walls, locomotor time 20.10.10.1-0.20.20.3
Bouts of movement, locomotor time 20.50.50.70.30.80.8
Total resting periods, locomotor time 20.20.20.30.30.50.5
Rest time, locomotor task time 20.50.60.90.3-0.9-1.0
Distance moved, locomotor task time 20.60.70.70.90.80.8
Vertical activity count, locomotor time 20.30.30.6-0.20.60.8
Weight adjusted by age0.30.41.0-1.00.10.2
Seeking ratio, delayed vs. immediate footshock3.23.75.41.02.32.2
Locomotion in novel chamber0.20.30.70.80.20.0
Locomotion in novel chamber post-restriction2.83.44.32.11.81.6
Progressive ratio0.00.10.1-0.3-0.2-0.2
Food seeking constrained by brief footshock4.75.78.6-0.82.82.9
Seeking ratio, punishment vs. effort1.21.52.40.01.51.5
Run reversals in cocaine runway, females0.40.41.01.00.40.3
Run reversals in cocaine runway, males0.00.00.00.1-0.0-0.1
Latency to leave start box in cocaine runway0.70.70.90.71.00.9
Latency to leave start box in cocaine runway, F0.00.00.0-0.2-0.1-0.1
Latency to leave start box in cocaine runway, M0.90.81.3-0.11.11.2
Cd content in liver0.91.01.01.01.01.0
Co content in liver1.51.72.1-1.1-1.5-1.3
Cu content in liver0.70.81.10.6-1.1-1.0
Fe content in liver1.01.23.5-1.9-0.30.1
K content in liver0.60.60.9-0.9-0.7-0.6
Mg content in liver0.50.50.6-0.5-0.7-0.8
Mn content in liver0.50.61.11.00.60.5
Na content in liver1.21.32.1-0.4-1.5-1.2
Rb content in liver3.84.86.4-1.3-2.5-2.5
Se content in liver2.12.63.01.41.61.7
Sr content in liver0.60.50.70.50.80.8
Zn content in liver0.40.51.11.00.50.4