Arfgap3

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 Arfgap3 0.03 0.02 4.4e-04 0.03 0.03 0.03 0.02 4.9e-04 6.9e-04 5.2e-04 1.1e-03
2 Adipose gene expression Arfgap3 0.21 0.16 7.1e-09 0.06 0.06 0.06 0.05 4.9e-07 7.4e-07 3.9e-07 1.7e-06
3 Liver gene expression Arfgap3 0.16 0.1 5.1e-03 0.03 0.01 0.01 0.02 5.1e-04 5.1e-02 8.5e-03 3.1e-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
Bone: apparent density0.20.30.50.6-0.70.1
Area under the delay curve0.70.81.91.4-0.6-0.3
BMI with tail0.92.96.5-2.50.61.4
BMI without tail0.30.61.7-1.30.4-0.1
Body weight0.93.68.4-2.91.30.8
Weight adjusted by age0.81.02.0-0.31.4-0.9
Bone surface0.00.00.0-0.00.10.0
Bone volume0.00.00.00.10.2-0.0
Breakpoint value in progressive ratio session0.40.50.8-0.4-0.90.7
Number of licking bursts0.10.10.20.4-0.2-0.3
Context. condit. distance diff. score3.84.67.7-2.52.80.0
Locomotion velocity, session 10.40.40.7-0.80.6-0.3
Locomotion distance, session 10.60.81.60.7-0.5-1.3
Locomotion velocity, session 20.40.51.3-1.10.4-0.0
Locomotion distance, session 21.72.45.31.2-2.30.5
Locomotion velocity, session 30.80.91.2-0.91.1-0.8
Locomotion distance, session 31.21.32.90.90.4-1.7
Stereotopy head waving bouts, day 30.50.61.0-1.00.20.8
Stereotopy head waving duration, day 32.42.96.2-2.51.30.8
Locomotion velocity, session 70.20.30.7-0.20.3-0.8
Locomotion distance, session 70.60.71.21.0-1.1-0.1
Stereotopy head waving bouts, day 73.03.45.7-2.42.1-0.3
Stereotopy head waving duration, day 72.32.84.2-2.02.0-0.7
Locomotion velocity, session 83.03.68.3-2.91.21.0
Locomotion distance, session 80.60.91.4-1.11.2-0.1
Degree of sensitization distance1.31.32.8-0.9-0.51.7
Degree of sensitization stereotypy2.62.94.2-2.11.9-0.8
Conditioned locomotion0.91.12.0-0.21.4-1.1
Cocaine response after cond. corrected0.20.20.50.10.7-0.4
Cocaine response after cond. not corrected0.30.30.60.10.8-0.5
Cocaine response before conditioning0.00.10.10.3-0.2-0.2
Saline control response0.70.91.9-0.41.4-0.8
Bone: connectivity density0.20.30.60.2-0.80.4
Bone: cortical apparent density0.71.01.91.4-1.0-0.0
Bone: cortical area0.81.22.1-1.50.90.8
Bone: cortical porosity0.30.40.8-0.90.5-0.0
Bone: cortical porosity0.70.81.4-1.20.90.3
Bone: cortical thickness0.71.12.2-0.3-1.11.5
Bone: cortical thickness0.50.61.4-0.4-0.41.2
Bone: cortical tissue density0.70.91.81.3-1.00.0
Condit. Reinf. active minus inactive responses1.21.41.81.3-1.30.7
Condit. Reinf. active-inactive response ratio0.10.10.3-0.0-0.10.5
Condit. Reinf. active responses2.12.55.02.2-1.60.3
Condit. Reinf. inactive responses1.82.14.42.1-1.4-0.4
Incentive salience index mean1.92.33.21.8-1.80.7
Condit. Reinf. lever presses1.52.13.61.9-1.60.1
Condit. Reinf. active minus inactive responses1.31.62.7-0.3-1.41.6
Condit. Reinf. active-inactive response ratio2.32.44.4-0.2-1.72.1
Condit. Reinf. active responses0.60.81.4-0.9-0.21.2
Condit. Reinf. inactive responses0.60.71.2-0.91.1-0.2
Condit. Reinf. lever presses0.81.11.70.6-1.31.1
Condit. Reinf. lever reinforcers received0.50.81.8-0.3-0.61.3
Conditioned reinforcement - actives0.40.40.90.51.0-0.1
Conditioned reinforcement - inactives0.50.60.90.1-0.90.9
Conditioned locomotion0.70.80.9-0.80.91.0
Patch foraging indifference point 0 sec0.61.01.70.3-1.31.1
Patch foraging indifference point AUC0.10.10.20.4-0.30.2
Delay disc. indifference point, 0s delay0.30.30.6-0.70.50.3
Delay disc. indifference point, 16s delay1.81.94.02.0-1.2-0.4
Delay disc. indifference point, 2s delay0.10.10.30.6-0.1-0.3
Delay disc. indifference point, 24s delay0.30.30.50.70.2-0.6
Delay disc. indifference point, 4s delay0.70.71.50.4-0.71.2
Delay disc. indifference point, 8s delay1.41.43.01.7-0.9-0.7
Indifference point function ln k0.71.02.6-1.60.50.4
Indifference point function log k0.71.02.6-1.60.50.4
Patch foraging total patch changes 0 sec0.61.01.90.3-1.41.0
Patch foraging total patch changes 12 sec0.40.51.1-0.0-0.71.0
Patch foraging total patch changes 18 sec1.01.22.00.0-1.41.3
Patch foraging total patch changes 24 sec0.10.10.20.4-0.30.2
Patch foraging total patch changes 6 sec0.60.81.8-0.1-0.91.3
Patch foraging time to switch 0 sec0.30.50.70.9-0.2-0.8
Patch foraging water rate 0 sec0.60.91.6-1.1-0.21.3
Patch foraging water rate 12 sec0.20.30.9-0.9-0.20.2
Patch foraging water rate 18 sec0.10.20.40.3-0.60.3
Patch foraging water rate 24 sec1.31.82.9-1.7-0.51.5
Patch foraging water rate 6 sec0.10.10.20.3-0.1-0.4
Seeking ratio, delayed vs. immediate footshock2.52.86.41.5-2.5-0.0
Distance traveled before self-admin0.80.91.90.4-1.40.8
Distance traveled after self-admin0.91.02.1-0.4-0.81.4
Extensor digitorum longus weight0.00.10.1-0.30.1-0.3
Bone: elastic displacement1.11.21.8-1.31.4-0.5
Bone: elastic work2.12.75.4-2.31.31.0
Bone: endosteal estimation1.83.87.4-1.92.7-0.6
Bone: endosteal perimeter2.34.89.8-1.83.1-1.1
Epididymis fat weight1.43.25.9-1.82.4-0.6
Delta time in closed arm before/after self-admin0.20.20.40.00.60.5
Delta time in open arm before/after self-admin0.40.40.8-0.20.6-0.9
Diff in mean of infusions in LGA sessions0.60.61.31.1-0.7-0.1
Delay discount exponential model param0.70.71.7-1.30.50.3
Extinction: sum of active levers before priming0.20.20.60.70.20.2
Active lever presses in extinction session 60.20.20.4-0.70.10.4
Bone: final force1.01.74.0-1.0-0.12.0
Bone: final moment1.32.14.6-1.30.02.2
Food consumed during 24 hour testing period1.11.32.6-1.60.21.1
Glucose0.40.71.60.6-1.30.2
Heart weight1.62.23.2-1.80.61.8
Delay discount hyperbolic model param0.50.51.3-1.10.40.2
Intermittent access intake day 1-15 change0.40.40.80.9-0.50.0
Intermittent access intake escalation0.30.30.60.8-0.60.1
Intermittent access intake escalation 20.10.10.20.4-0.1-0.1
Intermitt. access day 1 inactive lever presses1.21.22.6-0.9-0.51.6
Intermitt. access day 15 inactive lever presses1.82.04.8-0.5-1.02.2
Intermitt. access escalation Index0.40.40.40.5-0.70.6
Intermittent access day 1 total infusions0.60.71.0-1.00.31.0
Intermittent access day 15 total infusions0.30.30.8-0.2-0.40.9
Intermittent access terminal intake (last 3 days)0.00.00.1-0.10.30.1
Intermittent access total infusions0.20.20.4-0.40.20.6
Intermittent access day 1 locomotion0.20.20.5-0.3-0.00.7
Intermittent access day 15 total locomotion0.10.10.2-0.30.20.5
Intermittent access total locomotion0.30.40.9-0.5-0.20.9
Intermittent access standard deviation0.50.51.1-0.6-0.11.1
Left kidney weight7.120.037.5-6.13.73.0
Right kidney weight7.821.841.1-6.43.73.2
Cocaine induced anxiety1.31.52.2-1.4-0.51.5
Post-drug Anxiety1.11.22.3-1.5-0.51.0
Baseline Anxiety0.80.92.00.8-0.3-1.4
Tail length0.10.30.9-0.00.2-0.9
Length with tail0.20.61.3-1.10.70.0
Length without tail0.40.81.4-1.10.01.2
Times rat made contact with spout0.91.02.3-1.50.20.8
Lifetime Intake0.60.71.7-0.6-0.11.3
Liver weight, left0.91.43.2-0.41.8-0.9
Liver weight, right1.93.17.1-0.62.7-1.4
Locomotor activity1.52.43.9-2.01.70.5
Locomotor testing distance0.00.00.10.20.2-0.1
Locomotor testing rearing0.91.43.8-0.62.0-0.2
Locomotion in novel chamber2.02.54.90.21.6-2.2
Locomotion in novel chamber post-restriction0.81.01.71.1-0.3-1.3
Fecal boli incidents, locomotor time 10.20.20.50.70.2-0.2
Change in fecal boli incidents, locomotor task0.60.60.8-0.90.9-0.4
Time >=10cm from walls, locomotor time 10.00.00.00.00.20.1
Bouts of movement, locomotor time 10.10.10.20.4-0.2-0.1
Total resting periods, locomotor time 10.30.40.60.7-0.80.1
Rest time, locomotor task time 10.30.40.80.2-0.90.5
Distance moved, locomotor task time 10.60.61.8-0.31.3-0.2
Vertical activity count, locomotor time 10.00.00.1-0.20.20.1
Time >=10cm from walls, locomotor time 20.20.30.50.50.2-0.7
Bouts of movement, locomotor time 20.40.40.60.4-0.80.7
Total resting periods, locomotor time 20.50.61.00.3-1.00.8
Rest time, locomotor task time 20.30.30.80.3-0.90.2
Distance moved, locomotor task time 20.80.91.8-0.81.4-0.5
Vertical activity count, locomotor time 20.60.61.1-0.81.1-0.3
Light reinforcement 10.40.71.3-0.61.2-0.6
Light reinforcement 20.20.30.7-0.80.4-0.4
Bone: marrow area1.84.07.6-2.02.8-0.5
Bone: maximum diameter3.05.510.0-3.22.31.0
Bone: maximum force1.72.94.3-2.00.62.1
Bone: maximum moment2.13.65.4-2.30.82.2
Mean time between licks in bursts0.50.71.71.3-0.1-0.6
Mean num. licks in bursts1.01.22.7-1.60.80.6
Cd content in liver2.12.34.4-1.42.1-0.6
Co content in liver0.50.50.8-0.90.70.5
Cu content in liver2.93.67.72.8-1.7-0.5
Fe content in liver0.20.30.5-0.70.60.1
K content in liver1.01.01.50.6-1.21.1
Mg content in liver2.52.55.00.8-2.21.4
Mn content in liver0.40.40.7-0.10.9-0.8
Na content in liver1.21.32.11.2-1.5-0.4
Rb content in liver0.30.40.7-0.1-0.60.9
Se content in liver0.60.81.61.30.2-0.8
Sr content in liver0.70.61.00.9-0.1-1.0
Zn content in liver0.40.50.91.0-0.3-0.7
Bone: minimum diameter0.50.92.1-0.81.5-0.3
Time in familiar zone, hab. session 10.30.30.5-0.30.7-0.6
Time in novel zone, hab. session 10.80.81.2-1.01.10.2
Total zone transitions, hab. session 11.31.92.81.7-0.8-1.5
Total locomotion distance, hab. session 11.01.43.50.80.2-1.9
Locomotion velocity, hab. session 10.81.12.30.9-0.4-1.5
Time in familiar zone, hab. session 22.02.14.10.41.4-2.0
Time in novel zone, hab. session 21.81.73.5-1.1-0.81.9
Total zone transitions, hab. session 20.20.20.60.2-0.70.2
Total locomotion distance, hab. session 20.20.20.50.4-0.7-0.1
Locomotion velocity, hab. session 20.40.51.00.7-1.0-0.2
Novel to familiar place preference ratio2.52.64.2-1.82.10.4
Novelty place preference3.33.45.8-2.12.40.3
Time in novel zone, NPP test4.24.36.9-2.42.60.4
Total zone transitions, NPP test0.60.91.21.1-0.6-1.1
Total locomotion distance, NPP test0.30.40.60.7-0.7-0.4
Locomotion velocity, NPP test0.91.32.01.4-0.9-1.0
Intraocular pressure0.20.30.6-0.80.5-0.2
Delta distance traveled before/after self-admin1.31.42.5-1.61.30.4
Delta ambulatory time before/after self-admin1.82.03.9-2.01.30.7
Parametrial fat weight0.00.10.10.1-0.30.4
Pavlov. Cond. lever latency1.72.24.3-2.11.5-0.1
Pavlov. Cond. magazine entry latency1.41.82.71.6-1.60.2
Pavlov. Cond. change in total contacts2.22.44.11.6-2.00.8
Pavlov. Cond. index score1.41.82.81.5-1.70.7
Pavlov. Cond. latency score1.21.52.21.4-1.50.7
Pavlov. Cond. lever contacts2.12.44.12.0-1.80.1
Pavlov. Cond. magazine entry number1.21.52.2-1.51.5-0.2
Pavlov. Cond. intertrial magazine entries0.50.60.90.8-1.00.6
Pavlov. Cond. lever-magazine prob. diff.1.62.03.11.6-1.80.4
Pavlov. Cond. response bias2.12.63.92.0-2.00.3
Pavlov. Cond. lever latency1.01.42.4-0.61.6-1.1
Pavlov. Cond. magazine entry latency4.65.38.82.0-3.01.7
Pavlov. Cond. change in total contacts3.75.18.40.6-2.52.9
Pavlov. Cond. index score3.24.17.11.5-2.71.7
Pavlov. Cond. latency score3.94.98.61.6-2.91.9
Pavlov. Cond. lever contacts1.52.03.70.6-1.91.4
Pavlov. Cond. magazine entry number3.54.36.6-1.72.6-1.9
Pavlov. Cond. intertrial magazine entries1.31.73.7-1.90.90.7
Pavlov. Cond. lever-magazine prob. diff.3.24.17.01.6-2.61.6
Pavlov. Cond. response bias2.12.94.90.9-2.21.7
Time in closed arm before self-admin2.42.74.81.7-2.2-0.5
Time in closed arm after self-admin0.10.10.20.20.4-0.2
Time in open arm before self-admin0.50.50.70.20.8-0.9
Time in open arm after self-admin0.70.81.60.10.9-1.3
Bone: periosteal estimation1.63.35.5-2.12.40.1
Bone: periosteal perimeter2.54.27.6-2.22.8-0.3
Bone: post-yield work0.50.61.2-0.9-0.11.1
Progressive ratio test 1 active lever presses0.60.61.2-0.2-0.71.1
Progressive ratio test 1 breakpoint0.20.20.40.0-0.60.6
Progressive ratio test 1 inactive lever presses1.41.53.1-0.1-1.21.8
Progressive ratio test 2 active lever presses0.80.91.4-0.3-1.11.2
Progressive ratio test 2 breakpoint1.11.22.2-0.4-1.11.5
Progressive ratio test 2 inactive lever presses1.82.13.40.1-1.91.7
Incentive Sensitization - Responses1.01.01.2-0.7-1.11.1
Incentive Sensitization - Breakpoint1.11.11.6-0.8-1.11.3
Sum of active levers in priming session hrs 5-60.00.00.10.30.2-0.0
Progressive ratio0.30.30.50.2-0.70.7
Food seeking constrained by brief footshock0.40.50.8-0.90.60.5
Seeking ratio, punishment vs. effort0.20.20.3-0.50.60.0
Retroperitoneal fat weight0.82.74.2-1.92.00.6
Reaction time number correct1.21.72.91.50.4-1.7
Reaction time mean minus median0.50.71.1-0.81.0-0.6
Reaction time mean minus median AUC0.81.01.6-1.11.3-0.6
Reaction time num false alarms1.01.42.5-0.01.6-1.3
Reaction time num false alarms AUC0.91.32.4-0.01.6-1.2
Reaction time trials correct on left1.21.72.91.50.4-1.7
Reaction time trials on left1.31.93.11.50.4-1.8
Reaction time mean0.00.00.00.1-0.2-0.1
Reaction time mean AUC0.00.00.00.1-0.2-0.2
Median of all reaction times0.10.20.40.4-0.60.1
Reaction time omissions0.40.50.80.60.5-0.9
Reaction time false alarm rate0.40.61.1-0.71.1-0.2
Reaction time premature initiation rate1.31.73.2-0.0-1.41.8
Reaction time premature initiations0.50.81.10.6-1.10.9
Std. dev. reaction times0.30.51.1-0.51.0-0.3
Reaction time trials completed1.31.93.11.50.4-1.8
Reaction time trials AUC1.01.42.31.30.3-1.5
Run reversals in cocaine runway, females1.31.32.91.00.3-1.7
Run reversals in cocaine runway, males1.31.22.1-1.21.4-0.3
Latency to leave start box in cocaine runway0.20.20.4-0.60.60.0
Latency to leave start box in cocaine runway, F0.10.10.20.30.1-0.4
Latency to leave start box in cocaine runway, M0.80.81.3-1.10.51.0
Std. dev. time between licks in bursts1.21.42.31.1-1.50.9
Total sessions with >9 infusions0.70.81.8-0.70.21.3
Short access day 1 total inactive lever presses1.51.72.7-1.50.51.7
Short access day 10 total inactive lever presses1.11.22.9-1.70.80.4
Short access day 1 total infusions1.01.12.0-1.10.21.4
Short access day 10 total infusions0.20.20.60.1-0.10.8
Short access total infusions1.21.33.1-1.0-0.11.8
Short access day 1 locomotion0.20.20.40.3-0.10.7
Short access day 10 total locomotion0.50.51.51.2-0.3-0.0
Short access total locomotion0.30.30.70.30.00.8
One hour access (0.3 mA shock)0.10.10.30.5-0.2-0.2
Compulsive drug intake0.30.30.70.8-0.4-0.3
One hour access (shock baseline)0.00.10.10.3-0.1-0.2
Social response proportion0.50.61.1-0.5-0.51.1
Social responses0.20.20.30.50.5-0.3
Social time1.62.14.02.0-1.5-0.5
Soleus weight0.10.30.4-0.6-0.50.6
Bone: stiffness0.71.22.3-1.10.31.5
Tibialis anterior weight0.20.81.50.9-1.20.3
Time to tail flick, vehicle, before self-admin0.30.30.9-0.40.9-0.1
Time to tail flick, vehicle, after self-admin2.22.33.50.81.7-1.9
Time to tail flick, test, before self-admin1.11.11.8-0.31.3-1.2
Time to tail flick, test, after self-admin1.51.63.81.9-0.1-1.0
Delta time to tail flick, vehicle, before/after SA0.00.00.00.20.00.0
Delta time to tail flick, test, before/after SA1.81.63.71.9-1.0-0.1
Tibia length0.51.42.6-1.60.51.2
Ambulatory time before self-admin0.50.51.10.2-1.10.6
Ambulatory time after self-admin0.40.50.8-0.4-0.70.9
Bone: tissue strength0.30.20.5-0.50.10.7
Total heroin consumption0.30.30.5-0.7-0.10.6
Bone: trabecular number0.20.30.70.30.4-0.8
Bone: trabecular spacing0.40.60.9-0.9-0.00.9
Bone: trabecular thickness0.10.10.30.6-0.3-0.1
Bone: trabecular tissue density0.70.91.31.0-1.10.8
Water consumed over 24 hours1.92.36.1-2.50.50.7
Number of responses in last shaping day2.02.14.80.8-2.20.9