Rnf4

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 Rnf4 0.06 0.04 1.5e-08 0.06 0.06 0.06 0.06 5.0e-07 1.1e-07 5.0e-07 6.4e-07
2 Brain intron excision ratio chr14_80639985_80647017 0.03 0.03 1.8e-03 0.01 0.01 0 0.01 1.3e-02 2.4e-02 3.5e-01 6.2e-02
3 Liver gene expression Rnf4 0.02 0.01 8.1e-03 0.01 0.01 0 0 2.5e-02 4.3e-02 1.5e-01 7.3e-02
4 BLA intron excision ratio chr14_80639985_80647011 0.28 0.17 3.7e-03 0 0.05 0.03 0.03 2.8e-01 1.0e-03 7.8e-03 1.3e-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 density0.71.21.91.4-0.91.11.0
Area under the delay curve0.80.92.7-0.50.6-0.6-1.6
BMI with tail2.06.79.4-3.02.4-1.6-3.1
BMI without tail1.34.16.2-2.52.1-1.0-2.2
Body weight5.524.130.4-5.55.1-4.9-4.0
Weight adjusted by age2.53.84.4-2.12.0-1.8-1.9
Bone surface0.20.30.7-0.20.6-0.8-0.2
Bone volume0.00.10.10.3-0.20.10.3
Breakpoint value in progressive ratio session0.10.10.10.2-0.30.30.0
Number of licking bursts1.21.93.6-1.41.5-1.9-0.1
Context. condit. distance diff. score0.30.30.80.6-0.90.30.3
Locomotion velocity, session 11.11.21.51.2-1.01.11.1
Locomotion distance, session 10.30.40.70.8-0.20.80.3
Locomotion velocity, session 24.65.37.62.8-1.81.92.6
Locomotion distance, session 21.82.55.22.3-1.11.80.7
Locomotion velocity, session 30.10.10.30.5-0.3-0.1-0.2
Locomotion distance, session 30.10.10.3-0.00.4-0.3-0.6
Stereotopy head waving bouts, day 31.61.82.90.8-1.71.70.9
Stereotopy head waving duration, day 31.31.52.80.7-1.61.70.5
Locomotion velocity, session 71.21.34.4-0.80.4-2.10.0
Locomotion distance, session 70.10.20.40.5-0.2-0.6-0.1
Stereotopy head waving bouts, day 70.91.12.2-1.30.5-0.4-1.5
Stereotopy head waving duration, day 71.72.13.2-1.81.0-1.1-1.7
Locomotion velocity, session 81.92.34.01.5-2.00.81.5
Locomotion distance, session 81.52.13.61.9-1.41.31.2
Degree of sensitization distance1.21.22.21.1-1.10.31.5
Degree of sensitization stereotypy1.81.92.7-1.61.1-1.0-1.6
Conditioned locomotion0.70.82.2-0.20.4-0.8-1.5
Cocaine response after cond. corrected1.21.42.41.3-1.21.50.2
Cocaine response after cond. not corrected0.50.51.00.8-0.71.00.1
Cocaine response before conditioning0.70.91.3-1.01.1-1.20.1
Saline control response0.20.30.40.5-0.40.50.7
Bone: connectivity density0.30.51.21.1-0.50.70.5
Bone: cortical apparent density0.40.51.1-0.7-0.20.7-1.1
Bone: cortical area5.58.511.8-3.03.4-3.2-1.5
Bone: cortical porosity0.40.40.90.7-1.00.30.3
Bone: cortical porosity0.00.00.10.2-0.30.2-0.2
Bone: cortical thickness3.86.39.4-2.63.1-2.4-1.8
Bone: cortical thickness0.60.72.5-0.2-0.2-0.4-1.6
Bone: cortical tissue density0.40.61.2-0.6-0.30.8-1.1
Condit. Reinf. active minus inactive responses1.41.52.61.2-1.41.60.3
Condit. Reinf. active-inactive response ratio2.83.05.01.8-1.72.20.9
Condit. Reinf. active responses0.60.81.30.7-1.11.10.1
Condit. Reinf. inactive responses1.01.22.1-1.30.8-1.5-0.5
Incentive salience index mean0.20.20.40.3-0.60.6-0.1
Condit. Reinf. lever presses0.50.71.0-1.00.6-0.9-0.8
Condit. Reinf. active minus inactive responses0.30.40.6-0.70.6-0.80.4
Condit. Reinf. active-inactive response ratio0.10.20.20.2-0.50.4-0.5
Condit. Reinf. active responses0.20.20.70.2-0.4-0.20.9
Condit. Reinf. inactive responses0.40.51.20.4-0.8-0.01.1
Condit. Reinf. lever presses0.20.30.5-0.70.6-0.6-0.4
Condit. Reinf. lever reinforcers received0.00.10.2-0.0-0.1-0.40.3
Conditioned reinforcement - actives0.50.91.6-0.80.8-0.8-1.3
Conditioned reinforcement - inactives0.50.80.9-1.01.0-1.0-0.6
Conditioned locomotion1.11.41.5-1.21.2-1.2-1.2
Patch foraging indifference point 0 sec0.10.20.3-0.1-0.60.40.5
Patch foraging indifference point AUC0.40.50.80.6-0.40.90.9
Delay disc. indifference point, 0s delay2.52.89.6-0.60.7-0.7-3.1
Delay disc. indifference point, 16s delay0.10.10.10.3-0.30.4-0.3
Delay disc. indifference point, 2s delay0.60.72.70.10.1-0.0-1.6
Delay disc. indifference point, 24s delay0.80.93.1-0.30.4-0.3-1.7
Delay disc. indifference point, 4s delay0.20.20.40.4-0.30.3-0.6
Delay disc. indifference point, 8s delay0.80.91.0-1.01.0-1.0-0.8
Indifference point function ln k0.30.50.80.6-0.90.30.8
Indifference point function log k0.30.50.80.6-0.90.30.8
Patch foraging total patch changes 0 sec0.10.10.3-0.2-0.40.30.5
Patch foraging total patch changes 12 sec0.20.20.5-0.70.3-0.4-0.4
Patch foraging total patch changes 18 sec0.10.10.2-0.1-0.50.50.3
Patch foraging total patch changes 24 sec0.10.20.6-0.2-0.00.4-0.8
Patch foraging total patch changes 6 sec0.20.20.8-0.3-0.10.40.9
Patch foraging time to switch 0 sec1.53.15.8-1.41.6-1.4-2.4
Patch foraging water rate 0 sec0.51.03.2-0.60.2-0.51.8
Patch foraging water rate 12 sec0.20.51.30.2-0.40.81.1
Patch foraging water rate 18 sec0.20.30.9-0.3-0.00.40.9
Patch foraging water rate 24 sec0.60.82.5-0.80.2-0.01.6
Patch foraging water rate 6 sec0.50.81.5-1.20.7-0.60.9
Seeking ratio, delayed vs. immediate footshock2.83.44.91.7-1.71.72.2
Distance traveled before self-admin0.91.21.81.3-1.31.10.4
Distance traveled after self-admin0.30.41.30.3-0.20.1-1.2
Extensor digitorum longus weight1.76.712.0-3.52.6-2.5-1.4
Bone: elastic displacement1.11.32.5-1.01.6-1.3-0.3
Bone: elastic work3.34.36.2-2.32.5-2.3-0.6
Bone: endosteal estimation0.91.94.8-1.31.1-2.20.2
Bone: endosteal perimeter1.02.24.5-1.31.5-2.10.0
Epididymis fat weight1.75.97.6-2.82.1-2.4-2.4
Delta time in closed arm before/after self-admin0.60.60.80.9-0.90.9-0.0
Delta time in open arm before/after self-admin1.61.61.7-1.31.3-1.3-1.1
Diff in mean of infusions in LGA sessions0.81.01.51.2-1.11.1-0.4
Delay discount exponential model param0.60.72.30.4-0.50.51.5
Extinction: sum of active levers before priming1.01.11.4-1.01.0-1.0-1.2
Active lever presses in extinction session 60.40.41.7-0.10.10.0-1.3
Bone: final force4.87.711.4-2.83.1-3.4-1.3
Bone: final moment3.96.28.8-2.62.9-3.0-0.9
Food consumed during 24 hour testing period0.40.62.00.1-0.5-0.11.4
Glucose0.60.92.00.1-0.6-1.11.4
Heart weight1.21.82.8-1.31.6-1.7-0.4
Delay discount hyperbolic model param0.60.72.30.3-0.40.41.5
Intermittent access intake day 1-15 change2.24.55.82.4-2.32.31.2
Intermittent access intake escalation1.53.03.92.0-1.91.91.0
Intermittent access intake escalation 22.73.13.41.9-1.81.81.5
Intermitt. access day 1 inactive lever presses0.10.50.60.7-0.80.80.7
Intermitt. access day 15 inactive lever presses0.40.80.80.9-0.90.90.9
Intermitt. access escalation Index0.60.91.21.1-1.01.00.7
Intermittent access day 1 total infusions1.11.73.2-1.11.1-1.1-1.8
Intermittent access day 15 total infusions0.00.00.20.1-0.00.0-0.4
Intermittent access terminal intake (last 3 days)0.00.10.10.3-0.30.30.1
Intermittent access total infusions0.10.20.2-0.40.4-0.4-0.4
Intermittent access day 1 locomotion0.81.01.3-0.90.9-0.9-1.2
Intermittent access day 15 total locomotion0.40.71.9-0.60.6-0.6-1.4
Intermittent access total locomotion0.10.10.3-0.10.1-0.1-0.5
Intermittent access standard deviation0.30.60.80.9-0.80.80.5
Left kidney weight3.918.124.2-4.94.9-4.2-2.7
Right kidney weight3.315.018.4-4.34.3-3.6-3.2
Cocaine induced anxiety0.60.81.00.9-0.80.81.0
Post-drug Anxiety0.20.20.30.5-0.40.4-0.5
Baseline Anxiety2.83.37.1-1.41.4-1.4-2.7
Tail length0.83.04.8-1.92.2-1.9-0.1
Length with tail3.113.519.0-4.24.0-4.4-1.3
Length without tail2.78.812.9-3.33.0-3.6-1.5
Times rat made contact with spout1.51.82.81.2-1.40.91.7
Lifetime Intake0.10.20.2-0.40.4-0.4-0.3
Liver weight, left0.40.71.1-0.90.7-1.1-0.6
Liver weight, right2.13.76.5-2.52.0-1.4-1.5
Locomotor activity0.60.93.3-0.20.1-0.61.8
Locomotor testing distance0.40.71.2-1.10.5-1.10.1
Locomotor testing rearing0.71.42.4-1.51.0-1.50.3
Locomotion in novel chamber0.30.40.70.8-0.80.70.1
Locomotion in novel chamber post-restriction0.10.20.50.4-0.1-0.1-0.7
Fecal boli incidents, locomotor time 10.40.60.90.7-0.80.71.0
Change in fecal boli incidents, locomotor task0.50.50.90.7-0.50.50.9
Time >=10cm from walls, locomotor time 12.52.75.2-1.41.3-1.3-2.3
Bouts of movement, locomotor time 10.40.41.3-0.40.3-0.2-1.2
Total resting periods, locomotor time 10.40.41.4-0.40.3-0.3-1.2
Rest time, locomotor task time 11.21.52.2-1.51.3-1.5-0.3
Distance moved, locomotor task time 10.10.10.20.3-0.10.50.2
Vertical activity count, locomotor time 10.51.21.71.3-1.11.20.8
Time >=10cm from walls, locomotor time 20.60.80.9-0.90.9-1.0-0.8
Bouts of movement, locomotor time 20.10.10.30.1-0.20.2-0.6
Total resting periods, locomotor time 20.10.20.6-0.20.2-0.1-0.8
Rest time, locomotor task time 20.91.21.6-1.21.2-1.2-0.3
Distance moved, locomotor task time 20.40.40.70.8-0.60.80.2
Vertical activity count, locomotor time 21.21.72.41.6-1.41.40.6
Light reinforcement 11.53.65.4-2.32.0-1.8-1.3
Light reinforcement 21.92.94.6-2.11.8-1.8-0.9
Bone: marrow area0.81.84.6-1.21.0-2.10.1
Bone: maximum diameter3.05.78.3-2.82.9-2.3-0.9
Bone: maximum force3.15.58.3-2.52.5-2.9-0.9
Bone: maximum moment2.44.26.0-2.32.3-2.4-0.4
Mean time between licks in bursts1.12.65.51.4-1.31.22.3
Mean num. licks in bursts2.84.45.92.2-2.32.41.2
Cd content in liver0.10.10.30.3-0.1-0.10.6
Co content in liver0.70.82.3-0.40.8-1.5-0.4
Cu content in liver0.60.81.61.3-1.00.60.4
Fe content in liver2.83.45.62.4-2.31.60.5
K content in liver0.40.41.00.10.6-0.4-1.0
Mg content in liver1.81.83.6-1.11.9-1.1-1.1
Mn content in liver0.40.40.80.7-0.50.40.9
Na content in liver0.40.40.50.6-0.7-0.3-0.7
Rb content in liver0.50.51.3-0.30.7-1.1-0.5
Se content in liver0.30.31.00.2-0.41.0-0.1
Sr content in liver1.31.12.1-1.51.3-0.9-0.2
Zn content in liver0.30.30.4-0.4-0.50.70.6
Bone: minimum diameter1.32.44.6-1.41.7-2.20.1
Time in familiar zone, hab. session 10.60.60.80.9-0.80.90.4
Time in novel zone, hab. session 10.20.20.6-0.80.6-0.20.0
Total zone transitions, hab. session 10.10.10.20.5-0.40.30.3
Total locomotion distance, hab. session 10.50.71.11.0-0.80.60.8
Locomotion velocity, hab. session 10.10.20.50.7-0.2-0.10.4
Time in familiar zone, hab. session 23.33.55.42.0-2.32.10.5
Time in novel zone, hab. session 25.25.38.6-2.72.9-2.1-0.6
Total zone transitions, hab. session 20.00.00.1-0.2-0.10.20.3
Total locomotion distance, hab. session 20.10.20.60.0-0.10.30.8
Locomotion velocity, hab. session 20.10.10.30.1-0.10.20.6
Novel to familiar place preference ratio0.00.00.10.4-0.10.1-0.1
Novelty place preference0.00.00.00.20.1-0.00.0
Time in novel zone, NPP test0.00.00.00.10.1-0.00.1
Total zone transitions, NPP test0.00.10.10.3-0.30.3-0.2
Total locomotion distance, NPP test0.30.40.60.8-0.60.8-0.1
Locomotion velocity, NPP test0.50.61.11.0-0.80.9-0.2
Intraocular pressure0.20.30.7-0.70.9-0.2-0.2
Delta distance traveled before/after self-admin1.21.32.9-0.80.9-0.8-1.7
Delta ambulatory time before/after self-admin0.10.10.50.2-0.10.2-0.7
Parametrial fat weight0.10.30.50.7-0.60.7-0.2
Pavlov. Cond. lever latency0.81.01.61.1-0.81.30.8
Pavlov. Cond. magazine entry latency1.01.31.80.9-1.31.31.0
Pavlov. Cond. change in total contacts0.00.00.00.1-0.10.2-0.2
Pavlov. Cond. index score0.10.10.50.2-0.70.20.0
Pavlov. Cond. latency score0.00.10.2-0.0-0.5-0.1-0.1
Pavlov. Cond. lever contacts0.50.61.2-0.80.6-1.1-0.6
Pavlov. Cond. magazine entry number1.31.72.5-1.21.6-1.4-0.9
Pavlov. Cond. intertrial magazine entries0.30.40.5-0.70.7-0.2-0.7
Pavlov. Cond. lever-magazine prob. diff.0.00.10.20.1-0.40.1-0.0
Pavlov. Cond. response bias0.20.20.40.4-0.60.50.3
Pavlov. Cond. lever latency0.60.91.1-0.81.1-0.8-1.0
Pavlov. Cond. magazine entry latency1.31.62.0-1.31.4-1.4-0.8
Pavlov. Cond. change in total contacts0.00.00.1-0.1-0.30.10.0
Pavlov. Cond. index score0.00.00.1-0.1-0.20.00.2
Pavlov. Cond. latency score0.00.00.1-0.1-0.20.00.2
Pavlov. Cond. lever contacts0.91.31.71.2-1.31.01.0
Pavlov. Cond. magazine entry number1.31.72.61.6-1.31.40.5
Pavlov. Cond. intertrial magazine entries0.71.11.71.2-1.30.70.9
Pavlov. Cond. lever-magazine prob. diff.0.00.00.0-0.2-0.2-0.10.2
Pavlov. Cond. response bias0.10.10.10.2-0.30.20.3
Time in closed arm before self-admin0.10.10.1-0.40.3-0.30.3
Time in closed arm after self-admin0.30.30.50.6-0.70.70.3
Time in open arm before self-admin0.10.10.2-0.40.4-0.50.1
Time in open arm after self-admin1.51.72.1-1.41.4-1.4-0.8
Bone: periosteal estimation3.16.511.3-2.62.7-3.4-0.8
Bone: periosteal perimeter3.96.810.5-2.62.9-3.2-1.3
Bone: post-yield work0.91.32.40.8-1.61.11.0
Progressive ratio test 1 active lever presses0.91.11.1-1.11.1-1.1-1.0
Progressive ratio test 1 breakpoint0.91.11.1-1.01.0-1.0-1.0
Progressive ratio test 1 inactive lever presses0.20.20.3-0.50.5-0.5-0.3
Progressive ratio test 2 active lever presses0.10.10.5-0.10.2-0.2-0.7
Progressive ratio test 2 breakpoint0.20.20.6-0.20.2-0.2-0.8
Progressive ratio test 2 inactive lever presses0.40.71.0-0.70.8-0.8-1.0
Incentive Sensitization - Responses0.10.10.20.3-0.20.2-0.4
Incentive Sensitization - Breakpoint0.10.10.20.2-0.20.2-0.4
Sum of active levers in priming session hrs 5-60.30.31.00.0-0.10.2-1.0
Progressive ratio0.20.30.5-0.40.6-0.7-0.4
Food seeking constrained by brief footshock1.62.03.2-1.41.4-1.8-1.1
Seeking ratio, punishment vs. effort0.00.00.1-0.0-0.1-0.10.3
Retroperitoneal fat weight0.62.54.7-1.31.4-1.2-2.2
Reaction time number correct0.61.23.0-1.10.4-0.61.7
Reaction time mean minus median0.61.51.91.3-1.41.20.8
Reaction time mean minus median AUC0.10.10.4-0.30.2-0.2-0.6
Reaction time num false alarms1.82.55.8-1.21.4-1.0-2.4
Reaction time num false alarms AUC2.23.47.0-1.61.6-1.2-2.7
Reaction time trials correct on left0.61.23.0-1.10.4-0.61.7
Reaction time trials on left0.61.13.1-1.00.3-0.51.8
Reaction time mean0.61.01.91.4-1.01.0-0.0
Reaction time mean AUC0.60.91.81.3-1.01.0-0.1
Median of all reaction times0.50.71.51.2-0.70.8-0.3
Reaction time omissions0.50.71.50.7-0.91.20.2
Reaction time false alarm rate2.43.39.9-0.91.3-0.7-3.1
Reaction time premature initiation rate0.10.10.5-0.2-0.00.2-0.7
Reaction time premature initiations0.10.20.6-0.80.1-0.10.2
Std. dev. reaction times0.40.81.21.0-1.11.1-0.0
Reaction time trials completed0.61.13.1-1.00.3-0.51.8
Reaction time trials AUC0.61.23.4-1.00.3-0.41.9
Run reversals in cocaine runway, females1.01.01.31.1-1.00.7-1.1
Run reversals in cocaine runway, males0.20.20.3-0.50.6-0.3-0.5
Latency to leave start box in cocaine runway1.31.51.9-1.21.2-1.4-1.2
Latency to leave start box in cocaine runway, F2.63.03.2-1.81.7-1.8-1.6
Latency to leave start box in cocaine runway, M0.00.00.10.0-0.0-0.20.1
Std. dev. time between licks in bursts0.30.51.30.6-0.4-0.11.2
Total sessions with >9 infusions0.10.20.4-0.30.4-0.4-0.6
Short access day 1 total inactive lever presses0.00.00.0-0.20.2-0.20.1
Short access day 10 total inactive lever presses0.81.94.11.0-1.11.12.0
Short access day 1 total infusions0.10.20.6-0.10.2-0.2-0.8
Short access day 10 total infusions0.00.00.0-0.10.1-0.10.2
Short access total infusions0.00.00.00.00.0-0.00.0
Short access day 1 locomotion0.40.50.5-0.70.7-0.7-0.7
Short access day 10 total locomotion1.42.52.61.6-1.61.61.5
Short access total locomotion0.50.60.60.8-0.80.80.7
One hour access (0.3 mA shock)0.00.00.1-0.20.2-0.20.3
Compulsive drug intake0.10.10.20.4-0.40.40.1
One hour access (shock baseline)0.00.00.0-0.20.2-0.20.1
Social response proportion1.92.23.41.2-1.31.51.8
Social responses0.40.52.1-0.1-0.10.31.4
Social time1.11.52.01.4-1.41.11.0
Soleus weight1.75.19.1-3.02.7-2.00.0
Bone: stiffness1.22.04.3-1.11.1-2.1-1.2
Tibialis anterior weight0.93.25.8-2.41.9-1.6-1.0
Time to tail flick, vehicle, before self-admin0.50.50.80.7-0.70.9-0.3
Time to tail flick, vehicle, after self-admin0.30.40.80.7-0.60.90.1
Time to tail flick, test, before self-admin0.10.10.1-0.30.3-0.30.2
Time to tail flick, test, after self-admin0.50.50.9-0.60.6-0.71.0
Delta time to tail flick, vehicle, before/after SA0.10.10.2-0.30.4-0.30.1
Delta time to tail flick, test, before/after SA0.30.31.1-0.00.1-0.01.0
Tibia length1.54.16.4-1.72.5-2.4-1.2
Ambulatory time before self-admin0.50.81.21.1-1.10.9-0.2
Ambulatory time after self-admin0.91.01.31.1-1.10.9-0.8
Bone: tissue strength1.61.62.3-1.31.5-1.11.1
Total heroin consumption0.30.30.6-0.80.6-0.6-0.1
Bone: trabecular number0.30.51.30.8-0.31.10.4
Bone: trabecular spacing1.21.62.8-1.41.2-1.7-0.3
Bone: trabecular thickness1.31.73.41.2-1.91.20.5
Bone: trabecular tissue density0.10.10.50.7-0.30.20.1
Water consumed over 24 hours1.82.56.31.2-1.10.92.5
Number of responses in last shaping day0.70.72.90.1-0.00.0-1.7