Lrfn3

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 Lrfn3 0.06 0.04 3.9e-06 0.03 0.06 0.04 0.04 1.3e-04 1.1e-06 1.1e-05 9.1e-06
2 NAcc gene expression Lrfn3 0.04 0.03 1.8e-05 0.04 0.04 0.04 0.04 1.5e-05 8.7e-06 6.8e-06 5.9e-06
3 OFC gene expression Lrfn3 0.37 0.24 4.0e-04 0.13 0.07 0.11 0.06 5.8e-04 1.1e-02 1.6e-03 1.7e-02
4 Brain gene expression Lrfn3 0.05 0.04 7.7e-05 0.05 0.04 0.04 0.04 2.1e-05 1.2e-04 2.4e-04 1.6e-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 4
Bone: apparent density0.71.11.60.31.2-1.2-1.3
Area under the delay curve0.40.41.51.20.2-0.1-0.0
BMI with tail0.20.60.7-0.7-0.70.90.8
BMI without tail0.00.00.10.20.3-0.1-0.1
Body weight2.510.512.32.63.5-3.4-3.4
Weight adjusted by age0.30.30.4-0.30.5-0.7-0.7
Bone surface1.73.03.31.61.8-1.7-1.8
Bone volume1.72.83.41.31.8-1.8-1.8
Breakpoint value in progressive ratio session1.61.74.62.20.9-0.9-0.8
Number of licking bursts2.32.83.1-1.6-1.71.61.8
Context. condit. distance diff. score0.00.00.10.3-0.20.00.1
Locomotion velocity, session 10.50.61.4-1.2-0.60.60.4
Locomotion distance, session 10.81.01.30.90.9-1.1-1.1
Locomotion velocity, session 20.81.01.3-0.6-1.11.11.0
Locomotion distance, session 21.11.51.9-0.8-1.31.41.3
Locomotion velocity, session 30.40.50.7-0.6-0.70.70.8
Locomotion distance, session 32.62.86.42.51.3-1.3-1.3
Stereotopy head waving bouts, day 31.01.22.1-1.4-0.71.01.0
Stereotopy head waving duration, day 31.82.23.6-1.9-1.11.41.4
Locomotion velocity, session 70.40.40.90.90.4-0.6-0.5
Locomotion distance, session 70.10.20.30.30.1-0.6-0.4
Stereotopy head waving bouts, day 70.80.91.4-0.6-0.91.21.0
Stereotopy head waving duration, day 72.12.53.2-1.5-1.51.81.6
Locomotion velocity, session 83.64.35.5-1.5-2.32.02.3
Locomotion distance, session 80.60.81.3-0.2-1.21.01.0
Degree of sensitization distance0.60.61.7-1.3-0.60.20.4
Degree of sensitization stereotypy0.91.01.6-0.6-1.01.21.0
Conditioned locomotion0.50.61.0-0.4-0.81.00.8
Cocaine response after cond. corrected0.30.30.6-0.8-0.40.50.5
Cocaine response after cond. not corrected0.20.20.7-0.8-0.20.30.3
Cocaine response before conditioning1.31.61.91.11.4-1.3-1.2
Saline control response0.00.00.0-0.2-0.10.0-0.1
Bone: connectivity density0.20.30.50.50.6-0.5-0.7
Bone: cortical apparent density1.72.32.7-1.4-1.61.41.6
Bone: cortical area1.01.52.01.11.1-1.4-1.2
Bone: cortical porosity1.41.52.3-0.5-1.21.51.4
Bone: cortical porosity1.81.92.8-0.6-1.51.71.6
Bone: cortical thickness0.10.20.30.20.4-0.6-0.4
Bone: cortical thickness0.91.01.6-1.3-0.90.81.0
Bone: cortical tissue density2.02.63.1-1.5-1.81.61.7
Condit. Reinf. active minus inactive responses0.20.20.3-0.4-0.40.60.4
Condit. Reinf. active-inactive response ratio0.30.30.5-0.7-0.40.70.4
Condit. Reinf. active responses2.02.43.0-1.2-1.61.71.7
Condit. Reinf. inactive responses2.02.43.2-0.8-1.71.61.8
Incentive salience index mean0.20.30.5-0.1-0.50.70.5
Condit. Reinf. lever presses0.10.20.40.6-0.10.40.2
Condit. Reinf. active minus inactive responses0.81.02.31.50.9-0.7-0.6
Condit. Reinf. active-inactive response ratio0.20.20.4-0.2-0.40.50.6
Condit. Reinf. active responses2.83.86.32.51.9-1.7-1.6
Condit. Reinf. inactive responses4.55.58.83.02.2-2.1-2.0
Condit. Reinf. lever presses6.38.69.83.13.1-2.8-2.7
Condit. Reinf. lever reinforcers received3.14.37.12.72.0-1.9-1.6
Conditioned reinforcement - actives0.10.10.1-0.4-0.30.30.3
Conditioned reinforcement - inactives0.80.93.31.80.4-0.4-0.4
Conditioned locomotion1.92.22.7-0.9-1.61.61.6
Patch foraging indifference point 0 sec0.10.10.40.60.10.1-0.0
Patch foraging indifference point AUC0.60.70.8-0.9-0.70.90.8
Delay disc. indifference point, 0s delay0.30.41.31.10.3-0.3-0.2
Delay disc. indifference point, 16s delay0.80.93.31.80.3-0.1-0.1
Delay disc. indifference point, 2s delay1.11.32.01.41.1-1.0-0.9
Delay disc. indifference point, 24s delay2.02.04.12.01.1-1.1-1.2
Delay disc. indifference point, 4s delay0.20.20.30.4-0.50.50.6
Delay disc. indifference point, 8s delay0.10.10.40.60.2-0.2-0.2
Indifference point function ln k0.30.40.70.80.7-0.6-0.6
Indifference point function log k0.30.40.70.80.7-0.6-0.6
Patch foraging total patch changes 0 sec0.10.20.70.80.2-0.1-0.2
Patch foraging total patch changes 12 sec0.10.10.20.1-0.30.50.3
Patch foraging total patch changes 18 sec0.00.00.00.1-0.0-0.1-0.1
Patch foraging total patch changes 24 sec1.01.21.41.21.0-1.1-1.2
Patch foraging total patch changes 6 sec0.00.00.00.1-0.20.20.1
Patch foraging time to switch 0 sec0.60.91.0-0.9-1.00.91.0
Patch foraging water rate 0 sec0.71.11.2-0.8-1.11.11.1
Patch foraging water rate 12 sec0.81.21.70.81.1-1.2-1.3
Patch foraging water rate 18 sec0.20.20.3-0.4-0.40.60.4
Patch foraging water rate 24 sec0.10.20.70.80.3-0.1-0.3
Patch foraging water rate 6 sec1.32.02.51.61.4-1.2-1.3
Seeking ratio, delayed vs. immediate footshock1.72.02.51.61.3-1.4-1.4
Distance traveled before self-admin0.00.00.00.20.10.0-0.0
Distance traveled after self-admin3.74.15.42.31.9-2.0-1.9
Extensor digitorum longus weight0.20.92.4-1.5-0.60.70.6
Bone: elastic displacement0.00.00.1-0.3-0.10.00.1
Bone: elastic work1.92.42.91.21.6-1.7-1.6
Bone: endosteal estimation1.63.53.71.91.8-1.8-1.9
Bone: endosteal perimeter1.42.94.12.01.6-1.6-1.5
Epididymis fat weight0.20.50.70.30.7-0.7-0.8
Delta time in closed arm before/after self-admin2.62.53.11.31.7-1.5-1.8
Delta time in open arm before/after self-admin0.70.71.3-1.1-0.70.60.7
Diff in mean of infusions in LGA sessions0.50.60.70.4-0.80.80.8
Delay discount exponential model param0.40.41.5-1.2-0.30.20.1
Extinction: sum of active levers before priming3.53.54.11.62.0-1.9-2.0
Active lever presses in extinction session 61.91.82.11.01.4-1.5-1.4
Bone: final force1.52.42.81.61.5-1.7-1.4
Bone: final moment1.93.03.51.71.7-1.9-1.6
Food consumed during 24 hour testing period1.01.22.21.50.9-0.8-0.9
Glucose0.20.31.0-1.0-0.20.10.4
Heart weight0.20.30.70.80.4-0.4-0.5
Delay discount hyperbolic model param0.30.31.2-1.1-0.20.20.1
Intermittent access intake day 1-15 change2.92.93.51.21.9-1.8-1.8
Intermittent access intake escalation3.02.93.51.31.9-1.8-1.8
Intermittent access intake escalation 21.71.61.91.11.4-1.3-1.3
Intermitt. access day 1 inactive lever presses2.42.65.42.31.3-1.3-1.3
Intermitt. access day 15 inactive lever presses0.40.51.91.40.1-0.2-0.2
Intermitt. access escalation Index0.00.00.00.1-0.20.10.1
Intermittent access day 1 total infusions1.41.62.0-0.7-1.41.41.4
Intermittent access day 15 total infusions0.10.10.50.70.1-0.1-0.1
Intermittent access terminal intake (last 3 days)0.10.10.20.4-0.30.40.4
Intermittent access total infusions0.20.20.30.2-0.60.50.5
Intermittent access day 1 locomotion0.80.91.10.2-1.11.11.1
Intermittent access day 15 total locomotion0.20.20.60.80.2-0.1-0.1
Intermittent access total locomotion0.81.01.3-0.2-1.11.11.1
Intermittent access standard deviation5.86.27.72.82.4-2.4-2.4
Left kidney weight2.98.310.91.53.2-3.2-3.3
Right kidney weight4.913.917.32.54.0-4.0-4.2
Cocaine induced anxiety0.30.30.40.70.6-0.5-0.5
Post-drug Anxiety0.40.40.6-0.1-0.70.70.7
Baseline Anxiety1.71.82.2-0.8-1.51.51.5
Tail length4.513.515.33.03.9-3.8-3.9
Length with tail7.828.430.94.75.6-5.6-5.5
Length without tail5.411.813.03.03.6-3.6-3.5
Times rat made contact with spout0.60.62.5-1.6-0.20.1-0.1
Lifetime Intake0.20.30.4-0.3-0.60.60.6
Liver weight, left0.50.82.0-1.4-0.70.70.6
Liver weight, right0.20.40.6-0.8-0.60.50.5
Locomotor activity0.61.01.9-1.4-0.71.00.7
Locomotor testing distance0.30.61.5-1.2-0.50.60.4
Locomotor testing rearing1.52.34.7-2.2-1.41.21.2
Locomotion in novel chamber0.60.71.0-0.2-0.91.01.0
Locomotion in novel chamber post-restriction0.20.20.30.6-0.40.40.4
Fecal boli incidents, locomotor time 12.93.23.9-1.1-2.01.92.0
Change in fecal boli incidents, locomotor task0.00.00.0-0.2-0.00.00.0
Time >=10cm from walls, locomotor time 10.00.00.1-0.3-0.20.20.2
Bouts of movement, locomotor time 10.80.92.21.50.7-0.7-0.7
Total resting periods, locomotor time 10.60.72.11.40.5-0.5-0.5
Rest time, locomotor task time 11.61.82.3-0.7-1.51.51.5
Distance moved, locomotor task time 10.20.30.4-0.10.6-0.6-0.6
Vertical activity count, locomotor time 12.32.42.71.31.6-1.6-1.6
Time >=10cm from walls, locomotor time 22.22.42.9-1.0-1.71.61.7
Bouts of movement, locomotor time 20.00.00.00.00.0-0.1-0.0
Total resting periods, locomotor time 20.00.00.1-0.1-0.20.20.2
Rest time, locomotor task time 20.70.81.1-0.5-1.01.01.0
Distance moved, locomotor task time 20.00.00.1-0.40.1-0.1-0.1
Vertical activity count, locomotor time 20.90.91.00.91.0-1.0-1.0
Light reinforcement 10.10.20.4-0.1-0.40.60.3
Light reinforcement 22.83.84.8-1.6-2.02.22.0
Bone: marrow area1.73.63.71.91.9-1.9-1.9
Bone: maximum diameter1.22.22.51.51.4-1.6-1.5
Bone: maximum force2.64.54.92.12.1-2.2-2.1
Bone: maximum moment2.95.15.52.22.2-2.3-2.2
Mean time between licks in bursts0.00.10.20.4-0.2-0.00.1
Mean num. licks in bursts1.31.62.50.41.4-1.3-1.6
Cd content in liver0.20.30.4-0.20.5-0.6-0.6
Co content in liver0.50.60.7-0.6-0.80.80.9
Cu content in liver0.60.70.90.70.9-0.9-1.0
Fe content in liver0.00.00.00.1-0.20.1-0.0
K content in liver0.10.10.10.30.10.30.2
Mg content in liver0.90.91.4-0.6-0.91.21.0
Mn content in liver1.41.51.9-1.2-1.11.41.3
Na content in liver1.61.72.41.51.2-1.2-1.2
Rb content in liver0.10.20.30.4-0.40.40.5
Se content in liver8.19.910.2-3.1-3.23.23.1
Sr content in liver1.00.91.0-1.0-0.91.00.9
Zn content in liver0.10.10.2-0.2-0.40.40.4
Bone: minimum diameter2.95.38.22.92.1-2.1-2.1
Time in familiar zone, hab. session 10.30.20.5-0.30.5-0.7-0.5
Time in novel zone, hab. session 11.11.11.9-0.3-1.11.41.1
Total zone transitions, hab. session 10.00.00.10.3-0.10.20.1
Total locomotion distance, hab. session 11.01.52.51.61.1-1.0-1.1
Locomotion velocity, hab. session 10.70.91.31.10.9-0.9-0.9
Time in familiar zone, hab. session 21.31.41.71.31.2-1.1-1.1
Time in novel zone, hab. session 21.01.01.4-1.2-0.91.00.9
Total zone transitions, hab. session 23.03.84.6-1.6-2.02.12.0
Total locomotion distance, hab. session 20.10.10.20.3-0.20.40.3
Locomotion velocity, hab. session 20.10.10.30.0-0.40.50.4
Novel to familiar place preference ratio0.10.10.20.50.40.10.0
Novelty place preference0.10.10.20.40.30.10.0
Time in novel zone, NPP test0.00.00.10.20.10.30.2
Total zone transitions, NPP test0.10.10.1-0.3-0.30.40.2
Total locomotion distance, NPP test2.33.13.61.61.9-1.7-1.9
Locomotion velocity, NPP test2.33.23.81.71.9-1.6-1.8
Intraocular pressure0.10.10.20.4-0.40.30.2
Delta distance traveled before/after self-admin4.34.65.12.32.1-2.2-2.0
Delta ambulatory time before/after self-admin5.25.76.02.42.4-2.5-2.4
Parametrial fat weight0.40.83.2-1.8-0.30.30.2
Pavlov. Cond. lever latency0.40.50.80.10.8-0.9-0.7
Pavlov. Cond. magazine entry latency0.30.40.6-0.8-0.60.80.5
Pavlov. Cond. change in total contacts0.60.61.00.1-0.81.00.9
Pavlov. Cond. index score0.70.81.3-0.6-0.91.10.9
Pavlov. Cond. latency score0.40.50.8-0.3-0.80.90.7
Pavlov. Cond. lever contacts0.20.20.30.5-0.40.60.4
Pavlov. Cond. magazine entry number0.50.60.90.80.7-0.9-0.6
Pavlov. Cond. intertrial magazine entries0.91.11.4-0.9-1.20.91.1
Pavlov. Cond. lever-magazine prob. diff.0.81.01.5-0.7-1.01.21.0
Pavlov. Cond. response bias0.30.40.6-0.5-0.50.80.5
Pavlov. Cond. lever latency4.76.47.2-2.7-2.62.42.4
Pavlov. Cond. magazine entry latency2.52.94.22.01.7-1.4-1.6
Pavlov. Cond. change in total contacts8.011.113.43.73.4-3.1-3.1
Pavlov. Cond. index score5.06.57.22.72.7-2.4-2.4
Pavlov. Cond. latency score4.75.87.02.62.5-2.2-2.3
Pavlov. Cond. lever contacts4.66.26.92.52.6-2.4-2.4
Pavlov. Cond. magazine entry number4.15.05.9-2.1-2.42.22.3
Pavlov. Cond. intertrial magazine entries1.01.41.4-1.1-1.21.11.2
Pavlov. Cond. lever-magazine prob. diff.4.96.37.12.62.7-2.4-2.4
Pavlov. Cond. response bias5.37.38.02.72.8-2.6-2.6
Time in closed arm before self-admin2.22.42.9-1.2-1.71.61.7
Time in closed arm after self-admin0.10.10.50.7-0.10.30.1
Time in open arm before self-admin3.63.94.31.82.1-2.0-2.1
Time in open arm after self-admin1.11.21.70.51.2-1.3-1.2
Bone: periosteal estimation1.83.74.11.91.9-2.0-1.9
Bone: periosteal perimeter1.01.62.01.41.2-1.3-1.2
Bone: post-yield work2.12.94.42.11.5-1.4-1.6
Progressive ratio test 1 active lever presses0.80.81.71.30.7-0.7-0.7
Progressive ratio test 1 breakpoint1.11.22.21.50.9-0.9-0.9
Progressive ratio test 1 inactive lever presses0.70.72.71.60.2-0.3-0.3
Progressive ratio test 2 active lever presses0.20.20.40.70.3-0.3-0.3
Progressive ratio test 2 breakpoint0.10.10.30.50.2-0.2-0.2
Progressive ratio test 2 inactive lever presses1.41.65.92.40.4-0.3-0.3
Incentive Sensitization - Responses0.00.00.00.00.1-0.0-0.0
Incentive Sensitization - Breakpoint0.00.00.0-0.00.1-0.1-0.1
Sum of active levers in priming session hrs 5-60.10.10.20.40.4-0.4-0.3
Progressive ratio0.00.00.10.4-0.10.10.1
Food seeking constrained by brief footshock2.83.54.92.21.8-1.7-1.7
Seeking ratio, punishment vs. effort0.50.70.90.90.8-0.7-0.7
Retroperitoneal fat weight1.65.29.3-3.0-2.01.92.0
Reaction time number correct0.00.10.2-0.50.0-0.1-0.1
Reaction time mean minus median0.50.61.10.50.8-1.0-0.7
Reaction time mean minus median AUC1.21.52.30.51.3-1.5-1.3
Reaction time num false alarms0.60.81.2-1.1-0.90.80.8
Reaction time num false alarms AUC0.81.21.3-1.1-1.11.11.0
Reaction time trials correct on left0.00.10.2-0.50.0-0.1-0.1
Reaction time trials on left0.00.10.3-0.50.0-0.1-0.1
Reaction time mean0.40.60.80.10.8-0.9-0.9
Reaction time mean AUC0.30.40.60.00.6-0.7-0.7
Median of all reaction times0.20.30.5-0.00.5-0.6-0.7
Reaction time omissions0.10.10.3-0.60.1-0.3-0.3
Reaction time false alarm rate0.50.70.9-0.7-0.80.90.8
Reaction time premature initiation rate0.20.20.90.90.10.10.0
Reaction time premature initiations0.10.10.40.60.00.00.0
Std. dev. reaction times0.91.31.90.71.2-1.4-1.2
Reaction time trials completed0.00.10.3-0.50.0-0.1-0.1
Reaction time trials AUC0.10.10.5-0.7-0.1-0.0-0.0
Run reversals in cocaine runway, females0.90.91.10.61.0-1.1-1.1
Run reversals in cocaine runway, males0.50.51.7-1.3-0.20.40.4
Latency to leave start box in cocaine runway0.50.50.70.40.7-0.8-0.9
Latency to leave start box in cocaine runway, F0.00.00.00.20.2-0.2-0.2
Latency to leave start box in cocaine runway, M0.30.30.4-0.10.4-0.7-0.7
Std. dev. time between licks in bursts0.60.82.91.7-0.2-0.00.3
Total sessions with >9 infusions0.91.01.4-1.2-1.00.90.9
Short access day 1 total inactive lever presses0.50.62.41.50.0-0.0-0.0
Short access day 10 total inactive lever presses1.41.53.81.90.9-0.9-0.9
Short access day 1 total infusions0.00.00.1-0.2-0.20.20.2
Short access day 10 total infusions0.20.20.3-0.5-0.50.50.5
Short access total infusions0.60.71.2-1.1-0.80.70.7
Short access day 1 locomotion0.30.30.4-0.6-0.50.50.5
Short access day 10 total locomotion0.80.92.51.60.6-0.5-0.5
Short access total locomotion0.91.01.2-0.6-1.11.11.1
One hour access (0.3 mA shock)1.51.73.31.81.1-1.1-1.1
Compulsive drug intake0.00.00.00.10.2-0.2-0.1
One hour access (shock baseline)0.20.20.70.80.2-0.2-0.2
Social response proportion1.51.74.02.01.1-0.9-0.8
Social responses0.40.52.11.40.20.20.2
Social time2.73.55.22.31.8-1.5-1.8
Soleus weight0.10.40.6-0.8-0.50.60.6
Bone: stiffness1.32.12.41.51.4-1.4-1.4
Tibialis anterior weight0.10.51.8-1.3-0.2-0.0-0.0
Time to tail flick, vehicle, before self-admin0.80.91.0-0.8-1.00.91.0
Time to tail flick, vehicle, after self-admin0.20.20.30.3-0.40.50.5
Time to tail flick, test, before self-admin0.00.00.0-0.1-0.0-0.1-0.0
Time to tail flick, test, after self-admin0.00.00.0-0.1-0.00.10.0
Delta time to tail flick, vehicle, before/after SA0.40.40.80.90.5-0.4-0.5
Delta time to tail flick, test, before/after SA0.60.50.6-0.8-0.60.80.7
Tibia length3.39.210.92.33.3-3.1-3.3
Ambulatory time before self-admin0.00.00.10.2-0.20.20.3
Ambulatory time after self-admin7.48.110.73.32.7-2.7-2.6
Bone: tissue strength3.93.84.62.21.8-1.8-1.9
Total heroin consumption0.60.61.61.30.6-0.6-0.6
Bone: trabecular number1.72.73.51.31.7-1.7-1.9
Bone: trabecular spacing0.10.10.10.30.4-0.2-0.2
Bone: trabecular thickness0.10.10.3-0.60.1-0.2-0.2
Bone: trabecular tissue density2.83.97.6-2.8-1.61.71.6
Water consumed over 24 hours0.60.71.10.50.8-1.0-0.8
Number of responses in last shaping day0.10.10.40.6-0.20.20.2