Smc3

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 NAcc gene expression Smc3 0.03 0.02 9.8e-03 0.01 0.01 0.02 0.01 6.7e-03 1.3e-02 4.5e-03 6.6e-03
2 Liver gene expression Smc3 0.03 0.02 6.0e-03 0.01 0.01 0.01 0.01 3.4e-02 1.8e-02 1.5e-02 2.0e-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
Bone: apparent density1.01.63.21.80.0
Area under the delay curve0.80.91.61.30.3
BMI with tail1.65.18.62.91.3
BMI without tail1.32.84.12.01.2
Body weight3.313.726.65.20.9
Weight adjusted by age1.01.12.11.4-0.3
Bone surface0.00.10.10.30.2
Bone volume1.01.83.51.9-0.1
Breakpoint value in progressive ratio session0.30.30.50.70.4
Number of licking bursts1.01.21.41.0-1.2
Context. condit. distance diff. score0.70.91.5-1.2-0.5
Locomotion velocity, session 11.21.32.1-0.6-1.5
Locomotion distance, session 10.20.30.4-0.3-0.6
Locomotion velocity, session 20.30.40.8-0.90.0
Locomotion distance, session 20.91.22.30.4-1.5
Locomotion velocity, session 31.11.31.8-0.8-1.4
Locomotion distance, session 32.72.95.3-0.7-2.3
Stereotopy head waving bouts, day 30.50.60.8-0.70.9
Stereotopy head waving duration, day 30.60.70.8-0.80.9
Locomotion velocity, session 71.11.21.9-0.6-1.4
Locomotion distance, session 71.41.82.0-1.3-1.4
Stereotopy head waving bouts, day 70.30.30.5-0.3-0.7
Stereotopy head waving duration, day 70.20.20.50.1-0.7
Locomotion velocity, session 80.20.30.5-0.7-0.2
Locomotion distance, session 80.60.81.2-0.7-1.1
Degree of sensitization distance0.80.81.0-0.71.0
Degree of sensitization stereotypy1.11.22.3-0.3-1.5
Conditioned locomotion1.11.32.5-0.3-1.6
Cocaine response after cond. corrected2.52.84.9-2.20.9
Cocaine response after cond. not corrected3.43.77.1-2.70.6
Cocaine response before conditioning0.20.20.3-0.5-0.4
Saline control response0.30.40.9-0.9-0.1
Bone: connectivity density0.10.20.30.40.5
Bone: cortical apparent density0.30.40.8-0.9-0.3
Bone: cortical area1.21.83.50.4-1.9
Bone: cortical porosity0.00.00.10.00.2
Bone: cortical porosity0.10.10.10.4-0.2
Bone: cortical thickness1.32.14.1-0.3-2.0
Bone: cortical thickness0.91.12.0-0.5-1.4
Bone: cortical tissue density0.30.40.8-0.9-0.3
Condit. Reinf. active minus inactive responses1.11.21.3-1.1-1.1
Condit. Reinf. active-inactive response ratio0.80.81.7-1.3-0.1
Condit. Reinf. active responses1.41.83.1-0.7-1.7
Condit. Reinf. inactive responses0.81.01.70.4-1.3
Incentive salience index mean1.41.71.8-1.3-1.3
Condit. Reinf. lever presses0.50.71.3-0.3-1.1
Condit. Reinf. active minus inactive responses3.03.74.5-1.7-2.1
Condit. Reinf. active-inactive response ratio3.53.74.8-2.2-1.6
Condit. Reinf. active responses2.02.84.5-1.0-2.1
Condit. Reinf. inactive responses0.60.81.10.6-1.0
Condit. Reinf. lever presses3.04.16.5-1.3-2.5
Condit. Reinf. lever reinforcers received2.23.04.4-1.3-2.1
Conditioned reinforcement - actives0.80.81.50.31.2
Conditioned reinforcement - inactives1.01.11.11.1-1.0
Conditioned locomotion2.93.54.81.52.2
Patch foraging indifference point 0 sec0.20.30.6-0.80.2
Patch foraging indifference point AUC1.82.13.90.5-2.0
Delay disc. indifference point, 0s delay0.30.30.60.80.2
Delay disc. indifference point, 16s delay0.10.10.10.40.1
Delay disc. indifference point, 2s delay0.50.61.11.0-0.3
Delay disc. indifference point, 24s delay1.81.73.11.8-0.6
Delay disc. indifference point, 4s delay0.20.20.30.5-0.4
Delay disc. indifference point, 8s delay1.61.62.61.60.8
Indifference point function ln k0.60.81.4-0.41.2
Indifference point function log k0.60.81.4-0.41.2
Patch foraging total patch changes 0 sec0.10.20.3-0.5-0.3
Patch foraging total patch changes 12 sec0.91.22.40.0-1.5
Patch foraging total patch changes 18 sec1.11.42.8-0.1-1.7
Patch foraging total patch changes 24 sec1.11.32.00.8-1.4
Patch foraging total patch changes 6 sec0.20.30.50.2-0.7
Patch foraging time to switch 0 sec0.81.22.4-0.11.6
Patch foraging water rate 0 sec0.40.71.10.5-1.1
Patch foraging water rate 12 sec0.20.40.50.70.5
Patch foraging water rate 18 sec0.20.30.40.50.6
Patch foraging water rate 24 sec0.20.30.30.60.5
Patch foraging water rate 6 sec0.10.20.30.30.6
Seeking ratio, delayed vs. immediate footshock0.50.60.70.80.7
Distance traveled before self-admin0.70.81.3-1.1-0.5
Distance traveled after self-admin0.80.81.30.61.2
Extensor digitorum longus weight1.24.85.82.0-2.4
Bone: elastic displacement0.00.00.1-0.00.3
Bone: elastic work0.30.30.50.70.3
Bone: endosteal estimation0.71.41.61.31.1
Bone: endosteal perimeter0.61.32.31.5-0.4
Epididymis fat weight3.78.616.94.1-0.6
Delta time in closed arm before/after self-admin2.12.13.9-2.00.5
Delta time in open arm before/after self-admin0.80.71.51.20.0
Diff in mean of infusions in LGA sessions2.93.26.1-2.50.5
Delay discount exponential model param1.11.12.2-1.5-0.1
Extinction: sum of active levers before priming0.10.10.1-0.40.3
Active lever presses in extinction session 61.71.72.90.7-1.7
Bone: final force0.20.40.60.70.4
Bone: final moment0.30.60.80.90.5
Food consumed during 24 hour testing period0.20.20.30.40.6
Glucose3.14.69.13.0-0.4
Heart weight2.94.15.0-2.2-1.8
Delay discount hyperbolic model param0.91.01.9-1.4-0.2
Intermittent access intake day 1-15 change1.61.62.31.51.0
Intermittent access intake escalation1.81.82.81.70.9
Intermittent access intake escalation 23.53.55.22.31.3
Intermitt. access day 1 inactive lever presses3.33.64.11.7-2.0
Intermitt. access day 15 inactive lever presses0.30.40.70.1-0.9
Intermitt. access escalation Index0.80.71.41.20.3
Intermittent access day 1 total infusions0.10.10.10.2-0.3
Intermittent access day 15 total infusions1.01.22.31.50.2
Intermittent access terminal intake (last 3 days)2.12.33.81.90.9
Intermittent access total infusions0.91.12.01.40.2
Intermittent access day 1 locomotion0.20.20.30.10.6
Intermittent access day 15 total locomotion0.60.71.31.1-0.2
Intermittent access total locomotion0.80.91.20.71.1
Intermittent access standard deviation3.53.76.82.60.7
Left kidney weight1.74.95.32.32.1
Right kidney weight1.43.85.62.41.4
Cocaine induced anxiety0.20.30.5-0.70.2
Post-drug Anxiety0.10.10.1-0.30.2
Baseline Anxiety1.21.21.70.9-1.3
Tail length0.41.41.91.4-0.9
Length with tail1.65.811.53.4-0.3
Length without tail1.63.46.82.6-0.3
Times rat made contact with spout1.01.21.41.2-1.0
Lifetime Intake0.80.91.71.30.3
Liver weight, left1.42.23.01.2-1.7
Liver weight, right4.16.913.53.70.5
Locomotor activity0.00.00.10.1-0.3
Locomotor testing distance0.10.10.2-0.20.5
Locomotor testing rearing0.40.61.2-0.01.1
Locomotion in novel chamber1.21.42.8-1.7-0.1
Locomotion in novel chamber post-restriction0.91.11.3-0.91.1
Fecal boli incidents, locomotor time 10.30.30.60.70.2
Change in fecal boli incidents, locomotor task0.40.40.4-0.6-0.5
Time >=10cm from walls, locomotor time 10.20.20.5-0.10.7
Bouts of movement, locomotor time 10.40.40.60.50.8
Total resting periods, locomotor time 10.30.30.60.80.3
Rest time, locomotor task time 10.60.60.9-0.6-1.0
Distance moved, locomotor task time 11.11.22.41.50.1
Vertical activity count, locomotor time 10.50.51.0-1.00.1
Time >=10cm from walls, locomotor time 20.80.81.50.4-1.2
Bouts of movement, locomotor time 20.00.00.00.10.1
Total resting periods, locomotor time 20.10.10.10.10.3
Rest time, locomotor task time 20.80.91.90.11.4
Distance moved, locomotor task time 20.30.30.5-0.4-0.7
Vertical activity count, locomotor time 21.21.31.9-0.9-1.4
Light reinforcement 10.81.42.3-1.5-0.8
Light reinforcement 20.81.11.1-1.0-1.0
Bone: marrow area0.71.51.61.31.1
Bone: maximum diameter1.12.03.20.9-1.8
Bone: maximum force0.10.20.30.60.0
Bone: maximum moment0.20.30.60.80.1
Mean time between licks in bursts0.50.71.1-0.51.0
Mean num. licks in bursts0.30.40.7-0.20.9
Cd content in liver6.16.713.3-3.60.1
Co content in liver0.70.91.2-1.10.8
Cu content in liver1.01.22.01.40.6
Fe content in liver0.70.91.6-1.2-0.4
K content in liver1.41.42.61.60.3
Mg content in liver1.21.22.41.5-0.3
Mn content in liver1.11.31.9-0.8-1.4
Na content in liver0.60.61.1-0.3-1.1
Rb content in liver0.20.30.3-0.50.5
Se content in liver0.60.71.3-0.41.1
Sr content in liver3.22.94.6-1.12.2
Zn content in liver0.40.40.6-0.8-0.4
Bone: minimum diameter0.40.70.90.9-0.8
Time in familiar zone, hab. session 12.32.24.1-0.62.0
Time in novel zone, hab. session 13.13.04.41.3-2.1
Total zone transitions, hab. session 11.01.52.90.1-1.7
Total locomotion distance, hab. session 10.50.71.30.4-1.1
Locomotion velocity, hab. session 10.50.81.5-0.0-1.2
Time in familiar zone, hab. session 20.70.71.21.1-0.4
Time in novel zone, hab. session 20.30.30.4-0.70.4
Total zone transitions, hab. session 20.20.30.60.0-0.8
Total locomotion distance, hab. session 20.50.61.10.3-1.0
Locomotion velocity, hab. session 20.50.71.30.2-1.2
Novel to familiar place preference ratio0.20.20.30.50.4
Novelty place preference0.70.71.11.10.5
Time in novel zone, NPP test0.90.91.51.20.5
Total zone transitions, NPP test1.72.44.50.5-2.1
Total locomotion distance, NPP test1.41.93.30.7-1.8
Locomotion velocity, NPP test0.91.32.40.5-1.5
Intraocular pressure0.20.20.40.3-0.6
Delta distance traveled before/after self-admin2.83.14.21.42.0
Delta ambulatory time before/after self-admin2.22.42.51.51.6
Parametrial fat weight1.32.65.12.3-0.1
Pavlov. Cond. lever latency0.00.00.10.20.1
Pavlov. Cond. magazine entry latency0.40.50.80.9-0.5
Pavlov. Cond. change in total contacts0.10.20.20.5-0.3
Pavlov. Cond. index score0.30.40.50.7-0.6
Pavlov. Cond. latency score0.20.20.30.6-0.3
Pavlov. Cond. lever contacts0.00.00.00.1-0.1
Pavlov. Cond. magazine entry number0.60.71.4-1.20.2
Pavlov. Cond. intertrial magazine entries0.30.40.7-0.3-0.8
Pavlov. Cond. lever-magazine prob. diff.0.50.60.60.7-0.8
Pavlov. Cond. response bias0.30.40.70.8-0.3
Pavlov. Cond. lever latency2.33.15.70.82.4
Pavlov. Cond. magazine entry latency0.40.50.80.9-0.4
Pavlov. Cond. change in total contacts0.91.22.4-0.2-1.5
Pavlov. Cond. index score0.71.01.90.0-1.4
Pavlov. Cond. latency score0.70.91.60.4-1.3
Pavlov. Cond. lever contacts2.73.66.6-0.8-2.6
Pavlov. Cond. magazine entry number0.40.50.9-0.90.4
Pavlov. Cond. intertrial magazine entries0.81.01.7-1.3-0.6
Pavlov. Cond. lever-magazine prob. diff.0.81.01.90.2-1.4
Pavlov. Cond. response bias1.82.54.4-0.8-2.1
Time in closed arm before self-admin0.80.91.71.3-0.3
Time in closed arm after self-admin1.01.01.7-1.30.5
Time in open arm before self-admin0.70.81.1-0.7-1.1
Time in open arm after self-admin0.40.40.50.7-0.6
Bone: periosteal estimation0.40.81.61.3-0.2
Bone: periosteal perimeter1.42.33.21.8-1.2
Bone: post-yield work0.20.20.3-0.4-0.6
Progressive ratio test 1 active lever presses0.40.40.50.60.7
Progressive ratio test 1 breakpoint0.20.20.30.30.5
Progressive ratio test 1 inactive lever presses1.41.61.81.2-1.3
Progressive ratio test 2 active lever presses2.02.12.71.21.7
Progressive ratio test 2 breakpoint1.82.02.51.21.6
Progressive ratio test 2 inactive lever presses1.82.13.82.00.6
Incentive Sensitization - Responses1.41.41.71.31.1
Incentive Sensitization - Breakpoint1.31.31.71.31.0
Sum of active levers in priming session hrs 5-60.50.51.0-0.0-1.0
Progressive ratio1.11.32.1-1.4-0.7
Food seeking constrained by brief footshock0.60.71.0-1.0-0.6
Seeking ratio, punishment vs. effort0.30.30.70.8-0.0
Retroperitoneal fat weight5.016.327.85.32.2
Reaction time number correct1.42.12.21.41.5
Reaction time mean minus median0.30.30.70.10.8
Reaction time mean minus median AUC0.81.01.70.51.3
Reaction time num false alarms1.21.63.1-0.3-1.8
Reaction time num false alarms AUC1.52.03.2-0.9-1.8
Reaction time trials correct on left1.42.12.21.41.5
Reaction time trials on left1.52.12.41.31.5
Reaction time mean0.50.71.50.11.2
Reaction time mean AUC0.50.71.3-0.31.2
Median of all reaction times0.60.91.70.21.3
Reaction time omissions1.41.93.6-0.51.9
Reaction time false alarm rate2.73.85.5-1.4-2.3
Reaction time premature initiation rate0.60.81.60.3-1.2
Reaction time premature initiations0.40.61.01.0-0.3
Std. dev. reaction times0.50.71.30.31.1
Reaction time trials completed1.52.12.41.31.5
Reaction time trials AUC1.52.12.21.41.5
Run reversals in cocaine runway, females2.12.14.10.12.0
Run reversals in cocaine runway, males0.50.50.5-0.7-0.7
Latency to leave start box in cocaine runway0.20.20.3-0.6-0.1
Latency to leave start box in cocaine runway, F0.80.91.8-1.30.1
Latency to leave start box in cocaine runway, M0.10.10.20.40.2
Std. dev. time between licks in bursts0.10.10.1-0.3-0.2
Total sessions with >9 infusions2.12.33.81.90.9
Short access day 1 total inactive lever presses1.92.14.12.00.0
Short access day 10 total inactive lever presses1.31.51.51.2-1.2
Short access day 1 total infusions2.72.84.72.21.0
Short access day 10 total infusions0.40.50.80.9-0.4
Short access total infusions0.50.61.01.00.4
Short access day 1 locomotion2.12.33.81.90.9
Short access day 10 total locomotion2.32.63.92.01.1
Short access total locomotion1.11.21.70.81.3
One hour access (0.3 mA shock)3.23.86.22.51.1
Compulsive drug intake0.30.30.5-0.4-0.7
One hour access (shock baseline)1.92.23.21.81.1
Social response proportion7.98.69.33.12.8
Social responses2.33.03.21.71.8
Social time3.14.17.90.62.8
Soleus weight1.85.310.13.20.7
Bone: stiffness0.00.00.0-0.0-0.0
Tibialis anterior weight0.41.42.60.6-1.6
Time to tail flick, vehicle, before self-admin0.80.91.71.30.2
Time to tail flick, vehicle, after self-admin0.10.10.2-0.50.2
Time to tail flick, test, before self-admin0.10.10.10.30.4
Time to tail flick, test, after self-admin0.20.30.5-0.1-0.7
Delta time to tail flick, vehicle, before/after SA1.00.91.9-1.40.2
Delta time to tail flick, test, before/after SA0.30.30.5-0.1-0.7
Tibia length0.10.30.40.60.4
Ambulatory time before self-admin0.30.30.4-0.6-0.5
Ambulatory time after self-admin2.22.43.11.81.3
Bone: tissue strength0.30.30.3-0.50.6
Total heroin consumption0.20.20.20.4-0.5
Bone: trabecular number0.71.01.71.30.6
Bone: trabecular spacing0.91.21.9-0.7-1.4
Bone: trabecular thickness4.04.89.23.0-0.5
Bone: trabecular tissue density0.10.20.40.0-0.6
Water consumed over 24 hours1.31.62.71.70.7
Number of responses in last shaping day0.10.10.3-0.00.5