Smtnl2

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 ENSRNOG00000015157 0.03 0.03 3.6e-03 0.02 0.02 0.02 0.02 2.2e-03 3.2e-03 6.4e-03 3.3e-03
2 BLA gene expression ENSRNOG00000015157 0.07 0.06 6.9e-03 0.01 0.02 0.02 0.01 1.2e-01 4.0e-02 4.3e-02 7.6e-02
3 Brain gene expression ENSRNOG00000015157 0.15 0.09 1.6e-12 0.13 0.14 0.12 0.13 4.5e-12 1.4e-12 1.9e-11 3.3e-12
4 Eye gene expression ENSRNOG00000015157 0.49 0.35 2.2e-03 0.17 0.15 0.22 0.16 1.4e-03 2.4e-03 2.6e-04 1.8e-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 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 4
BMI with tail0.20.51.0-0.51.00.5-0.9
BMI without tail0.61.21.7-0.91.30.8-1.3
Body weight1.87.79.1-3.02.62.9-2.6
Epididymis fat weight2.35.510.4-1.43.21.7-2.5
Glucose3.45.27.52.7-1.8-2.32.1
Heart weight0.30.41.2-0.11.10.3-0.6
Left kidney weight0.00.10.4-0.0-0.1-0.6-0.4
Right kidney weight0.00.10.2-0.1-0.2-0.5-0.4
Tail length3.410.412.0-3.53.13.3-3.0
Length with tail2.28.111.3-3.42.33.0-2.6
Length without tail1.83.85.0-2.21.72.0-1.8
Liver weight, left0.81.32.1-1.40.71.2-1.0
Liver weight, right1.42.23.1-1.51.51.1-1.8
Parametrial fat weight9.117.829.2-3.15.43.2-4.7
Retroperitoneal fat weight0.10.20.50.60.1-0.7-0.1
Intraocular pressure1.31.84.42.1-0.1-1.40.9
Extensor digitorum longus weight1.56.111.2-1.23.30.7-3.3
Soleus weight4.713.716.0-3.93.73.2-4.0
Tibialis anterior weight2.79.115.4-2.23.92.1-3.5
Tibia length0.72.13.9-2.00.61.9-0.7
Number of licking bursts0.40.40.80.7-0.6-0.40.9
Food consumed during 24 hour testing period0.40.51.3-1.1-0.10.7-0.5
Times rat made contact with spout0.30.40.90.1-0.70.30.9
Mean time between licks in bursts1.82.63.9-1.51.71.0-2.0
Mean num. licks in bursts0.10.20.3-0.50.20.5-0.2
Std. dev. time between licks in bursts0.50.71.0-0.70.90.5-1.0
Water consumed over 24 hours0.80.91.6-1.3-0.91.00.3
Indifference point 0 sec0.61.02.70.4-0.80.61.6
Indifference point AUC0.80.92.01.2-0.1-1.40.1
Indifference point function ln k1.01.42.1-1.4-1.11.40.7
Indifference point function log k1.01.42.1-1.4-1.11.40.7
Delay discounting total patch changes 0 sec0.50.82.40.5-0.70.51.5
Delay discounting total patch changes 12 sec0.40.61.61.30.4-0.60.5
Delay discounting total patch changes 18 sec0.20.20.60.80.3-0.20.4
Delay discounting total patch changes 24 sec0.50.61.01.0-0.3-0.90.6
Delay discounting total patch changes 6 sec0.91.43.31.80.0-1.20.9
Delay discounting time to switch 0 sec0.40.71.7-0.11.30.2-1.0
Delay discounting water rate 0 sec0.30.51.10.3-1.0-0.40.8
Delay discounting water rate 12 sec0.40.71.1-0.61.00.8-0.7
Delay discounting water rate 18 sec1.01.32.2-1.50.61.5-0.7
Delay discounting water rate 24 sec0.00.00.10.00.2-0.1-0.3
Delay discounting water rate 6 sec0.10.10.2-0.4-0.4-0.1-0.2
Locomotor activity0.20.30.80.10.90.2-0.5
Locomotor testing distance0.61.02.50.61.6-0.3-1.0
Locomotor testing rearing0.60.91.51.11.2-0.8-0.6
Light reinforcement 10.30.51.30.61.1-0.1-0.5
Light reinforcement 20.10.10.30.5-0.0-0.50.1
Reaction time number correct0.20.40.4-0.60.60.6-0.6
Reaction time mean minus median1.92.54.31.9-1.2-1.02.1
Reaction time mean minus median AUC0.81.11.81.3-0.6-0.61.3
Reaction time num false alarms1.31.83.51.2-1.3-0.61.9
Reaction time num false alarms AUC1.01.42.41.1-1.2-0.71.5
Reaction time trials correct on left0.20.40.4-0.60.60.6-0.6
Reaction time trials on left0.20.30.4-0.60.50.5-0.6
Reaction time mean0.50.71.31.0-0.7-0.51.1
Reaction time mean AUC1.11.52.21.3-1.1-0.81.5
Median of all reaction times0.20.30.40.6-0.5-0.40.6
Reaction time omissions0.10.20.50.70.3-0.30.2
Reaction time false alarm rate1.11.62.71.2-1.2-0.71.7
Reaction time premature initiation rate0.30.40.8-0.7-0.40.90.4
Reaction time premature initiations0.40.61.2-1.0-0.11.1-0.0
Std. dev. reaction times1.82.54.31.6-1.5-0.92.1
Reaction time trials completed0.20.30.4-0.60.50.5-0.6
Reaction time trials AUC0.20.30.3-0.50.50.5-0.6
Social response proportion2.62.86.2-1.81.12.5-0.6
Social responses1.51.93.9-0.72.01.5-1.0
Social time1.41.93.1-1.01.81.5-1.1
Conditioned locomotion1.11.31.61.1-1.3-1.01.2
Cocaine response after cond. corrected0.30.30.8-0.60.00.90.2
Cocaine response after cond. not corrected0.30.30.8-0.60.30.90.1
Cocaine response before conditioning0.30.30.8-0.20.90.2-0.7
Saline control response0.10.20.60.20.80.3-0.2
Condit. Reinf. active minus inactive responses0.20.20.6-0.2-0.00.70.5
Condit. Reinf. active-inactive response ratio0.30.41.00.2-0.40.51.0
Condit. Reinf. active responses0.10.10.3-0.30.00.60.1
Condit. Reinf. inactive responses0.00.10.10.20.0-0.4-0.2
Condit. Reinf. lever presses0.91.21.61.3-1.0-0.91.2
Condit. Reinf. lever reinforcers received0.00.10.1-0.0-0.10.30.3
Pavlov. Cond. lever latency2.33.14.2-1.71.91.3-2.1
Pavlov. Cond. magazine entry latency0.50.61.10.5-1.0-0.41.0
Pavlov. Cond. change in total contacts0.50.71.20.6-1.1-0.51.0
Pavlov. Cond. index score2.02.62.81.7-1.7-1.51.7
Pavlov. Cond. latency score2.53.13.31.8-1.8-1.71.8
Pavlov. Cond. lever contacts1.01.41.71.2-1.1-0.91.3
Pavlov. Cond. magazine entry number0.70.91.2-0.81.10.7-1.1
Pavlov. Cond. intertrial magazine entries0.60.81.6-0.51.30.7-0.9
Pavlov. Cond. lever-magazine prob. diff.2.02.62.91.6-1.7-1.41.7
Pavlov. Cond. response bias1.11.52.01.2-1.3-0.91.4
Conditioned reinforcement - actives0.60.61.1-0.51.00.3-1.1
Conditioned reinforcement - inactives0.40.51.20.81.1-0.1-0.1
Conditioned locomotion0.30.41.20.4-0.2-1.1-0.4
Intermittent access intake day 1-15 change1.61.63.11.8-0.4-1.60.8
Intermittent access intake escalation1.41.42.71.5-0.6-1.60.6
Intermittent access intake escalation 22.02.03.11.5-1.2-1.81.0
Intermitt. access day 1 inactive lever presses2.22.44.22.0-0.9-1.31.7
Intermitt. access day 15 inactive lever presses0.20.30.70.5-0.00.30.8
Intermitt. access escalation Index1.91.72.3-1.21.41.5-1.0
Intermittent access day 1 total infusions0.80.91.9-0.31.40.3-1.2
Intermittent access day 15 total infusions0.91.11.61.00.9-1.3-0.9
Intermittent access terminal intake (last 3 days)0.91.02.10.21.5-0.3-1.3
Intermittent access total infusions0.60.71.30.21.0-0.5-1.2
Intermittent access day 1 locomotion0.60.61.30.11.1-0.2-1.1
Intermittent access day 15 total locomotion0.40.51.10.40.3-1.0-0.8
Intermittent access total locomotion0.30.30.70.10.6-0.4-0.9
Intermittent access standard deviation1.71.84.61.6-0.1-2.1-0.3
Cocaine induced anxiety0.91.11.90.6-1.4-0.41.4
Post-drug Anxiety0.70.82.20.8-0.50.21.5
Baseline Anxiety0.20.20.70.40.80.20.0
Lifetime Intake0.80.91.70.41.3-0.5-1.2
Incentive Sensitization - Responses0.10.10.2-0.10.40.1-0.4
Incentive Sensitization - Breakpoint0.10.10.1-0.00.40.1-0.3
Progressive ratio test 1 active lever presses1.31.32.4-0.91.30.6-1.5
Progressive ratio test 1 breakpoint1.81.92.9-1.01.71.0-1.6
Progressive ratio test 1 inactive lever presses0.30.40.60.20.8-0.3-0.8
Progressive ratio test 2 active lever presses0.50.51.0-0.40.90.2-1.0
Progressive ratio test 2 breakpoint0.30.40.7-0.40.80.3-0.9
Progressive ratio test 2 inactive lever presses0.50.61.30.91.1-0.2-0.3
Total sessions with >9 infusions1.21.32.9-0.71.40.2-1.7
Short access day 1 total inactive lever presses0.20.20.60.70.3-0.10.5
Short access day 10 total inactive lever presses0.00.00.0-0.0-0.10.10.2
Short access day 1 total infusions0.90.91.61.30.5-1.3-0.3
Short access day 10 total infusions0.40.41.10.31.0-0.1-0.7
Short access total infusions0.80.91.21.11.1-0.8-0.6
Short access day 1 locomotion0.60.61.51.20.1-1.00.3
Short access day 10 total locomotion0.30.30.70.70.1-0.9-0.2
Short access total locomotion0.20.30.60.50.2-0.8-0.4
Compulsive drug intake0.20.20.6-0.2-0.20.80.5
One hour access (0.3 mA shock)0.30.41.00.31.0-0.2-0.7
One hour access (shock baseline)0.60.71.8-0.11.0-0.4-1.3
Number of responses in last shaping day1.01.02.01.4-0.3-1.10.8
Context. condit. distance diff. score1.11.32.1-0.91.51.0-1.2
Locomotion velocity, session 14.04.34.7-2.22.11.9-2.1
Locomotion distance, session 10.50.61.1-0.61.00.3-1.0
Locomotion velocity, session 20.50.61.2-1.10.31.0-0.5
Locomotion distance, session 20.50.80.9-0.90.90.9-0.7
Locomotion velocity, session 30.91.02.90.2-1.7-0.80.8
Locomotion distance, session 30.00.00.1-0.0-0.3-0.10.1
Stereotopy head waving bouts, day 30.20.20.4-0.70.10.3-0.5
Stereotopy head waving duration, day 30.50.71.70.7-0.7-1.30.1
Locomotion velocity, session 70.10.10.20.40.1-0.10.2
Locomotion distance, session 70.20.20.40.60.00.10.7
Stereotopy head waving bouts, day 70.91.01.6-0.81.20.6-1.3
Stereotopy head waving duration, day 71.31.62.4-1.11.40.8-1.5
Locomotion velocity, session 81.31.53.2-1.21.10.5-1.8
Locomotion distance, session 82.53.84.4-1.92.11.8-2.0
Degree of sensitization distance0.20.20.70.40.80.3-0.0
Degree of sensitization stereotypy1.61.82.4-1.21.61.2-1.3
Condit. Reinf. active minus inactive responses0.40.51.30.2-0.30.71.1
Condit. Reinf. active-inactive response ratio0.30.31.00.2-0.30.51.0
Condit. Reinf. active responses0.30.41.10.2-0.10.71.0
Condit. Reinf. inactive responses0.00.10.10.3-0.2-0.10.4
Incentive salience index mean0.50.61.3-0.2-0.11.11.0
Condit. Reinf. lever presses1.01.43.9-1.20.42.00.3
Time in familiar zone, hab. session 10.40.30.70.8-0.2-0.60.5
Time in novel zone, hab. session 10.20.20.4-0.60.00.6-0.2
Total zone transitions, hab. session 10.91.22.70.41.7-0.4-1.4
Total locomotion distance, hab. session 10.10.10.40.20.60.1-0.2
Locomotion velocity, hab. session 10.10.10.30.30.6-0.1-0.2
Time in familiar zone, hab. session 20.20.20.3-0.60.10.6-0.1
Time in novel zone, hab. session 20.70.71.01.0-0.7-0.71.0
Total zone transitions, hab. session 20.81.12.5-0.31.60.4-1.2
Total locomotion distance, hab. session 20.10.10.50.10.70.2-0.3
Locomotion velocity, hab. session 20.10.20.4-0.00.70.1-0.4
Novel to familiar place preference ratio0.30.30.50.7-0.2-0.60.4
Novelty place preference0.10.10.20.4-0.1-0.20.3
Time in novel zone, NPP test0.00.00.00.20.10.10.2
Total zone transitions, NPP test0.60.92.50.21.6-0.0-1.1
Total locomotion distance, NPP test0.30.40.90.9-0.1-0.70.4
Locomotion velocity, NPP test0.71.01.81.3-0.5-1.10.8
Pavlov. Cond. lever latency0.60.82.2-0.10.8-0.7-1.5
Pavlov. Cond. magazine entry latency0.70.91.7-0.9-0.61.30.9
Pavlov. Cond. change in total contacts1.51.63.81.0-1.3-0.22.0
Pavlov. Cond. index score0.60.71.6-0.6-0.31.30.9
Pavlov. Cond. latency score0.70.92.1-0.8-0.21.50.8
Pavlov. Cond. lever contacts0.50.61.60.1-0.50.81.3
Pavlov. Cond. magazine entry number0.40.61.40.00.7-0.6-1.2
Pavlov. Cond. intertrial magazine entries0.50.61.00.81.0-0.7-0.7
Pavlov. Cond. lever-magazine prob. diff.0.50.61.2-0.5-0.41.11.0
Pavlov. Cond. response bias0.60.71.6-0.1-0.60.91.3
Bone: apparent density1.11.82.9-1.31.41.7-0.9
Bone surface0.91.52.5-0.91.61.0-1.3
Bone volume1.01.73.0-0.91.71.0-1.5
Bone: connectivity density1.42.32.9-1.41.71.7-1.2
Bone: cortical apparent density1.11.52.31.0-1.4-0.81.5
Bone: cortical area0.50.71.10.9-0.8-1.00.6
Bone: cortical porosity0.60.61.3-1.1-0.21.10.1
Bone: cortical porosity0.40.40.7-0.8-0.40.90.2
Bone: cortical thickness1.32.13.71.0-1.9-0.81.8
Bone: cortical thickness0.80.91.8-0.2-1.30.51.3
Bone: cortical tissue density0.91.21.90.9-1.2-0.61.4
Bone: elastic displacement0.91.01.31.1-0.9-0.91.1
Bone: elastic work1.31.72.41.1-1.6-1.01.4
Bone: endosteal estimation0.51.11.60.61.2-1.0-1.3
Bone: endosteal perimeter0.61.11.90.51.3-0.8-1.4
Bone: final force0.10.20.50.20.7-0.1-0.4
Bone: final moment0.10.20.30.40.6-0.3-0.3
Bone: marrow area0.51.11.60.61.2-1.0-1.3
Bone: maximum diameter0.20.41.20.7-0.0-1.1-0.3
Bone: maximum force0.10.20.40.30.6-0.3-0.4
Bone: maximum moment0.10.20.30.50.5-0.5-0.3
Bone: minimum diameter0.50.82.0-0.11.1-0.5-1.4
Bone: periosteal estimation0.30.61.20.70.4-1.1-0.6
Bone: periosteal perimeter0.20.30.60.50.3-0.8-0.4
Bone: post-yield work0.60.81.3-0.71.11.0-0.8
Bone: stiffness2.13.34.8-1.52.21.5-2.0
Bone: tissue strength0.60.61.11.1-0.4-0.80.7
Bone: trabecular number0.61.02.1-1.00.81.5-0.4
Bone: trabecular spacing0.30.40.90.6-0.5-1.00.1
Bone: trabecular thickness0.30.30.4-0.50.60.6-0.6
Bone: trabecular tissue density1.82.53.81.2-1.9-1.31.7
Breakpoint value in progressive ratio session0.80.91.4-0.71.21.2-0.5
Distance traveled before self-admin0.50.51.60.6-0.5-1.2-0.1
Distance traveled after self-admin1.31.53.10.11.6-0.6-1.8
Delta time in closed arm before/after self-admin0.30.30.7-0.40.4-0.3-0.9
Delta time in open arm before/after self-admin0.30.30.70.60.90.20.0
Diff in mean of infusions in LGA sessions0.50.51.4-0.50.61.20.0
Extinction: sum of active levers before priming2.02.02.9-1.21.71.6-1.1
Active lever presses in extinction session 61.51.42.1-1.21.20.8-1.5
Delta distance traveled before/after self-admin2.02.14.8-0.52.20.9-1.6
Delta ambulatory time before/after self-admin1.21.33.3-0.31.80.8-1.1
Time in closed arm before self-admin0.60.61.9-0.50.61.40.3
Time in closed arm after self-admin0.00.00.1-0.3-0.10.0-0.1
Time in open arm before self-admin1.71.92.51.2-1.6-1.51.2
Time in open arm after self-admin1.51.63.41.8-0.4-1.41.0
Sum of active levers in priming session hrs 5-62.01.93.4-1.41.31.9-0.8
Time to tail flick, vehicle, before self-admin1.41.42.1-1.31.01.4-0.9
Time to tail flick, vehicle, after self-admin0.10.10.10.40.2-0.00.1
Time to tail flick, test, before self-admin0.70.71.2-0.4-0.80.91.1
Time to tail flick, test, after self-admin0.20.20.4-0.6-0.20.70.3
Delta time to tail flick, vehicle, before/after SA1.21.22.01.4-0.5-1.40.6
Delta time to tail flick, test, before/after SA0.30.30.70.00.5-0.6-0.8
Ambulatory time before self-admin0.40.41.00.4-0.6-1.00.1
Ambulatory time after self-admin1.41.62.9-0.71.70.4-1.7
Total heroin consumption2.63.15.7-1.71.72.4-0.9
Area under the delay curve0.10.10.30.1-0.4-0.5-0.1
Delay disc. indifference point, 0s delay0.70.81.5-0.41.20.1-1.2
Delay disc. indifference point, 16s delay0.30.30.6-0.3-0.1-0.7-0.8
Delay disc. indifference point, 2s delay0.30.30.40.5-0.6-0.40.6
Delay disc. indifference point, 24s delay0.20.20.60.0-0.8-0.10.6
Delay disc. indifference point, 4s delay0.10.10.30.50.4-0.20.1
Delay disc. indifference point, 8s delay0.00.00.0-0.0-0.1-0.2-0.1
Delay discount exponential model param0.10.10.10.00.40.3-0.0
Delay discount hyperbolic model param0.10.10.1-0.10.30.4-0.1
Fecal boli incidents, locomotor time 10.10.10.4-0.6-0.50.1-0.2
Change in fecal boli incidents, locomotor task0.30.30.80.5-0.6-0.00.9
Time >=10cm from walls, locomotor time 10.10.10.1-0.2-0.30.20.3
Bouts of movement, locomotor time 10.20.30.6-0.8-0.20.6-0.1
Total resting periods, locomotor time 10.30.30.5-0.6-0.70.60.4
Rest time, locomotor task time 10.40.50.80.5-0.9-0.50.8
Distance moved, locomotor task time 10.20.20.70.20.90.0-0.4
Vertical activity count, locomotor time 10.30.31.00.11.00.2-0.5
Time >=10cm from walls, locomotor time 20.20.20.4-0.2-0.70.00.4
Bouts of movement, locomotor time 20.30.30.6-0.0-0.70.30.8
Total resting periods, locomotor time 20.10.10.2-0.3-0.40.40.3
Rest time, locomotor task time 20.20.30.8-0.1-0.9-0.20.5
Distance moved, locomotor task time 20.30.40.50.70.7-0.6-0.4
Vertical activity count, locomotor time 20.10.10.40.10.6-0.1-0.4
Weight adjusted by age0.70.72.40.41.50.3-0.6
Seeking ratio, delayed vs. immediate footshock0.60.71.00.7-1.0-0.71.0
Locomotion in novel chamber2.83.45.72.3-1.2-2.41.2
Locomotion in novel chamber post-restriction0.50.61.00.8-0.7-0.51.0
Progressive ratio0.40.41.11.00.1-0.60.4
Food seeking constrained by brief footshock0.10.10.20.1-0.5-0.20.2
Seeking ratio, punishment vs. effort0.20.30.7-0.9-0.50.4-0.1
Run reversals in cocaine runway, females0.10.10.20.4-0.3-0.20.5
Run reversals in cocaine runway, males1.01.02.21.50.1-1.30.3
Latency to leave start box in cocaine runway0.10.10.2-0.4-0.10.2-0.1
Latency to leave start box in cocaine runway, F0.50.51.2-1.10.30.8-0.5
Latency to leave start box in cocaine runway, M0.10.10.3-0.30.3-0.0-0.6
Cd content in liver0.70.71.3-0.51.10.4-1.1
Co content in liver0.40.50.8-0.70.60.3-0.9
Cu content in liver0.60.81.70.0-1.10.31.3
Fe content in liver0.60.71.3-0.90.71.1-0.4
K content in liver1.21.22.1-1.40.61.0-1.1
Mg content in liver0.00.00.10.2-0.2-0.30.1
Mn content in liver0.30.30.5-0.7-0.50.60.3
Na content in liver0.20.20.40.3-0.4-0.70.0
Rb content in liver0.10.20.40.20.6-0.2-0.4
Se content in liver0.91.01.60.8-1.3-0.61.2
Sr content in liver1.11.01.7-0.61.30.5-1.3
Zn content in liver0.40.50.90.8-0.5-0.30.9