Sptlc3

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 Brain gene expression ENSRNOG00000004443 0.06 0.04 3.5e-05 0.03 0.05 0.05 0.05 5.6e-04 2.9e-05 1.6e-05 1.0e-05
2 Eye gene expression ENSRNOG00000004443 0.59 0.16 3.2e-04 0 0.06 0 0.02 2.7e-01 4.9e-02 3.2e-01 1.5e-01
3 PL gene expression ENSRNOG00000004443 0.06 0.03 1.2e-04 0.02 0.04 0.03 0.03 7.8e-03 2.9e-04 5.2e-03 3.3e-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
BMI with tail2.47.715.3-3.9-0.8-2.7
BMI without tail1.83.77.3-2.7-0.6-1.9
Body weight3.313.927.4-5.2-2.1-3.2
Epididymis fat weight4.39.920.1-4.5-0.7-3.0
Glucose0.91.42.7-1.60.2-1.2
Heart weight0.91.32.4-1.5-0.9-0.7
Left kidney weight0.30.91.4-1.2-0.9-0.7
Right kidney weight0.41.01.8-1.0-1.3-0.4
Tail length0.51.62.7-1.6-1.2-0.9
Length with tail1.24.48.0-2.8-1.6-1.5
Length without tail0.71.63.3-1.8-0.5-1.1
Liver weight, left0.40.61.3-1.1-0.1-0.7
Liver weight, right1.21.94.9-0.7-2.20.7
Parametrial fat weight1.32.55.2-2.3-0.7-1.3
Retroperitoneal fat weight3.712.323.8-4.9-1.3-3.4
Intraocular pressure0.30.40.6-0.7-0.8-0.4
Extensor digitorum longus weight0.00.10.2-0.10.3-0.4
Soleus weight0.20.50.60.8-0.30.8
Tibialis anterior weight0.20.81.3-1.10.5-1.0
Tibia length2.77.514.7-3.8-1.6-2.3
Number of licking bursts0.40.51.4-0.3-1.20.2
Food consumed during 24 hour testing period5.97.19.2-1.93.0-2.9
Times rat made contact with spout0.40.51.2-0.11.1-0.5
Mean time between licks in bursts1.72.46.2-0.6-2.50.9
Mean num. licks in bursts1.01.22.9-0.21.7-0.7
Std. dev. time between licks in bursts0.20.30.60.1-0.80.4
Water consumed over 24 hours1.31.52.4-0.71.6-1.3
Indifference point 0 sec0.91.53.11.80.90.6
Indifference point AUC7.28.512.13.5-1.43.4
Indifference point function ln k4.36.19.2-2.81.2-3.0
Indifference point function log k4.36.19.2-2.81.2-3.0
Delay discounting total patch changes 0 sec1.22.04.42.10.81.0
Delay discounting total patch changes 12 sec2.02.65.22.30.11.6
Delay discounting total patch changes 18 sec6.58.615.84.0-0.33.2
Delay discounting total patch changes 24 sec4.96.211.53.4-0.22.7
Delay discounting total patch changes 6 sec3.85.89.93.1-0.92.6
Delay discounting time to switch 0 sec2.84.27.4-2.70.7-2.2
Delay discounting water rate 0 sec3.35.39.33.1-0.82.4
Delay discounting water rate 12 sec1.31.93.31.8-0.71.4
Delay discounting water rate 18 sec1.72.23.11.1-1.81.5
Delay discounting water rate 24 sec4.25.86.52.2-2.52.6
Delay discounting water rate 6 sec1.31.94.70.2-2.21.0
Locomotor activity0.60.92.40.51.5-0.3
Locomotor testing distance0.91.43.21.01.80.0
Locomotor testing rearing1.42.23.51.91.50.9
Light reinforcement 10.71.33.50.41.9-0.4
Light reinforcement 20.50.61.2-0.41.1-0.7
Reaction time number correct1.01.41.90.8-1.41.3
Reaction time mean minus median1.11.52.0-1.40.8-1.4
Reaction time mean minus median AUC0.20.30.4-0.60.4-0.7
Reaction time num false alarms0.20.30.40.7-0.00.6
Reaction time num false alarms AUC0.70.91.41.2-0.31.1
Reaction time trials correct on left1.01.41.90.8-1.41.3
Reaction time trials on left1.01.52.00.8-1.41.3
Reaction time mean0.60.81.2-1.00.6-1.1
Reaction time mean AUC0.60.81.2-0.90.6-1.1
Median of all reaction times0.40.50.6-0.70.6-0.8
Reaction time omissions0.20.30.40.6-0.30.7
Reaction time false alarm rate0.20.30.50.70.30.4
Reaction time premature initiation rate0.20.30.6-0.50.2-0.8
Reaction time premature initiations0.20.20.50.3-0.70.3
Std. dev. reaction times0.71.01.6-1.00.5-1.2
Reaction time trials completed1.01.52.00.8-1.41.3
Reaction time trials AUC1.01.41.90.8-1.41.3
Social response proportion0.70.81.3-1.1-0.1-1.0
Social responses0.00.00.10.1-0.20.3
Social time0.60.81.0-0.81.0-0.8
Conditioned locomotion0.81.01.9-1.4-0.6-0.7
Cocaine response after cond. corrected0.20.30.40.2-0.60.6
Cocaine response after cond. not corrected0.10.10.20.3-0.10.5
Cocaine response before conditioning0.50.71.70.21.3-0.5
Saline control response0.00.00.00.10.10.1
Condit. Reinf. active minus inactive responses0.10.10.30.60.20.3
Condit. Reinf. active-inactive response ratio0.10.10.30.60.10.4
Condit. Reinf. active responses0.10.10.40.60.20.2
Condit. Reinf. inactive responses0.10.10.30.50.10.2
Condit. Reinf. lever presses1.21.74.20.92.0-0.3
Condit. Reinf. lever reinforcers received0.30.40.80.90.40.4
Pavlov. Cond. lever latency1.52.02.80.8-1.61.7
Pavlov. Cond. magazine entry latency1.51.73.90.12.0-1.1
Pavlov. Cond. change in total contacts0.10.10.20.20.5-0.1
Pavlov. Cond. index score1.01.32.3-0.31.5-1.2
Pavlov. Cond. latency score0.81.01.8-0.11.3-1.0
Pavlov. Cond. lever contacts1.21.73.2-0.41.8-1.3
Pavlov. Cond. magazine entry number0.60.71.10.3-1.11.0
Pavlov. Cond. intertrial magazine entries0.10.10.40.10.60.0
Pavlov. Cond. lever-magazine prob. diff.0.91.21.9-0.41.4-1.2
Pavlov. Cond. response bias0.91.22.2-0.31.5-1.2
Conditioned reinforcement - actives0.90.91.21.01.10.6
Conditioned reinforcement - inactives0.70.81.41.20.70.7
Conditioned locomotion1.01.12.21.50.80.8
Intermittent access intake day 1-15 change3.13.16.0-0.72.5-1.6
Intermittent access intake escalation4.04.08.4-0.62.9-1.8
Intermittent access intake escalation 25.04.99.8-0.93.1-2.0
Intermitt. access day 1 inactive lever presses0.30.30.70.80.40.2
Intermitt. access day 15 inactive lever presses1.21.32.2-1.10.8-1.5
Intermitt. access escalation Index0.70.61.1-1.0-0.1-0.9
Intermittent access day 1 total infusions0.60.71.0-1.0-0.3-1.0
Intermittent access day 15 total infusions2.32.63.7-1.21.6-1.9
Intermittent access terminal intake (last 3 days)1.92.13.1-1.11.4-1.8
Intermittent access total infusions1.31.42.3-1.10.9-1.5
Intermittent access day 1 locomotion0.60.61.1-0.70.4-1.0
Intermittent access day 15 total locomotion1.01.02.3-0.11.5-0.9
Intermittent access total locomotion0.50.61.0-0.21.0-0.9
Intermittent access standard deviation3.53.79.30.13.1-1.3
Cocaine induced anxiety0.80.91.90.81.4-0.1
Post-drug Anxiety0.10.10.20.50.40.1
Baseline Anxiety1.11.21.8-1.2-1.3-0.5
Lifetime Intake0.70.81.4-0.80.7-1.2
Incentive Sensitization - Responses0.20.20.50.20.70.1
Incentive Sensitization - Breakpoint0.20.20.60.30.80.2
Progressive ratio test 1 active lever presses0.00.10.10.00.2-0.3
Progressive ratio test 1 breakpoint0.00.00.10.20.2-0.2
Progressive ratio test 1 inactive lever presses0.30.40.80.20.9-0.4
Progressive ratio test 2 active lever presses0.30.40.90.10.9-0.4
Progressive ratio test 2 breakpoint0.10.10.3-0.00.5-0.3
Progressive ratio test 2 inactive lever presses2.22.56.0-0.12.5-1.3
Total sessions with >9 infusions0.60.61.3-0.11.1-0.8
Short access day 1 total inactive lever presses2.22.43.4-1.41.4-1.8
Short access day 10 total inactive lever presses0.50.51.0-0.01.0-0.8
Short access day 1 total infusions0.20.30.4-0.20.6-0.6
Short access day 10 total infusions0.00.00.10.3-0.0-0.2
Short access total infusions0.20.20.4-0.30.1-0.6
Short access day 1 locomotion0.20.20.30.4-0.50.5
Short access day 10 total locomotion1.11.22.11.41.00.7
Short access total locomotion1.11.12.31.50.40.9
Compulsive drug intake0.30.30.50.7-0.20.7
One hour access (0.3 mA shock)1.01.23.00.41.7-0.5
One hour access (shock baseline)1.11.32.3-0.41.5-1.3
Number of responses in last shaping day0.80.81.5-0.41.2-0.9
Context. condit. distance diff. score0.10.10.2-0.50.1-0.4
Locomotion velocity, session 10.20.30.50.40.70.3
Locomotion distance, session 11.92.55.91.22.4-0.2
Locomotion velocity, session 20.70.91.31.11.00.6
Locomotion distance, session 21.72.43.51.91.80.7
Locomotion velocity, session 30.30.30.50.50.7-0.3
Locomotion distance, session 30.00.00.00.0-0.0-0.2
Stereotopy head waving bouts, day 30.91.11.6-1.00.7-1.3
Stereotopy head waving duration, day 30.40.50.7-0.70.5-0.8
Locomotion velocity, session 70.40.40.60.8-0.60.6
Locomotion distance, session 70.10.10.2-0.4-0.2-0.4
Stereotopy head waving bouts, day 70.10.10.2-0.30.2-0.4
Stereotopy head waving duration, day 70.50.71.1-0.41.0-0.9
Locomotion velocity, session 80.30.40.70.80.40.6
Locomotion distance, session 80.40.61.20.81.10.1
Degree of sensitization distance0.30.30.4-0.30.6-0.6
Degree of sensitization stereotypy0.10.10.1-0.4-0.1-0.3
Condit. Reinf. active minus inactive responses1.21.32.1-1.10.6-1.5
Condit. Reinf. active-inactive response ratio0.50.60.9-0.90.0-1.0
Condit. Reinf. active responses0.00.00.10.00.1-0.3
Condit. Reinf. inactive responses0.60.71.31.10.00.9
Incentive salience index mean0.50.61.30.31.2-0.5
Condit. Reinf. lever presses1.11.53.01.71.00.8
Time in familiar zone, hab. session 11.21.22.6-0.11.6-0.9
Time in novel zone, hab. session 10.70.60.80.6-0.90.8
Total zone transitions, hab. session 10.10.10.10.40.30.0
Total locomotion distance, hab. session 10.50.71.31.10.20.9
Locomotion velocity, hab. session 10.50.81.11.0-0.41.0
Time in familiar zone, hab. session 21.31.32.9-0.11.7-1.0
Time in novel zone, hab. session 20.50.51.2-0.1-1.10.5
Total zone transitions, hab. session 20.50.61.60.31.3-0.4
Total locomotion distance, hab. session 21.41.92.71.61.60.7
Locomotion velocity, hab. session 21.52.03.61.91.01.2
Novel to familiar place preference ratio0.10.10.1-0.4-0.3-0.0
Novelty place preference0.20.20.4-0.5-0.70.1
Time in novel zone, NPP test0.20.20.4-0.6-0.6-0.1
Total zone transitions, NPP test0.60.81.21.11.00.6
Total locomotion distance, NPP test1.92.64.22.11.51.1
Locomotion velocity, NPP test2.13.05.32.31.21.5
Pavlov. Cond. lever latency0.81.01.8-1.3-0.7-0.8
Pavlov. Cond. magazine entry latency0.70.91.5-1.00.4-1.2
Pavlov. Cond. change in total contacts0.60.70.80.7-0.90.8
Pavlov. Cond. index score0.10.10.30.30.5-0.1
Pavlov. Cond. latency score0.20.20.50.70.40.2
Pavlov. Cond. lever contacts0.91.02.01.40.60.8
Pavlov. Cond. magazine entry number0.60.71.11.10.01.0
Pavlov. Cond. intertrial magazine entries0.60.81.10.9-0.51.1
Pavlov. Cond. lever-magazine prob. diff.0.10.20.50.30.7-0.2
Pavlov. Cond. response bias0.20.20.3-0.30.5-0.6
Bone: apparent density1.82.94.3-1.71.3-2.1
Bone surface2.13.65.9-1.02.4-2.0
Bone volume1.72.93.8-1.41.7-2.0
Bone: connectivity density3.35.16.4-1.62.5-2.5
Bone: cortical apparent density1.41.85.0-0.4-2.20.5
Bone: cortical area2.74.17.8-2.1-2.8-0.2
Bone: cortical porosity2.12.23.3-1.80.9-1.6
Bone: cortical porosity1.71.93.8-1.90.1-1.3
Bone: cortical thickness5.79.416.9-3.3-4.1-0.5
Bone: cortical thickness2.73.15.3-1.9-2.3-0.8
Bone: cortical tissue density1.31.74.5-0.2-2.10.6
Bone: elastic displacement0.80.92.4-0.2-1.60.5
Bone: elastic work1.82.33.9-2.0-1.5-0.9
Bone: endosteal estimation2.04.210.30.13.2-1.5
Bone: endosteal perimeter1.12.25.70.62.4-0.7
Bone: final force1.82.94.1-2.0-2.0-0.8
Bone: final moment1.62.74.3-2.1-1.7-1.0
Bone: marrow area1.84.09.80.23.1-1.4
Bone: maximum diameter0.10.20.3-0.5-0.6-0.1
Bone: maximum force1.62.85.1-2.3-1.4-1.1
Bone: maximum moment1.62.75.4-2.3-0.9-1.4
Bone: minimum diameter0.51.01.8-1.30.1-1.1
Bone: periosteal estimation0.40.81.2-1.10.2-1.0
Bone: periosteal perimeter0.00.00.1-0.3-0.10.0
Bone: post-yield work1.82.53.0-1.41.7-1.6
Bone: stiffness1.11.72.7-1.6-1.4-0.6
Bone: tissue strength0.10.10.2-0.10.4-0.1
Bone: trabecular number2.33.65.1-1.91.5-2.2
Bone: trabecular spacing2.83.65.61.1-2.42.0
Bone: trabecular thickness1.11.42.5-1.60.1-1.3
Bone: trabecular tissue density0.30.40.60.1-0.80.7
Breakpoint value in progressive ratio session0.60.71.4-1.2-0.7-0.2
Distance traveled before self-admin0.20.30.50.5-0.10.7
Distance traveled after self-admin3.03.36.30.5-2.51.8
Delta time in closed arm before/after self-admin0.10.10.20.1-0.5-0.0
Delta time in open arm before/after self-admin0.80.81.3-1.1-1.0-0.4
Diff in mean of infusions in LGA sessions0.00.00.00.1-0.20.0
Extinction: sum of active levers before priming0.40.40.7-0.2-0.80.7
Active lever presses in extinction session 61.11.12.2-1.5-0.1-1.0
Delta distance traveled before/after self-admin2.02.14.40.6-2.11.3
Delta ambulatory time before/after self-admin1.51.63.50.5-1.91.0
Time in closed arm before self-admin0.20.20.3-0.30.5-0.6
Time in closed arm after self-admin0.10.10.2-0.2-0.4-0.3
Time in open arm before self-admin0.70.81.21.10.11.1
Time in open arm after self-admin1.31.52.40.3-1.51.4
Sum of active levers in priming session hrs 5-60.10.00.1-0.1-0.20.3
Time to tail flick, vehicle, before self-admin1.51.53.7-0.9-1.90.4
Time to tail flick, vehicle, after self-admin0.10.10.1-0.40.2-0.3
Time to tail flick, test, before self-admin3.03.03.8-1.41.8-1.9
Time to tail flick, test, after self-admin4.74.85.9-1.82.3-2.4
Delta time to tail flick, vehicle, before/after SA0.60.61.60.51.3-0.3
Delta time to tail flick, test, before/after SA0.30.20.60.00.8-0.3
Ambulatory time before self-admin0.00.00.10.10.10.3
Ambulatory time after self-admin2.32.55.30.4-2.31.4
Total heroin consumption0.20.30.4-0.3-0.70.5
Area under the delay curve0.20.30.40.60.70.1
Delay disc. indifference point, 0s delay0.00.10.1-0.20.3-0.1
Delay disc. indifference point, 16s delay0.90.91.71.30.50.8
Delay disc. indifference point, 2s delay1.01.12.70.81.7-0.2
Delay disc. indifference point, 24s delay0.10.10.10.40.30.2
Delay disc. indifference point, 4s delay0.00.10.10.10.3-0.2
Delay disc. indifference point, 8s delay0.20.20.3-0.20.6-0.4
Delay discount exponential model param0.20.20.3-0.6-0.6-0.2
Delay discount hyperbolic model param0.20.30.5-0.5-0.7-0.1
Fecal boli incidents, locomotor time 10.00.00.10.1-0.20.3
Change in fecal boli incidents, locomotor task0.40.40.6-0.7-0.4-0.7
Time >=10cm from walls, locomotor time 10.10.10.2-0.10.4-0.1
Bouts of movement, locomotor time 11.21.42.11.3-0.61.4
Total resting periods, locomotor time 11.01.11.81.2-0.51.3
Rest time, locomotor task time 11.41.52.7-0.51.6-1.2
Distance moved, locomotor task time 12.93.24.51.2-2.11.9
Vertical activity count, locomotor time 10.00.00.1-0.10.1-0.3
Time >=10cm from walls, locomotor time 22.02.22.8-1.61.0-1.7
Bouts of movement, locomotor time 20.20.20.50.2-0.70.4
Total resting periods, locomotor time 20.20.20.50.1-0.70.4
Rest time, locomotor task time 20.30.30.60.2-0.80.5
Distance moved, locomotor task time 20.50.61.10.91.00.2
Vertical activity count, locomotor time 21.21.43.70.31.9-0.6
Weight adjusted by age0.30.30.7-0.8-0.4-0.3
Seeking ratio, delayed vs. immediate footshock1.41.62.1-1.40.9-1.5
Locomotion in novel chamber1.31.64.3-0.5-2.10.5
Locomotion in novel chamber post-restriction0.10.10.10.0-0.30.4
Progressive ratio0.10.20.20.5-0.30.5
Food seeking constrained by brief footshock1.51.83.61.90.31.3
Seeking ratio, punishment vs. effort0.40.40.70.90.70.4
Run reversals in cocaine runway, females0.40.40.6-0.60.6-0.7
Run reversals in cocaine runway, males0.40.30.60.3-0.60.7
Latency to leave start box in cocaine runway4.85.210.4-3.2-0.6-2.2
Latency to leave start box in cocaine runway, F5.66.111.7-3.40.1-2.6
Latency to leave start box in cocaine runway, M0.50.51.0-0.6-1.00.0
Cd content in liver2.52.74.3-2.10.5-1.9
Co content in liver0.50.60.90.9-0.21.0
Cu content in liver0.10.20.40.60.30.2
Fe content in liver0.40.51.40.01.2-0.3
K content in liver2.02.03.61.90.31.5
Mg content in liver0.30.30.50.7-0.10.5
Mn content in liver4.55.16.92.5-1.42.6
Na content in liver1.31.32.61.11.60.4
Rb content in liver1.21.42.1-1.5-1.2-0.8
Se content in liver0.60.70.9-0.9-0.9-0.5
Sr content in liver1.21.12.41.01.50.0
Zn content in liver1.11.22.0-1.40.6-1.2