Stap1

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 Eye gene expression Stap1 0.35 0.18 9.7e-03 0.18 0.03 0.06 0.18 1.0e-03 1.1e-01 5.1e-02 1.0e-03
2 IL alternative TSS XM_017599182.3 0.12 0.08 3.8e-03 0.11 0.13 0.13 0.13 1.2e-03 5.7e-04 4.3e-04 5.0e-04
3 Adipose gene expression Stap1 0.13 0.07 1.0e-05 0.02 0.05 0.05 0.05 3.3e-03 3.5e-06 6.9e-06 3.5e-06

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
Bone: apparent density0.51.01.9-1.4-0.5-0.8
Area under the delay curve0.71.02.1-1.40.3-0.9
BMI with tail1.75.88.2-2.8-2.9-1.1
BMI without tail0.52.65.4-1.4-2.3-0.6
Body weight0.20.91.2-1.1-0.7-0.9
Weight adjusted by age0.51.52.2-1.2-1.5-0.8
Bone surface0.30.71.2-1.1-0.4-0.8
Bone volume0.30.51.2-1.10.4-0.5
Breakpoint value in progressive ratio session0.30.50.90.40.70.9
Number of licking bursts0.20.50.7-0.8-0.5-0.7
Context. condit. distance diff. score1.51.84.02.00.11.2
Locomotion velocity, session 10.70.82.2-0.3-0.4-1.5
Locomotion distance, session 10.00.10.10.40.1-0.2
Locomotion velocity, session 20.00.00.0-0.2-0.10.2
Locomotion distance, session 20.10.10.2-0.20.1-0.4
Locomotion velocity, session 30.20.30.5-0.60.70.0
Locomotion distance, session 30.50.51.5-1.2-0.30.0
Stereotopy head waving bouts, day 30.30.30.50.3-0.6-0.7
Stereotopy head waving duration, day 30.60.72.2-0.30.1-1.5
Locomotion velocity, session 71.11.22.2-0.21.5-1.1
Locomotion distance, session 70.60.81.70.81.30.3
Stereotopy head waving bouts, day 70.10.10.4-0.2-0.1-0.6
Stereotopy head waving duration, day 70.30.40.7-0.7-0.3-0.8
Locomotion velocity, session 80.00.00.1-0.0-0.10.2
Locomotion distance, session 80.60.92.41.60.40.2
Degree of sensitization distance3.03.26.42.51.51.0
Degree of sensitization stereotypy0.10.10.20.40.20.4
Conditioned locomotion0.80.91.80.0-1.01.3
Cocaine response after cond. corrected0.60.91.80.91.3-0.2
Cocaine response after cond. not corrected0.40.61.10.71.1-0.6
Cocaine response before conditioning0.50.60.9-0.7-0.9-0.8
Saline control response0.60.81.50.80.51.2
Bone: connectivity density0.91.42.0-1.4-1.2-1.0
Bone: cortical apparent density0.50.72.01.40.2-0.4
Bone: cortical area0.50.81.4-0.80.7-1.2
Bone: cortical porosity0.50.51.4-0.0-1.20.3
Bone: cortical porosity0.91.02.9-0.4-1.7-0.1
Bone: cortical thickness0.40.71.1-1.1-1.0-0.3
Bone: cortical thickness0.00.00.10.30.10.0
Bone: cortical tissue density0.40.71.91.40.2-0.4
Condit. Reinf. active minus inactive responses1.11.31.71.3-1.01.1
Condit. Reinf. active-inactive response ratio1.61.74.60.5-2.10.5
Condit. Reinf. active responses1.11.43.01.70.01.1
Condit. Reinf. inactive responses1.21.62.81.31.70.5
Incentive salience index mean1.31.72.81.5-0.31.7
Condit. Reinf. lever presses0.71.02.70.6-0.11.7
Condit. Reinf. active minus inactive responses0.00.10.10.30.10.3
Condit. Reinf. active-inactive response ratio0.30.40.70.80.4-0.6
Condit. Reinf. active responses0.10.20.40.10.00.7
Condit. Reinf. inactive responses0.30.50.9-0.7-0.00.9
Condit. Reinf. lever presses0.50.81.9-1.40.70.2
Condit. Reinf. lever reinforcers received0.20.30.90.10.11.0
Conditioned reinforcement - actives0.00.10.2-0.5-0.1-0.0
Conditioned reinforcement - inactives0.51.41.81.01.21.3
Conditioned locomotion0.40.61.1-0.8-0.0-1.0
Patch foraging indifference point 0 sec0.10.40.60.70.8-0.1
Patch foraging indifference point AUC1.63.85.61.92.41.5
Delay disc. indifference point, 0s delay0.70.71.2-1.1-0.1-1.0
Delay disc. indifference point, 16s delay0.91.32.1-1.4-0.7-1.1
Delay disc. indifference point, 2s delay1.71.95.60.12.4-0.1
Delay disc. indifference point, 24s delay0.00.00.00.2-0.2-0.1
Delay disc. indifference point, 4s delay1.01.01.6-0.80.9-1.2
Delay disc. indifference point, 8s delay1.42.44.4-2.1-1.0-1.3
Indifference point function ln k0.62.02.7-1.6-1.5-1.0
Indifference point function log k0.62.02.7-1.6-1.5-1.0
Patch foraging total patch changes 0 sec0.20.50.90.90.8-0.0
Patch foraging total patch changes 12 sec0.20.30.50.50.70.5
Patch foraging total patch changes 18 sec0.81.94.02.00.91.0
Patch foraging total patch changes 24 sec0.51.72.91.71.20.9
Patch foraging total patch changes 6 sec0.91.54.00.62.0-0.0
Patch foraging time to switch 0 sec1.03.65.9-2.1-2.4-0.8
Patch foraging water rate 0 sec0.51.93.01.61.70.1
Patch foraging water rate 12 sec0.20.71.11.10.50.8
Patch foraging water rate 18 sec0.20.40.90.31.0-0.1
Patch foraging water rate 24 sec0.60.81.10.81.00.8
Patch foraging water rate 6 sec1.42.03.71.91.40.5
Seeking ratio, delayed vs. immediate footshock2.94.28.42.90.42.0
Distance traveled before self-admin0.71.53.3-1.8-0.9-0.6
Distance traveled after self-admin1.32.33.20.91.81.7
Extensor digitorum longus weight3.614.637.0-2.5-6.10.6
Bone: elastic displacement0.91.21.71.3-0.61.3
Bone: elastic work0.20.20.3-0.4-0.5-0.4
Bone: endosteal estimation0.71.73.90.62.0-0.8
Bone: endosteal perimeter1.02.43.9-1.41.0-2.0
Epididymis fat weight0.10.30.7-0.2-0.1-0.8
Delta time in closed arm before/after self-admin0.60.61.0-0.7-1.0-0.4
Delta time in open arm before/after self-admin0.40.40.6-0.80.4-0.7
Diff in mean of infusions in LGA sessions0.30.41.20.3-0.21.1
Delay discount exponential model param0.60.81.41.2-0.50.8
Extinction: sum of active levers before priming0.20.20.40.2-0.6-0.6
Active lever presses in extinction session 60.40.40.8-0.30.9-0.5
Bone: final force0.60.92.1-1.40.1-0.9
Bone: final moment0.60.91.6-1.30.1-1.1
Food consumed during 24 hour testing period0.51.11.9-1.11.40.0
Glucose1.21.93.01.71.60.2
Heart weight0.61.02.4-0.7-1.6-0.2
Delay discount hyperbolic model param0.70.91.41.2-0.80.7
Intermittent access intake day 1-15 change0.10.81.7-1.3-0.40.7
Intermittent access intake escalation0.21.01.9-1.4-0.80.6
Intermittent access intake escalation 20.61.02.8-1.70.3-0.1
Intermitt. access day 1 inactive lever presses0.22.64.31.01.62.1
Intermitt. access day 15 inactive lever presses0.21.33.80.41.90.0
Intermitt. access escalation Index0.10.30.80.2-0.9-0.1
Intermittent access day 1 total infusions0.10.30.7-0.30.5-0.8
Intermittent access day 15 total infusions0.10.30.6-0.70.30.3
Intermittent access terminal intake (last 3 days)0.30.50.8-0.90.80.1
Intermittent access total infusions0.10.20.3-0.50.4-0.4
Intermittent access day 1 locomotion0.20.30.80.20.9-0.4
Intermittent access day 15 total locomotion0.00.00.0-0.20.1-0.1
Intermittent access total locomotion0.30.40.8-0.60.1-0.9
Intermittent access standard deviation0.10.81.9-0.61.40.3
Left kidney weight0.10.50.7-0.8-0.4-0.8
Right kidney weight0.31.83.1-1.50.4-1.8
Cocaine induced anxiety0.61.62.6-1.2-0.8-1.6
Post-drug Anxiety0.50.60.9-0.90.2-0.9
Baseline Anxiety1.62.74.31.31.42.1
Tail length0.21.31.91.41.20.8
Length with tail0.41.92.81.51.70.8
Length without tail0.21.11.81.11.30.5
Times rat made contact with spout1.11.22.4-1.61.0-0.5
Lifetime Intake0.30.30.5-0.70.1-0.7
Liver weight, left1.42.52.9-1.71.3-1.7
Liver weight, right0.71.32.0-0.31.4-1.3
Locomotor activity1.42.23.6-1.70.2-1.9
Locomotor testing distance0.30.81.0-0.8-0.8-1.0
Locomotor testing rearing0.10.40.60.7-0.80.3
Locomotion in novel chamber1.31.74.32.10.40.9
Locomotion in novel chamber post-restriction0.41.12.01.41.00.4
Fecal boli incidents, locomotor time 10.41.12.5-1.0-1.60.0
Change in fecal boli incidents, locomotor task0.50.61.61.30.20.2
Time >=10cm from walls, locomotor time 10.81.02.11.4-0.9-0.2
Bouts of movement, locomotor time 10.30.40.6-0.7-0.8-0.4
Total resting periods, locomotor time 10.30.30.5-0.5-0.5-0.7
Rest time, locomotor task time 10.10.20.40.20.60.3
Distance moved, locomotor task time 10.00.10.1-0.2-0.30.2
Vertical activity count, locomotor time 10.10.61.2-0.70.5-1.1
Time >=10cm from walls, locomotor time 20.20.50.80.7-0.90.3
Bouts of movement, locomotor time 20.10.30.60.80.50.0
Total resting periods, locomotor time 20.00.20.30.60.5-0.1
Rest time, locomotor task time 20.20.40.90.90.20.5
Distance moved, locomotor task time 21.72.24.4-2.1-1.5-0.3
Vertical activity count, locomotor time 20.61.42.9-1.7-0.4-1.1
Light reinforcement 10.10.61.6-1.30.5-0.2
Light reinforcement 20.71.53.5-1.9-0.4-0.9
Bone: marrow area0.61.63.80.61.9-0.8
Bone: maximum diameter0.81.63.4-0.80.8-1.8
Bone: maximum force0.40.81.4-1.20.3-1.0
Bone: maximum moment0.50.91.7-1.00.4-1.3
Mean time between licks in bursts0.95.39.1-3.0-2.3-1.3
Mean num. licks in bursts0.20.71.90.01.40.3
Cd content in liver1.51.73.0-1.1-1.7-0.8
Co content in liver0.30.30.60.2-0.5-0.8
Cu content in liver0.20.20.30.4-0.40.6
Fe content in liver0.70.91.2-0.7-1.1-0.9
K content in liver0.70.61.21.10.20.8
Mg content in liver0.10.10.10.30.20.2
Mn content in liver2.32.64.62.2-0.41.7
Na content in liver0.91.02.21.50.80.4
Rb content in liver1.21.42.51.6-1.2-0.5
Se content in liver1.61.85.3-0.50.12.3
Sr content in liver0.30.30.50.4-0.70.4
Zn content in liver0.30.40.9-0.2-0.40.9
Bone: minimum diameter2.03.88.20.42.9-1.7
Time in familiar zone, hab. session 10.40.51.20.4-0.01.1
Time in novel zone, hab. session 10.50.61.7-0.1-0.2-1.3
Total zone transitions, hab. session 10.20.30.60.50.30.8
Total locomotion distance, hab. session 10.40.61.20.21.10.7
Locomotion velocity, hab. session 10.50.71.10.31.00.9
Time in familiar zone, hab. session 20.50.51.1-1.0-0.7-0.0
Time in novel zone, hab. session 20.40.50.91.00.3-0.6
Total zone transitions, hab. session 20.20.20.5-0.7-0.2-0.5
Total locomotion distance, hab. session 20.10.20.3-0.30.6-0.3
Locomotion velocity, hab. session 20.10.20.3-0.40.6-0.2
Novel to familiar place preference ratio0.10.10.30.10.50.1
Novelty place preference0.00.00.1-0.00.4-0.0
Time in novel zone, NPP test0.10.10.30.20.50.0
Total zone transitions, NPP test0.20.30.60.40.1-0.8
Total locomotion distance, NPP test0.10.20.30.40.0-0.5
Locomotion velocity, NPP test0.10.10.20.3-0.2-0.4
Intraocular pressure3.76.19.2-3.0-0.2-3.0
Delta distance traveled before/after self-admin3.63.95.02.22.11.6
Delta ambulatory time before/after self-admin1.32.24.02.01.40.9
Parametrial fat weight1.02.34.1-0.32.0-1.6
Pavlov. Cond. lever latency1.31.73.0-1.3-0.6-1.7
Pavlov. Cond. magazine entry latency1.72.15.60.9-0.22.4
Pavlov. Cond. change in total contacts2.83.05.91.8-0.22.4
Pavlov. Cond. index score2.32.96.31.50.12.5
Pavlov. Cond. latency score2.12.65.71.40.32.4
Pavlov. Cond. lever contacts1.31.53.11.10.61.8
Pavlov. Cond. magazine entry number2.22.85.3-1.80.1-2.3
Pavlov. Cond. intertrial magazine entries0.20.30.80.90.1-0.0
Pavlov. Cond. lever-magazine prob. diff.2.43.06.41.50.32.5
Pavlov. Cond. response bias1.62.04.21.30.22.0
Pavlov. Cond. lever latency1.31.84.92.20.60.3
Pavlov. Cond. magazine entry latency0.91.21.9-1.4-1.1-0.8
Pavlov. Cond. change in total contacts0.51.22.6-1.6-1.0-0.1
Pavlov. Cond. index score1.11.84.3-2.1-1.0-0.3
Pavlov. Cond. latency score1.11.83.8-2.0-1.2-0.2
Pavlov. Cond. lever contacts1.42.05.8-2.4-0.2-0.5
Pavlov. Cond. magazine entry number1.62.12.81.71.51.0
Pavlov. Cond. intertrial magazine entries0.51.12.30.71.50.7
Pavlov. Cond. lever-magazine prob. diff.1.21.94.6-2.2-1.0-0.3
Pavlov. Cond. response bias1.31.84.7-2.2-0.6-0.5
Time in closed arm before self-admin1.93.45.22.31.02.0
Time in closed arm after self-admin1.51.74.10.9-0.42.0
Time in open arm before self-admin0.30.40.7-0.3-0.8-0.6
Time in open arm after self-admin1.11.22.4-0.50.9-1.5
Bone: periosteal estimation0.51.32.2-0.21.5-1.2
Bone: periosteal perimeter1.12.23.9-1.40.9-2.0
Bone: post-yield work0.50.82.20.50.1-1.5
Progressive ratio test 1 active lever presses0.71.22.2-1.5-0.8-1.0
Progressive ratio test 1 breakpoint0.61.12.0-1.4-0.7-0.9
Progressive ratio test 1 inactive lever presses0.61.53.40.51.80.9
Progressive ratio test 2 active lever presses1.31.84.8-2.20.0-0.8
Progressive ratio test 2 breakpoint1.41.84.7-2.2-0.1-0.8
Progressive ratio test 2 inactive lever presses0.20.61.3-0.11.10.8
Incentive Sensitization - Responses0.41.23.4-1.80.1-0.3
Incentive Sensitization - Breakpoint0.51.23.5-1.90.0-0.3
Sum of active levers in priming session hrs 5-60.00.00.1-0.2-0.0-0.1
Progressive ratio0.41.23.4-1.9-0.2-0.0
Food seeking constrained by brief footshock0.10.10.3-0.0-0.6-0.1
Seeking ratio, punishment vs. effort0.41.02.51.60.3-0.5
Retroperitoneal fat weight0.41.84.3-0.60.9-2.1
Reaction time number correct0.31.13.0-0.7-0.1-1.7
Reaction time mean minus median0.10.40.70.8-0.6-0.4
Reaction time mean minus median AUC0.00.30.40.4-0.4-0.7
Reaction time num false alarms0.71.11.81.3-0.11.3
Reaction time num false alarms AUC0.61.32.01.4-0.41.3
Reaction time trials correct on left0.31.13.0-0.7-0.1-1.7
Reaction time trials on left0.31.23.1-0.7-0.1-1.7
Reaction time mean0.10.20.6-0.1-0.8-0.3
Reaction time mean AUC0.10.30.90.0-1.0-0.1
Median of all reaction times0.20.30.7-0.3-0.8-0.2
Reaction time omissions0.40.61.6-0.1-1.3-0.3
Reaction time false alarm rate1.41.93.61.4-0.31.9
Reaction time premature initiation rate0.91.43.9-0.20.42.0
Reaction time premature initiations0.10.40.7-0.50.50.8
Std. dev. reaction times0.10.20.50.4-0.7-0.4
Reaction time trials completed0.31.23.1-0.7-0.1-1.7
Reaction time trials AUC0.41.53.8-0.8-0.1-2.0
Run reversals in cocaine runway, females1.11.22.0-1.00.9-1.4
Run reversals in cocaine runway, males0.30.30.9-1.0-0.2-0.3
Latency to leave start box in cocaine runway2.02.85.31.72.30.2
Latency to leave start box in cocaine runway, F4.96.19.62.93.10.4
Latency to leave start box in cocaine runway, M0.40.41.1-1.00.0-0.1
Std. dev. time between licks in bursts0.61.22.4-1.0-1.60.2
Total sessions with >9 infusions2.43.04.0-1.7-1.4-2.0
Short access day 1 total inactive lever presses0.40.81.60.31.30.8
Short access day 10 total inactive lever presses0.10.91.30.71.10.9
Short access day 1 total infusions0.30.61.3-0.60.4-1.2
Short access day 10 total infusions0.40.61.1-0.7-0.4-1.0
Short access total infusions1.11.52.8-1.2-0.5-1.7
Short access day 1 locomotion0.91.53.1-0.8-0.7-1.8
Short access day 10 total locomotion0.10.51.3-1.1-0.0-0.3
Short access total locomotion1.11.63.3-1.1-0.6-1.8
One hour access (0.3 mA shock)0.20.30.50.10.70.6
Compulsive drug intake1.11.62.51.60.91.2
One hour access (shock baseline)0.20.51.0-1.00.1-0.7
Social response proportion1.01.22.81.01.7-0.2
Social responses1.41.82.41.51.50.9
Social time0.91.51.71.31.11.2
Soleus weight0.82.35.31.3-0.22.3
Bone: stiffness0.50.81.4-1.20.9-0.6
Tibialis anterior weight1.75.912.3-2.2-3.50.8
Time to tail flick, vehicle, before self-admin0.60.72.1-0.01.50.2
Time to tail flick, vehicle, after self-admin0.81.62.80.91.11.7
Time to tail flick, test, before self-admin1.11.23.30.5-0.31.8
Time to tail flick, test, after self-admin0.30.30.8-0.10.9-0.4
Delta time to tail flick, vehicle, before/after SA0.00.00.00.20.20.2
Delta time to tail flick, test, before/after SA0.81.01.7-0.31.1-1.3
Tibia length0.41.01.9-1.40.8-0.7
Ambulatory time before self-admin0.51.53.5-1.9-0.7-0.6
Ambulatory time after self-admin0.71.12.20.11.51.0
Bone: tissue strength0.30.30.90.10.9-0.2
Total heroin consumption0.40.51.00.61.00.3
Bone: trabecular number0.00.10.1-0.4-0.20.1
Bone: trabecular spacing0.00.00.00.2-0.1-0.1
Bone: trabecular thickness0.81.23.2-1.80.3-0.4
Bone: trabecular tissue density0.20.30.50.1-0.7-0.7
Water consumed over 24 hours0.91.82.3-1.51.5-0.8
Number of responses in last shaping day0.10.20.5-0.2-0.70.1