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 5.2e-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 5.3e-04
3 Adipose gene expression Stap1 0.13 0.07 1.0e-05 0.02 0.05 0.04 0.05 3.3e-03 3.5e-06 8.0e-06 3.7e-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 density0.61.01.91.40.5-0.8
Area under the delay curve0.91.02.11.4-0.3-0.9
BMI with tail1.75.88.22.82.9-1.1
BMI without tail0.82.65.41.42.3-0.6
Body weight0.20.91.21.10.7-0.9
Weight adjusted by age1.01.52.21.21.5-0.8
Bone surface0.40.71.21.10.4-0.8
Bone volume0.30.51.21.1-0.4-0.5
Breakpoint value in progressive ratio session0.40.50.9-0.4-0.70.9
Number of licking bursts0.30.50.70.80.5-0.7
Context. condit. distance diff. score1.51.84.0-2.0-0.11.2
Locomotion velocity, session 10.70.82.20.30.4-1.5
Locomotion distance, session 10.00.10.1-0.4-0.1-0.2
Locomotion velocity, session 20.00.00.00.20.10.2
Locomotion distance, session 20.10.10.20.2-0.1-0.4
Locomotion velocity, session 30.20.30.50.6-0.70.0
Locomotion distance, session 30.50.51.51.20.30.0
Stereotopy head waving bouts, day 30.30.30.5-0.30.6-0.7
Stereotopy head waving duration, day 30.60.72.20.3-0.1-1.5
Locomotion velocity, session 71.11.22.20.2-1.5-1.1
Locomotion distance, session 70.60.81.7-0.8-1.30.3
Stereotopy head waving bouts, day 70.10.10.40.20.1-0.6
Stereotopy head waving duration, day 70.40.40.70.70.3-0.8
Locomotion velocity, session 80.00.00.10.00.10.2
Locomotion distance, session 80.60.92.4-1.6-0.40.2
Degree of sensitization distance3.13.26.4-2.5-1.51.0
Degree of sensitization stereotypy0.10.10.2-0.4-0.20.4
Conditioned locomotion0.80.91.8-0.01.01.3
Cocaine response after cond. corrected0.70.91.8-0.9-1.3-0.2
Cocaine response after cond. not corrected0.50.61.1-0.7-1.1-0.6
Cocaine response before conditioning0.50.60.90.70.9-0.8
Saline control response0.60.81.5-0.8-0.51.2
Bone: connectivity density0.91.42.01.41.2-1.0
Bone: cortical apparent density0.50.72.0-1.4-0.2-0.4
Bone: cortical area0.50.81.40.8-0.7-1.2
Bone: cortical porosity0.50.51.40.01.20.3
Bone: cortical porosity1.01.02.90.41.7-0.1
Bone: cortical thickness0.40.71.11.11.0-0.3
Bone: cortical thickness0.00.00.1-0.3-0.10.0
Bone: cortical tissue density0.50.71.9-1.4-0.2-0.4
Condit. Reinf. active minus inactive responses1.11.31.7-1.31.01.1
Condit. Reinf. active-inactive response ratio1.61.74.6-0.52.10.5
Condit. Reinf. active responses1.11.43.0-1.7-0.01.1
Condit. Reinf. inactive responses1.31.62.8-1.3-1.70.5
Incentive salience index mean1.41.72.8-1.50.31.7
Condit. Reinf. lever presses0.71.02.7-0.60.11.7
Condit. Reinf. active minus inactive responses0.00.10.1-0.3-0.10.3
Condit. Reinf. active-inactive response ratio0.30.40.7-0.8-0.4-0.6
Condit. Reinf. active responses0.10.20.4-0.1-0.00.7
Condit. Reinf. inactive responses0.40.50.90.70.00.9
Condit. Reinf. lever presses0.60.81.91.4-0.70.2
Condit. Reinf. lever reinforcers received0.20.30.9-0.1-0.11.0
Conditioned reinforcement - actives0.00.10.20.50.1-0.0
Conditioned reinforcement - inactives1.01.41.8-1.0-1.21.3
Conditioned locomotion0.40.61.10.80.0-1.0
Patch foraging indifference point 0 sec0.20.40.6-0.7-0.8-0.1
Patch foraging indifference point AUC2.63.85.6-1.9-2.41.5
Delay disc. indifference point, 0s delay0.70.71.21.10.1-1.0
Delay disc. indifference point, 16s delay1.11.32.11.40.7-1.1
Delay disc. indifference point, 2s delay1.71.95.6-0.1-2.4-0.1
Delay disc. indifference point, 24s delay0.00.00.0-0.20.2-0.1
Delay disc. indifference point, 4s delay1.01.01.60.8-0.9-1.2
Delay disc. indifference point, 8s delay2.02.44.42.11.0-1.3
Indifference point function ln k1.12.02.71.61.5-1.0
Indifference point function log k1.12.02.71.61.5-1.0
Patch foraging total patch changes 0 sec0.30.50.9-0.9-0.8-0.0
Patch foraging total patch changes 12 sec0.20.30.5-0.5-0.70.5
Patch foraging total patch changes 18 sec1.31.94.0-2.0-0.91.0
Patch foraging total patch changes 24 sec1.01.72.9-1.7-1.20.9
Patch foraging total patch changes 6 sec1.01.54.0-0.6-2.0-0.0
Patch foraging time to switch 0 sec1.83.65.92.12.4-0.8
Patch foraging water rate 0 sec0.91.93.0-1.6-1.70.1
Patch foraging water rate 12 sec0.30.71.1-1.1-0.50.8
Patch foraging water rate 18 sec0.20.40.9-0.3-1.0-0.1
Patch foraging water rate 24 sec0.60.81.1-0.8-1.00.8
Patch foraging water rate 6 sec1.42.03.7-1.9-1.40.5
Seeking ratio, delayed vs. immediate footshock3.44.28.4-2.9-0.42.0
Distance traveled before self-admin1.11.53.31.80.9-0.6
Distance traveled after self-admin1.82.33.2-0.9-1.81.7
Extensor digitorum longus weight3.714.637.02.56.10.6
Bone: elastic displacement1.01.21.7-1.30.61.3
Bone: elastic work0.20.20.30.40.5-0.4
Bone: endosteal estimation0.81.73.9-0.6-2.0-0.8
Bone: endosteal perimeter1.12.43.91.4-1.0-2.0
Epididymis fat weight0.10.30.70.20.1-0.8
Delta time in closed arm before/after self-admin0.60.61.00.71.0-0.4
Delta time in open arm before/after self-admin0.40.40.60.8-0.4-0.7
Diff in mean of infusions in LGA sessions0.40.41.2-0.30.21.1
Delay discount exponential model param0.70.81.4-1.20.50.8
Extinction: sum of active levers before priming0.20.20.4-0.20.6-0.6
Active lever presses in extinction session 60.40.40.80.3-0.9-0.5
Bone: final force0.60.92.11.4-0.1-0.9
Bone: final moment0.60.91.61.3-0.1-1.1
Food consumed during 24 hour testing period0.81.11.91.1-1.40.0
Glucose1.21.93.0-1.7-1.60.2
Heart weight0.61.02.40.71.6-0.2
Delay discount hyperbolic model param0.80.91.4-1.20.80.7
Intermittent access intake day 1-15 change0.40.81.71.30.40.7
Intermittent access intake escalation0.51.01.91.40.80.6
Intermittent access intake escalation 20.81.02.81.7-0.3-0.1
Intermitt. access day 1 inactive lever presses0.72.64.3-1.0-1.62.1
Intermitt. access day 15 inactive lever presses0.61.33.8-0.4-1.90.0
Intermitt. access escalation Index0.20.30.8-0.20.9-0.1
Intermittent access day 1 total infusions0.20.30.70.3-0.5-0.8
Intermittent access day 15 total infusions0.20.30.60.7-0.30.3
Intermittent access terminal intake (last 3 days)0.40.50.80.9-0.80.1
Intermittent access total infusions0.10.20.30.5-0.4-0.4
Intermittent access day 1 locomotion0.30.30.8-0.2-0.9-0.4
Intermittent access day 15 total locomotion0.00.00.00.2-0.1-0.1
Intermittent access total locomotion0.30.40.80.6-0.1-0.9
Intermittent access standard deviation0.40.81.90.6-1.40.3
Left kidney weight0.10.50.70.80.4-0.8
Right kidney weight0.41.83.11.5-0.4-1.8
Cocaine induced anxiety1.11.62.61.20.8-1.6
Post-drug Anxiety0.50.60.90.9-0.2-0.9
Baseline Anxiety2.32.74.3-1.3-1.42.1
Tail length0.31.31.9-1.4-1.20.8
Length with tail0.41.92.8-1.5-1.70.8
Length without tail0.31.11.8-1.1-1.30.5
Times rat made contact with spout1.11.22.41.6-1.0-0.5
Lifetime Intake0.30.30.50.7-0.1-0.7
Liver weight, left1.52.52.91.7-1.3-1.7
Liver weight, right0.71.32.00.3-1.4-1.3
Locomotor activity1.42.23.61.7-0.2-1.9
Locomotor testing distance0.40.81.00.80.8-1.0
Locomotor testing rearing0.20.40.6-0.70.80.3
Locomotion in novel chamber1.41.74.3-2.1-0.40.9
Locomotion in novel chamber post-restriction0.71.12.0-1.4-1.00.4
Fecal boli incidents, locomotor time 10.81.12.51.01.60.0
Change in fecal boli incidents, locomotor task0.60.61.6-1.3-0.20.2
Time >=10cm from walls, locomotor time 10.91.02.1-1.40.9-0.2
Bouts of movement, locomotor time 10.40.40.60.70.8-0.4
Total resting periods, locomotor time 10.30.30.50.50.5-0.7
Rest time, locomotor task time 10.10.20.4-0.2-0.60.3
Distance moved, locomotor task time 10.00.10.10.20.30.2
Vertical activity count, locomotor time 10.30.61.20.7-0.5-1.1
Time >=10cm from walls, locomotor time 20.30.50.8-0.70.90.3
Bouts of movement, locomotor time 20.20.30.6-0.8-0.50.0
Total resting periods, locomotor time 20.10.20.3-0.6-0.5-0.1
Rest time, locomotor task time 20.30.40.9-0.9-0.20.5
Distance moved, locomotor task time 21.92.24.42.11.5-0.3
Vertical activity count, locomotor time 21.01.42.91.70.4-1.1
Light reinforcement 10.30.61.61.3-0.5-0.2
Light reinforcement 21.01.53.51.90.4-0.9
Bone: marrow area0.71.63.8-0.6-1.9-0.8
Bone: maximum diameter0.81.63.40.8-0.8-1.8
Bone: maximum force0.50.81.41.2-0.3-1.0
Bone: maximum moment0.50.91.71.0-0.4-1.3
Mean time between licks in bursts2.25.39.13.02.3-1.3
Mean num. licks in bursts0.40.71.9-0.0-1.40.3
Cd content in liver1.51.73.01.11.7-0.8
Co content in liver0.30.30.6-0.20.5-0.8
Cu content in liver0.20.20.3-0.40.40.6
Fe content in liver0.70.91.20.71.1-0.9
K content in liver0.70.61.2-1.1-0.20.8
Mg content in liver0.10.10.1-0.3-0.20.2
Mn content in liver2.42.64.6-2.20.41.7
Na content in liver0.91.02.2-1.5-0.80.4
Rb content in liver1.21.42.5-1.61.2-0.5
Se content in liver1.61.85.30.5-0.12.3
Sr content in liver0.30.30.5-0.40.70.4
Zn content in liver0.30.40.90.20.40.9
Bone: minimum diameter2.13.88.2-0.4-2.9-1.7
Time in familiar zone, hab. session 10.50.51.2-0.40.01.1
Time in novel zone, hab. session 10.60.61.70.10.2-1.3
Total zone transitions, hab. session 10.20.30.6-0.5-0.30.8
Total locomotion distance, hab. session 10.40.61.2-0.2-1.10.7
Locomotion velocity, hab. session 10.50.71.1-0.3-1.00.9
Time in familiar zone, hab. session 20.50.51.11.00.7-0.0
Time in novel zone, hab. session 20.50.50.9-1.0-0.3-0.6
Total zone transitions, hab. session 20.20.20.50.70.2-0.5
Total locomotion distance, hab. session 20.10.20.30.3-0.6-0.3
Locomotion velocity, hab. session 20.10.20.30.4-0.6-0.2
Novel to familiar place preference ratio0.10.10.3-0.1-0.50.1
Novelty place preference0.00.00.10.0-0.4-0.0
Time in novel zone, NPP test0.10.10.3-0.2-0.50.0
Total zone transitions, NPP test0.20.30.6-0.4-0.1-0.8
Total locomotion distance, NPP test0.10.20.3-0.4-0.0-0.5
Locomotion velocity, NPP test0.10.10.2-0.30.2-0.4
Intraocular pressure4.26.19.23.00.2-3.0
Delta distance traveled before/after self-admin3.73.95.0-2.2-2.11.6
Delta ambulatory time before/after self-admin1.82.24.0-2.0-1.40.9
Parametrial fat weight1.02.34.10.3-2.0-1.6
Pavlov. Cond. lever latency1.31.73.01.30.6-1.7
Pavlov. Cond. magazine entry latency1.72.15.6-0.90.22.4
Pavlov. Cond. change in total contacts2.93.05.9-1.80.22.4
Pavlov. Cond. index score2.32.96.3-1.5-0.12.5
Pavlov. Cond. latency score2.12.65.7-1.4-0.32.4
Pavlov. Cond. lever contacts1.31.53.1-1.1-0.61.8
Pavlov. Cond. magazine entry number2.22.85.31.8-0.1-2.3
Pavlov. Cond. intertrial magazine entries0.20.30.8-0.9-0.1-0.0
Pavlov. Cond. lever-magazine prob. diff.2.43.06.4-1.5-0.32.5
Pavlov. Cond. response bias1.62.04.2-1.3-0.22.0
Pavlov. Cond. lever latency1.31.84.9-2.2-0.60.3
Pavlov. Cond. magazine entry latency1.01.21.91.41.1-0.8
Pavlov. Cond. change in total contacts0.71.22.61.61.0-0.1
Pavlov. Cond. index score1.31.84.32.11.0-0.3
Pavlov. Cond. latency score1.31.83.82.01.2-0.2
Pavlov. Cond. lever contacts1.52.05.82.40.2-0.5
Pavlov. Cond. magazine entry number1.72.12.8-1.7-1.51.0
Pavlov. Cond. intertrial magazine entries0.71.12.3-0.7-1.50.7
Pavlov. Cond. lever-magazine prob. diff.1.41.94.62.21.0-0.3
Pavlov. Cond. response bias1.31.84.72.20.6-0.5
Time in closed arm before self-admin2.63.45.2-2.3-1.02.0
Time in closed arm after self-admin1.61.74.1-0.90.42.0
Time in open arm before self-admin0.30.40.70.30.8-0.6
Time in open arm after self-admin1.11.22.40.5-0.9-1.5
Bone: periosteal estimation0.61.32.20.2-1.5-1.2
Bone: periosteal perimeter1.32.23.91.4-0.9-2.0
Bone: post-yield work0.60.82.2-0.5-0.1-1.5
Progressive ratio test 1 active lever presses1.01.22.21.50.8-1.0
Progressive ratio test 1 breakpoint0.91.12.01.40.7-0.9
Progressive ratio test 1 inactive lever presses1.01.53.4-0.5-1.80.9
Progressive ratio test 2 active lever presses1.61.84.82.2-0.0-0.8
Progressive ratio test 2 breakpoint1.61.84.72.20.1-0.8
Progressive ratio test 2 inactive lever presses0.40.61.30.1-1.10.8
Incentive Sensitization - Responses0.81.23.41.8-0.1-0.3
Incentive Sensitization - Breakpoint0.91.23.51.9-0.0-0.3
Sum of active levers in priming session hrs 5-60.00.00.10.20.0-0.1
Progressive ratio0.71.23.41.90.2-0.0
Food seeking constrained by brief footshock0.10.10.30.00.6-0.1
Seeking ratio, punishment vs. effort0.71.02.5-1.6-0.3-0.5
Retroperitoneal fat weight0.41.84.30.6-0.9-2.1
Reaction time number correct0.61.13.00.70.1-1.7
Reaction time mean minus median0.20.40.7-0.80.6-0.4
Reaction time mean minus median AUC0.10.30.4-0.40.4-0.7
Reaction time num false alarms0.81.11.8-1.30.11.3
Reaction time num false alarms AUC0.81.32.0-1.40.41.3
Reaction time trials correct on left0.61.13.00.70.1-1.7
Reaction time trials on left0.61.23.10.70.1-1.7
Reaction time mean0.20.20.60.10.8-0.3
Reaction time mean AUC0.20.30.9-0.01.0-0.1
Median of all reaction times0.20.30.70.30.8-0.2
Reaction time omissions0.40.61.60.11.3-0.3
Reaction time false alarm rate1.41.93.6-1.40.31.9
Reaction time premature initiation rate1.01.43.90.2-0.42.0
Reaction time premature initiations0.20.40.70.5-0.50.8
Std. dev. reaction times0.10.20.5-0.40.7-0.4
Reaction time trials completed0.61.23.10.70.1-1.7
Reaction time trials AUC0.81.53.80.80.1-2.0
Run reversals in cocaine runway, females1.21.22.01.0-0.9-1.4
Run reversals in cocaine runway, males0.30.30.91.00.2-0.3
Latency to leave start box in cocaine runway2.42.85.3-1.7-2.30.2
Latency to leave start box in cocaine runway, F5.36.19.6-2.9-3.10.4
Latency to leave start box in cocaine runway, M0.40.41.11.0-0.0-0.1
Std. dev. time between licks in bursts0.91.22.41.01.60.2
Total sessions with >9 infusions2.53.04.01.71.4-2.0
Short access day 1 total inactive lever presses0.60.81.6-0.3-1.30.8
Short access day 10 total inactive lever presses0.40.91.3-0.7-1.10.9
Short access day 1 total infusions0.50.61.30.6-0.4-1.2
Short access day 10 total infusions0.50.61.10.70.4-1.0
Short access total infusions1.21.52.81.20.5-1.7
Short access day 1 locomotion1.21.53.10.80.7-1.8
Short access day 10 total locomotion0.20.51.31.10.0-0.3
Short access total locomotion1.41.63.31.10.6-1.8
One hour access (0.3 mA shock)0.20.30.5-0.1-0.70.6
Compulsive drug intake1.31.62.5-1.6-0.91.2
One hour access (shock baseline)0.30.51.01.0-0.1-0.7
Social response proportion1.11.22.8-1.0-1.7-0.2
Social responses1.41.82.4-1.5-1.50.9
Social time1.11.51.7-1.3-1.11.2
Soleus weight0.82.35.3-1.30.22.3
Bone: stiffness0.50.81.41.2-0.9-0.6
Tibialis anterior weight1.75.912.32.23.50.8
Time to tail flick, vehicle, before self-admin0.70.72.10.0-1.50.2
Time to tail flick, vehicle, after self-admin1.21.62.8-0.9-1.11.7
Time to tail flick, test, before self-admin1.21.23.3-0.50.31.8
Time to tail flick, test, after self-admin0.30.30.80.1-0.9-0.4
Delta time to tail flick, vehicle, before/after SA0.00.00.0-0.2-0.20.2
Delta time to tail flick, test, before/after SA1.01.01.70.3-1.1-1.3
Tibia length0.41.01.91.4-0.8-0.7
Ambulatory time before self-admin1.01.53.51.90.7-0.6
Ambulatory time after self-admin0.91.12.2-0.1-1.51.0
Bone: tissue strength0.30.30.9-0.1-0.9-0.2
Total heroin consumption0.40.51.0-0.6-1.00.3
Bone: trabecular number0.00.10.10.40.20.1
Bone: trabecular spacing0.00.00.0-0.20.1-0.1
Bone: trabecular thickness0.91.23.21.8-0.3-0.4
Bone: trabecular tissue density0.20.30.5-0.10.7-0.7
Water consumed over 24 hours1.31.82.31.5-1.5-0.8
Number of responses in last shaping day0.20.20.50.20.70.1