Hmbox1

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 ENSRNOG00000013326 0.07 0.04 2.1e-06 0.06 0.04 0.04 0.04 2.4e-06 2.6e-04 2.2e-04 5.4e-05
2 Eye intron excision ratio chr15:39081531:39082559 0.42 0.18 2.1e-03 0.09 0.06 -0.02 0.05 1.7e-02 3.9e-02 8.0e-01 6.0e-02
3 Liver isoform ratio ENSRNOT00000109493 0.05 0.05 6.4e-04 0.02 0.01 0.02 0.02 3.3e-03 7.4e-03 4.8e-03 4.6e-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 tail0.82.74.72.21.7-0.6
BMI without tail0.20.30.4-0.5-0.60.6
Body weight1.77.19.53.12.7-2.2
Epididymis fat weight0.10.20.50.2-0.10.7
Glucose0.30.40.70.50.50.8
Heart weight0.00.10.10.10.3-0.3
Left kidney weight1.74.86.31.92.2-2.5
Right kidney weight2.46.710.72.12.2-3.3
Tail length0.30.91.4-1.2-1.1-0.3
Length with tail0.62.33.91.11.3-2.0
Length without tail4.08.710.23.13.2-2.6
Liver weight, left2.94.86.02.32.5-1.7
Liver weight, right1.62.63.81.81.9-0.9
Parametrial fat weight3.36.58.4-2.5-2.22.9
Retroperitoneal fat weight0.62.04.7-0.8-0.82.2
Intraocular pressure1.92.74.0-2.0-2.00.7
Extensor digitorum longus weight6.024.131.95.65.4-3.4
Soleus weight0.31.01.51.21.20.2
Tibialis anterior weight6.422.227.15.25.0-3.8
Tibia length1.44.19.71.40.8-3.1
Number of licking bursts0.30.40.60.80.70.1
Food consumed during 24 hour testing period0.10.10.4-0.00.1-0.6
Times rat made contact with spout0.10.10.1-0.20.20.4
Mean time between licks in bursts2.63.76.6-2.6-2.10.4
Mean num. licks in bursts0.30.40.8-0.9-0.60.3
Std. dev. time between licks in bursts0.91.12.2-1.5-1.00.1
Water consumed over 24 hours1.21.51.81.21.4-1.1
Indifference point 0 sec0.20.30.70.2-0.1-0.8
Indifference point AUC0.40.51.4-0.2-0.11.2
Indifference point function ln k0.81.11.80.80.9-1.4
Indifference point function log k0.81.11.80.80.9-1.4
Delay discounting total patch changes 0 sec0.30.51.10.50.3-1.0
Delay discounting total patch changes 12 sec0.00.10.10.4-0.2-0.1
Delay discounting total patch changes 18 sec0.40.60.7-0.6-0.80.9
Delay discounting total patch changes 24 sec0.10.20.20.30.4-0.5
Delay discounting total patch changes 6 sec0.00.00.00.1-0.2-0.0
Delay discounting time to switch 0 sec0.20.20.5-0.2-0.70.4
Delay discounting water rate 0 sec0.61.01.10.91.0-1.1
Delay discounting water rate 12 sec0.20.30.50.20.6-0.7
Delay discounting water rate 18 sec4.25.67.42.52.7-1.7
Delay discounting water rate 24 sec0.10.10.2-0.00.10.5
Delay discounting water rate 6 sec0.91.21.60.81.3-1.2
Locomotor activity3.65.76.52.32.3-2.5
Locomotor testing distance0.50.81.90.40.5-1.4
Locomotor testing rearing0.81.33.2-0.6-0.5-1.8
Light reinforcement 10.00.10.1-0.3-0.40.1
Light reinforcement 20.30.40.6-0.7-0.40.8
Reaction time number correct0.20.30.5-0.7-0.70.2
Reaction time mean minus median0.81.11.30.91.0-1.1
Reaction time mean minus median AUC0.40.51.10.50.5-1.1
Reaction time num false alarms1.01.32.21.20.7-1.5
Reaction time num false alarms AUC0.91.21.51.20.8-1.2
Reaction time trials correct on left0.20.30.5-0.7-0.70.2
Reaction time trials on left0.30.40.6-0.8-0.80.3
Reaction time mean0.20.30.7-0.30.0-0.8
Reaction time mean AUC0.40.51.5-0.00.3-1.2
Median of all reaction times0.20.30.5-0.7-0.3-0.6
Reaction time omissions1.52.13.1-1.8-1.80.1
Reaction time false alarm rate1.01.52.11.41.0-1.1
Reaction time premature initiation rate0.30.40.70.60.8-0.0
Reaction time premature initiations0.00.00.10.10.30.2
Std. dev. reaction times0.10.10.30.00.3-0.5
Reaction time trials completed0.30.40.6-0.8-0.80.3
Reaction time trials AUC0.40.60.9-0.9-0.90.3
Social response proportion2.73.03.2-1.8-1.81.6
Social responses3.44.45.5-2.1-2.31.9
Social time0.60.81.9-0.5-0.6-1.4
Conditioned locomotion0.40.40.8-0.6-0.30.9
Cocaine response after cond. corrected0.50.61.80.10.21.3
Cocaine response after cond. not corrected0.40.41.10.30.01.0
Cocaine response before conditioning0.30.41.10.4-0.0-1.1
Saline control response0.00.00.1-0.1-0.0-0.3
Condit. Reinf. active minus inactive responses0.30.30.7-0.50.10.8
Condit. Reinf. active-inactive response ratio0.20.20.3-0.20.40.5
Condit. Reinf. active responses0.40.50.8-0.7-0.60.9
Condit. Reinf. inactive responses1.41.72.7-1.3-1.61.0
Condit. Reinf. lever presses0.20.31.0-0.0-0.2-1.0
Condit. Reinf. lever reinforcers received0.10.20.3-0.4-0.30.5
Pavlov. Cond. lever latency1.62.24.3-1.0-1.12.1
Pavlov. Cond. magazine entry latency1.61.92.91.71.1-1.3
Pavlov. Cond. change in total contacts3.54.96.82.01.9-2.6
Pavlov. Cond. index score2.63.34.71.81.5-2.2
Pavlov. Cond. latency score2.53.15.01.61.3-2.2
Pavlov. Cond. lever contacts1.31.84.00.90.8-2.0
Pavlov. Cond. magazine entry number0.60.71.4-1.2-0.70.6
Pavlov. Cond. intertrial magazine entries8.210.614.6-3.8-3.52.2
Pavlov. Cond. lever-magazine prob. diff.2.43.14.31.81.4-2.1
Pavlov. Cond. response bias1.82.53.21.51.4-1.8
Conditioned reinforcement - actives7.37.28.7-2.9-2.72.4
Conditioned reinforcement - inactives1.92.13.2-1.7-1.80.5
Conditioned locomotion2.63.25.1-1.4-1.52.3
Intermittent access intake day 1-15 change0.40.40.5-0.7-0.40.7
Intermittent access intake escalation0.50.50.9-0.7-0.50.9
Intermittent access intake escalation 20.20.20.3-0.5-0.30.3
Intermitt. access day 1 inactive lever presses0.80.81.3-1.0-1.20.3
Intermitt. access day 15 inactive lever presses0.70.72.2-0.10.1-1.5
Intermitt. access escalation Index0.80.71.7-0.4-0.51.3
Intermittent access day 1 total infusions0.70.81.8-0.5-0.61.3
Intermittent access day 15 total infusions2.02.24.2-1.2-1.12.0
Intermittent access terminal intake (last 3 days)1.51.63.2-1.0-0.81.8
Intermittent access total infusions2.52.85.1-1.3-1.22.3
Intermittent access day 1 locomotion0.10.10.20.30.40.4
Intermittent access day 15 total locomotion0.40.50.9-0.5-0.41.0
Intermittent access total locomotion0.20.20.50.10.20.7
Intermittent access standard deviation0.70.71.0-1.0-0.70.8
Cocaine induced anxiety0.30.30.70.40.5-0.8
Post-drug Anxiety1.01.23.10.30.5-1.8
Baseline Anxiety0.00.00.0-0.2-0.2-0.1
Lifetime Intake2.83.15.2-1.5-1.42.3
Incentive Sensitization - Responses1.81.82.8-1.7-1.40.6
Incentive Sensitization - Breakpoint1.81.82.9-1.7-1.50.6
Progressive ratio test 1 active lever presses0.91.02.7-0.3-0.31.7
Progressive ratio test 1 breakpoint1.01.03.1-0.2-0.11.7
Progressive ratio test 1 inactive lever presses0.80.81.1-1.0-0.90.7
Progressive ratio test 2 active lever presses2.83.04.2-1.7-1.32.0
Progressive ratio test 2 breakpoint1.82.02.7-1.4-1.11.7
Progressive ratio test 2 inactive lever presses1.71.92.6-1.6-1.51.0
Total sessions with >9 infusions0.91.01.3-0.9-1.10.9
Short access day 1 total inactive lever presses0.70.81.4-0.7-0.61.2
Short access day 10 total inactive lever presses0.70.70.8-0.9-0.90.8
Short access day 1 total infusions3.53.73.9-1.8-2.01.9
Short access day 10 total infusions0.40.51.4-0.00.01.2
Short access total infusions0.80.91.8-0.7-0.71.3
Short access day 1 locomotion0.10.10.2-0.20.1-0.4
Short access day 10 total locomotion0.70.80.90.90.9-0.9
Short access total locomotion0.40.40.70.50.6-0.8
Compulsive drug intake0.10.10.10.30.30.3
One hour access (0.3 mA shock)1.41.74.2-0.7-0.62.0
One hour access (shock baseline)1.82.03.6-1.1-1.11.9
Number of responses in last shaping day0.10.10.20.50.4-0.2
Context. condit. distance diff. score2.53.15.4-1.2-1.52.3
Locomotion velocity, session 10.00.00.10.30.0-0.1
Locomotion distance, session 10.00.00.1-0.1-0.3-0.0
Locomotion velocity, session 20.10.20.20.50.50.2
Locomotion distance, session 20.10.10.1-0.4-0.4-0.1
Locomotion velocity, session 31.21.31.90.91.2-1.4
Locomotion distance, session 30.80.91.60.91.3-0.5
Stereotopy head waving bouts, day 30.30.30.8-0.40.1-0.9
Stereotopy head waving duration, day 31.31.62.70.81.2-1.6
Locomotion velocity, session 72.12.34.1-1.2-1.22.0
Locomotion distance, session 73.34.25.0-1.8-2.12.2
Stereotopy head waving bouts, day 72.52.83.91.52.0-1.5
Stereotopy head waving duration, day 74.15.06.21.92.5-2.3
Locomotion velocity, session 80.10.10.3-0.00.10.6
Locomotion distance, session 80.91.31.8-0.8-1.11.4
Degree of sensitization distance8.68.79.6-2.7-3.13.0
Degree of sensitization stereotypy2.12.33.91.52.0-1.0
Condit. Reinf. active minus inactive responses0.40.40.50.60.7-0.7
Condit. Reinf. active-inactive response ratio0.00.00.1-0.10.1-0.3
Condit. Reinf. active responses0.40.40.50.70.6-0.6
Condit. Reinf. inactive responses0.10.10.20.30.0-0.5
Incentive salience index mean1.72.12.41.51.5-1.2
Condit. Reinf. lever presses2.02.63.41.91.7-1.2
Time in familiar zone, hab. session 10.60.61.3-0.4-0.51.1
Time in novel zone, hab. session 11.81.82.71.31.6-1.0
Total zone transitions, hab. session 10.20.30.60.80.50.2
Total locomotion distance, hab. session 10.10.10.20.2-0.20.5
Locomotion velocity, hab. session 10.10.10.20.2-0.40.1
Time in familiar zone, hab. session 20.20.20.2-0.4-0.50.5
Time in novel zone, hab. session 20.00.00.10.10.30.0
Total zone transitions, hab. session 20.20.30.40.60.4-0.6
Total locomotion distance, hab. session 20.00.00.10.3-0.10.1
Locomotion velocity, hab. session 20.10.10.30.60.2-0.1
Novel to familiar place preference ratio0.50.51.0-0.5-0.71.0
Novelty place preference0.40.40.7-0.5-0.60.8
Time in novel zone, NPP test0.20.20.4-0.3-0.50.6
Total zone transitions, NPP test0.00.00.1-0.0-0.30.1
Total locomotion distance, NPP test1.52.13.9-1.4-2.00.8
Locomotion velocity, NPP test1.62.34.0-1.4-2.00.9
Pavlov. Cond. lever latency0.70.91.2-1.1-1.10.5
Pavlov. Cond. magazine entry latency0.91.11.40.91.2-1.0
Pavlov. Cond. change in total contacts2.52.63.71.91.8-1.0
Pavlov. Cond. index score2.73.54.02.02.0-1.6
Pavlov. Cond. latency score2.02.53.01.71.7-1.3
Pavlov. Cond. lever contacts1.51.82.01.41.4-1.2
Pavlov. Cond. magazine entry number2.02.53.0-1.6-1.71.4
Pavlov. Cond. intertrial magazine entries0.20.20.30.0-0.6-0.5
Pavlov. Cond. lever-magazine prob. diff.3.34.24.92.22.2-1.7
Pavlov. Cond. response bias2.83.54.11.92.0-1.6
Bone: apparent density0.40.71.2-1.0-1.1-0.1
Bone surface0.20.30.4-0.6-0.6-0.1
Bone volume0.10.10.2-0.3-0.40.2
Bone: connectivity density1.42.23.3-1.8-1.8-0.4
Bone: cortical apparent density0.10.10.30.40.50.1
Bone: cortical area1.01.52.11.51.50.5
Bone: cortical porosity2.42.63.11.81.7-1.3
Bone: cortical porosity1.92.02.51.51.6-1.0
Bone: cortical thickness1.72.74.22.02.00.2
Bone: cortical thickness1.82.13.81.21.12.0
Bone: cortical tissue density0.10.10.20.30.50.1
Bone: elastic displacement0.00.10.1-0.4-0.1-0.0
Bone: elastic work0.60.80.90.91.0-0.8
Bone: endosteal estimation0.00.10.1-0.3-0.20.2
Bone: endosteal perimeter0.20.50.8-0.9-0.70.4
Bone: final force1.01.62.51.51.60.0
Bone: final moment0.91.52.41.51.5-0.3
Bone: marrow area0.10.10.1-0.4-0.30.3
Bone: maximum diameter0.50.91.10.81.00.9
Bone: maximum force1.22.13.21.81.80.1
Bone: maximum moment1.12.03.01.71.7-0.2
Bone: minimum diameter0.40.71.10.91.00.3
Bone: periosteal estimation0.10.30.30.50.50.6
Bone: periosteal perimeter0.10.10.20.00.10.5
Bone: post-yield work1.92.67.70.20.12.8
Bone: stiffness0.81.32.01.41.4-0.3
Bone: tissue strength0.10.10.2-0.5-0.1-0.2
Bone: trabecular number0.61.01.5-1.2-1.20.1
Bone: trabecular spacing1.72.23.41.91.7-0.3
Bone: trabecular thickness0.20.30.50.70.5-0.3
Bone: trabecular tissue density1.82.63.41.91.7-1.2
Breakpoint value in progressive ratio session0.60.71.10.71.10.6
Distance traveled before self-admin0.10.10.2-0.5-0.2-0.2
Distance traveled after self-admin0.00.00.1-0.3-0.20.1
Delta time in closed arm before/after self-admin0.90.91.6-1.0-1.30.3
Delta time in open arm before/after self-admin0.00.00.1-0.00.00.2
Diff in mean of infusions in LGA sessions5.86.58.42.62.9-2.1
Extinction: sum of active levers before priming0.20.30.3-0.5-0.50.6
Active lever presses in extinction session 60.70.70.7-0.8-0.80.9
Delta distance traveled before/after self-admin0.10.10.30.50.4-0.1
Delta ambulatory time before/after self-admin0.10.10.10.30.20.3
Time in closed arm before self-admin3.23.63.91.81.9-2.0
Time in closed arm after self-admin0.60.71.40.60.4-1.2
Time in open arm before self-admin1.21.21.6-1.2-1.20.9
Time in open arm after self-admin0.40.40.6-0.7-0.80.4
Sum of active levers in priming session hrs 5-60.80.81.0-0.9-0.81.0
Time to tail flick, vehicle, before self-admin1.81.82.21.31.2-1.5
Time to tail flick, vehicle, after self-admin1.51.62.41.21.6-1.0
Time to tail flick, test, before self-admin0.40.41.10.20.4-1.0
Time to tail flick, test, after self-admin4.44.56.2-2.5-2.41.2
Delta time to tail flick, vehicle, before/after SA0.40.40.5-0.7-0.50.6
Delta time to tail flick, test, before/after SA5.04.55.5-2.3-2.31.6
Ambulatory time before self-admin0.00.00.1-0.3-0.00.1
Ambulatory time after self-admin0.20.20.40.50.7-0.2
Total heroin consumption0.50.60.80.80.9-0.6
Area under the delay curve4.85.28.02.72.8-0.2
Delay disc. indifference point, 0s delay0.10.10.30.30.20.5
Delay disc. indifference point, 16s delay2.52.53.81.91.9-0.1
Delay disc. indifference point, 2s delay0.70.81.21.11.10.0
Delay disc. indifference point, 24s delay3.33.24.92.12.20.5
Delay disc. indifference point, 4s delay3.43.65.32.22.3-0.8
Delay disc. indifference point, 8s delay6.87.111.53.03.4-0.7
Delay discount exponential model param5.55.99.3-2.9-3.00.3
Delay discount hyperbolic model param5.76.09.5-2.9-3.10.5
Fecal boli incidents, locomotor time 10.50.50.80.80.90.3
Change in fecal boli incidents, locomotor task0.20.20.3-0.3-0.2-0.5
Time >=10cm from walls, locomotor time 10.40.51.2-0.1-0.3-1.1
Bouts of movement, locomotor time 10.10.10.4-0.1-0.10.7
Total resting periods, locomotor time 10.50.51.5-0.3-0.31.2
Rest time, locomotor task time 10.10.10.30.10.20.6
Distance moved, locomotor task time 10.20.20.4-0.5-0.6-0.1
Vertical activity count, locomotor time 10.40.41.10.2-0.1-1.0
Time >=10cm from walls, locomotor time 20.40.40.8-0.5-0.4-0.9
Bouts of movement, locomotor time 21.92.03.61.51.90.2
Total resting periods, locomotor time 22.42.54.41.82.10.1
Rest time, locomotor task time 21.21.42.11.41.50.5
Distance moved, locomotor task time 20.80.91.4-1.1-1.2-0.2
Vertical activity count, locomotor time 20.30.30.5-0.5-0.6-0.7
Weight adjusted by age2.22.55.01.21.0-2.2
Seeking ratio, delayed vs. immediate footshock0.10.10.2-0.2-0.4-0.2
Locomotion in novel chamber0.91.21.31.11.1-1.0
Locomotion in novel chamber post-restriction0.10.10.20.5-0.10.4
Progressive ratio1.31.62.31.11.0-1.5
Food seeking constrained by brief footshock0.30.40.5-0.6-0.40.7
Seeking ratio, punishment vs. effort0.70.81.5-0.8-0.51.2
Run reversals in cocaine runway, females0.80.81.2-1.1-1.1-0.2
Run reversals in cocaine runway, males2.42.33.51.71.9-0.6
Latency to leave start box in cocaine runway1.21.31.8-1.2-1.30.8
Latency to leave start box in cocaine runway, F0.20.30.6-0.4-0.80.2
Latency to leave start box in cocaine runway, M1.01.01.6-1.3-1.10.1
Cd content in liver0.20.20.5-0.7-0.3-0.2
Co content in liver0.81.01.50.91.20.7
Cu content in liver0.30.30.40.50.6-0.6
Fe content in liver0.80.91.6-1.0-1.3-0.1
K content in liver0.40.40.8-0.5-0.40.9
Mg content in liver0.70.81.1-1.0-0.70.9
Mn content in liver1.41.62.1-1.2-1.21.4
Na content in liver6.26.68.22.62.3-2.9
Rb content in liver0.81.01.6-1.3-1.20.4
Se content in liver0.10.10.4-0.2-0.1-0.6
Sr content in liver1.51.42.2-1.5-1.4-0.0
Zn content in liver2.42.64.41.21.4-2.1