Hub : Genes

Sox6

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	ENSRNOG00000020514	0.03	0.03	7.1e-04	0.01	0.01	0.01	0.01	1.4e-02	3.0e-02	4e-02	4.8e-02
2	Liver	intron excision ratio	chr1:169943000:170010640	0.2	0.12	4.2e-03	0.01	0	0	0	2.2e-02	2.1e-01	8e-02	1.1e-01

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
BMI with tail	6.5	21.2	21.5	-4.6	4.6
BMI without tail	11.5	24.1	24.3	-4.9	4.9
Body weight	5.4	23.0	23.1	-4.8	4.8
Epididymis fat weight	1.8	4.1	4.4	-2.1	2.0
Glucose	0.0	0.0	0.0	0.2	-0.1
Heart weight	0.2	0.3	0.3	-0.5	0.6
Left kidney weight	8.0	22.9	23.1	-4.8	4.8
Right kidney weight	9.2	26.3	26.7	-5.1	5.2
Tail length	2.6	7.9	8.1	-2.8	2.8
Length with tail	1.1	4.0	4.1	-2.0	2.0
Length without tail	0.1	0.3	0.3	0.5	-0.5
Liver weight, left	3.1	5.0	5.1	-2.2	2.3
Liver weight, right	4.3	7.2	7.4	-2.7	2.7
Parametrial fat weight	10.4	20.4	20.7	-4.5	4.5
Retroperitoneal fat weight	2.9	9.7	9.8	-3.1	3.1
Intraocular pressure	0.3	0.4	0.5	-0.6	0.7
Extensor digitorum longus weight	2.8	11.1	11.6	-3.3	3.4
Soleus weight	1.3	3.6	4.0	-1.8	2.0
Tibialis anterior weight	4.5	15.6	16.0	-3.9	4.0
Tibia length	0.1	0.1	0.1	-0.4	0.4
Number of licking bursts	6.4	7.5	7.7	2.8	-2.7
Food consumed during 24 hour testing period	0.0	0.0	0.0	-0.1	0.0
Times rat made contact with spout	0.6	0.7	0.7	0.8	-0.8
Mean time between licks in bursts	1.4	1.9	2.0	-1.4	1.3
Mean num. licks in bursts	3.2	3.8	3.9	-2.0	1.9
Std. dev. time between licks in bursts	3.1	3.7	3.8	-1.9	1.9
Water consumed over 24 hours	3.9	4.6	4.6	2.1	-2.1
Indifference point 0 sec	0.0	0.1	0.1	-0.3	0.2
Indifference point AUC	1.3	1.5	1.5	-1.2	1.2
Indifference point function ln k	0.0	0.1	0.1	-0.3	0.2
Indifference point function log k	0.0	0.1	0.1	-0.3	0.2
Delay discounting total patch changes 0 sec	0.2	0.3	0.4	-0.6	0.5
Delay discounting total patch changes 12 sec	0.1	0.1	0.1	0.3	-0.3
Delay discounting total patch changes 18 sec	0.0	0.1	0.1	0.2	-0.3
Delay discounting total patch changes 24 sec	0.5	0.6	0.6	-0.8	0.8
Delay discounting total patch changes 6 sec	0.2	0.3	0.4	0.5	-0.6
Delay discounting time to switch 0 sec	4.3	6.6	6.6	2.6	-2.6
Delay discounting water rate 0 sec	1.0	1.5	1.5	-1.2	1.2
Delay discounting water rate 12 sec	5.4	8.1	8.5	-2.9	2.8
Delay discounting water rate 18 sec	2.6	3.4	3.5	-1.9	1.8
Delay discounting water rate 24 sec	0.4	0.6	0.6	-0.8	0.7
Delay discounting water rate 6 sec	0.5	0.7	0.7	-0.8	0.8
Locomotor activity	0.5	0.8	0.8	-0.9	0.9
Locomotor testing distance	0.1	0.2	0.2	-0.4	0.4
Locomotor testing rearing	0.1	0.1	0.1	-0.4	0.4
Light reinforcement 1	0.7	1.2	1.2	1.1	-1.1
Light reinforcement 2	0.3	0.4	0.4	0.6	-0.6
Reaction time number correct	0.3	0.5	0.5	-0.6	0.7
Reaction time mean minus median	0.7	0.9	0.9	-1.0	0.9
Reaction time mean minus median AUC	1.0	1.3	1.4	-1.2	1.1
Reaction time num false alarms	0.2	0.3	0.4	0.6	-0.5
Reaction time num false alarms AUC	0.0	0.0	0.1	0.3	-0.2
Reaction time trials correct on left	0.3	0.5	0.5	-0.6	0.7
Reaction time trials on left	0.4	0.5	0.5	-0.7	0.7
Reaction time mean	0.1	0.2	0.2	-0.5	0.4
Reaction time mean AUC	0.1	0.1	0.1	-0.3	0.2
Median of all reaction times	0.0	0.0	0.0	-0.1	0.0
Reaction time omissions	0.0	0.0	0.0	-0.2	0.1
Reaction time false alarm rate	0.4	0.5	0.6	0.7	-0.7
Reaction time premature initiation rate	0.0	0.0	0.1	-0.1	0.2
Reaction time premature initiations	0.1	0.1	0.2	-0.3	0.4
Std. dev. reaction times	0.8	1.1	1.2	-1.1	1.0
Reaction time trials completed	0.4	0.5	0.5	-0.7	0.7
Reaction time trials AUC	0.5	0.7	0.7	-0.8	0.9
Social response proportion	0.9	1.0	1.0	-1.0	1.0
Social responses	0.4	0.6	0.6	0.7	-0.8
Social time	0.3	0.4	0.4	0.6	-0.7
Conditioned locomotion	0.2	0.2	0.2	0.5	-0.4
Cocaine response after cond. corrected	0.5	0.6	0.6	0.7	-0.8
Cocaine response after cond. not corrected	0.4	0.4	0.5	-0.7	0.6
Cocaine response before conditioning	5.8	7.1	7.1	-2.7	2.7
Saline control response	0.6	0.7	0.8	-0.8	0.9
Condit. Reinf. active minus inactive responses	1.3	1.6	1.7	-1.3	1.2
Condit. Reinf. active-inactive response ratio	0.7	0.7	0.7	-0.9	0.8
Condit. Reinf. active responses	1.2	1.7	1.8	-1.3	1.3
Condit. Reinf. inactive responses	1.0	1.2	1.2	-1.1	1.1
Condit. Reinf. lever presses	3.6	5.0	5.0	-2.2	2.2
Condit. Reinf. lever reinforcers received	1.0	1.4	1.5	-1.2	1.1
Pavlov. Cond. lever latency	1.8	2.5	2.5	1.6	-1.5
Pavlov. Cond. magazine entry latency	0.0	0.0	0.0	-0.1	0.1
Pavlov. Cond. change in total contacts	0.5	0.7	0.8	-0.9	0.8
Pavlov. Cond. index score	0.6	0.8	0.8	-0.9	0.9
Pavlov. Cond. latency score	0.5	0.7	0.7	-0.8	0.8
Pavlov. Cond. lever contacts	3.4	4.7	4.8	-2.2	2.1
Pavlov. Cond. magazine entry number	0.4	0.4	0.4	-0.7	0.7
Pavlov. Cond. intertrial magazine entries	8.1	10.4	10.7	-3.2	3.3
Pavlov. Cond. lever-magazine prob. diff.	0.5	0.7	0.7	-0.8	0.8
Pavlov. Cond. response bias	1.3	1.9	1.9	-1.4	1.3
Conditioned reinforcement - actives	0.4	0.4	0.4	0.6	-0.7
Conditioned reinforcement - inactives	1.0	1.1	1.3	1.0	-1.1
Conditioned locomotion	1.2	1.5	1.5	1.2	-1.2
Intermittent access intake day 1-15 change	0.8	0.8	0.8	0.9	-0.9
Intermittent access intake escalation	0.5	0.5	0.5	0.7	-0.7
Intermittent access intake escalation 2	0.1	0.1	0.2	0.3	-0.4
Intermitt. access day 1 inactive lever presses	0.1	0.1	0.1	0.2	-0.4
Intermitt. access day 15 inactive lever presses	0.5	0.5	0.6	0.8	-0.7
Intermitt. access escalation Index	2.7	2.5	2.6	-1.5	1.6
Intermittent access day 1 total infusions	0.2	0.3	0.3	-0.4	0.6
Intermittent access day 15 total infusions	0.0	0.0	0.0	0.1	0.0
Intermittent access terminal intake (last 3 days)	0.1	0.1	0.1	-0.1	0.3
Intermittent access total infusions	0.2	0.2	0.2	-0.4	0.5
Intermittent access day 1 locomotion	0.7	0.7	0.9	-0.8	0.9
Intermittent access day 15 total locomotion	0.3	0.3	0.3	-0.5	0.6
Intermittent access total locomotion	0.7	0.8	0.9	-0.8	1.0
Intermittent access standard deviation	0.4	0.4	0.5	-0.7	0.6
Cocaine induced anxiety	1.4	1.6	1.6	-1.2	1.2
Post-drug Anxiety	0.4	0.4	0.4	-0.7	0.7
Baseline Anxiety	1.6	1.7	1.7	1.3	-1.3
Lifetime Intake	0.5	0.5	0.6	-0.7	0.8
Incentive Sensitization - Responses	0.7	0.7	0.7	0.8	-0.8
Incentive Sensitization - Breakpoint	0.7	0.7	0.7	0.8	-0.8
Progressive ratio test 1 active lever presses	0.1	0.2	0.2	-0.4	0.4
Progressive ratio test 1 breakpoint	0.3	0.3	0.3	-0.6	0.5
Progressive ratio test 1 inactive lever presses	0.3	0.4	0.5	-0.7	0.5
Progressive ratio test 2 active lever presses	0.0	0.0	0.0	0.0	-0.0
Progressive ratio test 2 breakpoint	0.0	0.0	0.0	-0.0	0.0
Progressive ratio test 2 inactive lever presses	0.1	0.1	0.1	0.2	-0.3
Total sessions with >9 infusions	0.5	0.6	0.6	-0.8	0.8
Short access day 1 total inactive lever presses	0.2	0.2	0.3	0.3	-0.5
Short access day 10 total inactive lever presses	0.7	0.8	0.9	0.8	-0.9
Short access day 1 total infusions	0.3	0.3	0.3	-0.6	0.6
Short access day 10 total infusions	0.1	0.1	0.1	-0.3	0.3
Short access total infusions	1.0	1.1	1.1	-1.1	1.1
Short access day 1 locomotion	0.1	0.1	0.1	0.3	-0.3
Short access day 10 total locomotion	1.9	2.1	2.1	-1.4	1.4
Short access total locomotion	1.9	1.9	1.9	-1.4	1.4
Compulsive drug intake	1.8	1.8	2.0	-1.3	1.4
One hour access (0.3 mA shock)	1.5	1.8	1.9	-1.3	1.4
One hour access (shock baseline)	0.1	0.1	0.1	0.4	-0.4
Number of responses in last shaping day	0.0	0.0	0.0	-0.1	0.2
Context. condit. distance diff. score	0.8	0.9	0.9	1.0	-1.0
Locomotion velocity, session 1	3.4	3.6	3.7	1.9	-1.9
Locomotion distance, session 1	0.0	0.1	0.1	0.2	-0.2
Locomotion velocity, session 2	4.0	4.7	4.9	2.1	-2.2
Locomotion distance, session 2	0.0	0.1	0.1	0.3	-0.2
Locomotion velocity, session 3	0.0	0.0	0.0	0.0	0.0
Locomotion distance, session 3	0.0	0.0	0.0	0.0	0.1
Stereotopy head waving bouts, day 3	1.4	1.7	1.8	1.3	-1.3
Stereotopy head waving duration, day 3	1.7	2.1	2.2	1.4	-1.5
Locomotion velocity, session 7	0.1	0.1	0.2	0.4	-0.3
Locomotion distance, session 7	0.8	1.0	1.1	1.1	-1.0
Stereotopy head waving bouts, day 7	0.5	0.5	0.6	0.7	-0.8
Stereotopy head waving duration, day 7	0.1	0.1	0.2	-0.4	0.3
Locomotion velocity, session 8	1.7	2.0	2.2	1.5	-1.4
Locomotion distance, session 8	0.9	1.4	1.4	1.2	-1.2
Degree of sensitization distance	0.6	0.6	0.6	0.7	-0.8
Degree of sensitization stereotypy	0.1	0.1	0.1	0.2	-0.3
Condit. Reinf. active minus inactive responses	0.2	0.2	0.2	-0.4	0.4
Condit. Reinf. active-inactive response ratio	1.0	1.1	1.1	-1.0	1.0
Condit. Reinf. active responses	0.0	0.0	0.0	-0.1	0.1
Condit. Reinf. inactive responses	0.0	0.0	0.0	-0.2	0.2
Incentive salience index mean	0.3	0.4	0.4	-0.7	0.6
Condit. Reinf. lever presses	0.0	0.0	0.0	-0.1	0.0
Time in familiar zone, hab. session 1	0.3	0.3	0.3	0.5	-0.5
Time in novel zone, hab. session 1	0.2	0.1	0.2	-0.4	0.4
Total zone transitions, hab. session 1	0.1	0.2	0.2	-0.3	0.5
Total locomotion distance, hab. session 1	0.5	0.7	0.8	-0.8	0.9
Locomotion velocity, hab. session 1	0.6	0.8	0.9	-0.8	1.0
Time in familiar zone, hab. session 2	0.4	0.4	0.5	-0.7	0.7
Time in novel zone, hab. session 2	0.0	0.0	0.0	0.0	-0.1
Total zone transitions, hab. session 2	0.2	0.3	0.3	-0.5	0.6
Total locomotion distance, hab. session 2	0.0	0.0	0.0	-0.2	0.2
Locomotion velocity, hab. session 2	0.0	0.0	0.0	-0.2	0.2
Novel to familiar place preference ratio	0.2	0.2	0.3	0.5	-0.4
Novelty place preference	0.4	0.5	0.5	0.7	-0.6
Time in novel zone, NPP test	0.3	0.3	0.3	0.6	-0.5
Total zone transitions, NPP test	0.0	0.1	0.1	-0.2	0.2
Total locomotion distance, NPP test	0.0	0.1	0.1	0.2	-0.2
Locomotion velocity, NPP test	0.0	0.0	0.0	0.2	-0.2
Pavlov. Cond. lever latency	1.7	2.2	2.2	1.5	-1.5
Pavlov. Cond. magazine entry latency	6.7	8.7	8.8	-3.0	2.9
Pavlov. Cond. change in total contacts	2.5	2.6	2.7	-1.6	1.6
Pavlov. Cond. index score	5.0	6.4	6.6	-2.6	2.5
Pavlov. Cond. latency score	4.8	6.2	6.3	-2.5	2.5
Pavlov. Cond. lever contacts	3.3	3.9	3.9	-2.0	2.0
Pavlov. Cond. magazine entry number	4.2	5.2	5.4	2.3	-2.3
Pavlov. Cond. intertrial magazine entries	0.4	0.4	0.5	0.6	-0.7
Pavlov. Cond. lever-magazine prob. diff.	5.7	7.1	7.3	-2.7	2.6
Pavlov. Cond. response bias	3.5	4.3	4.3	-2.1	2.1
Bone: apparent density	0.6	0.9	1.0	-0.9	1.0
Bone surface	0.8	1.4	1.5	-1.2	1.2
Bone volume	0.9	1.5	1.6	-1.2	1.3
Bone: connectivity density	0.9	1.4	1.5	-1.1	1.2
Bone: cortical apparent density	2.5	3.3	3.7	1.9	-1.7
Bone: cortical area	1.6	2.4	2.5	-1.6	1.5
Bone: cortical porosity	2.3	2.5	2.8	-1.5	1.7
Bone: cortical porosity	1.2	1.3	1.4	-1.1	1.2
Bone: cortical thickness	0.0	0.1	0.1	-0.2	0.3
Bone: cortical thickness	0.1	0.1	0.1	0.3	-0.4
Bone: cortical tissue density	2.6	3.3	3.8	1.9	-1.7
Bone: elastic displacement	3.9	4.4	4.6	2.2	-2.0
Bone: elastic work	0.4	0.5	0.6	0.7	-0.7
Bone: endosteal estimation	1.6	3.4	4.0	-2.0	1.7
Bone: endosteal perimeter	0.9	1.8	2.2	-1.5	1.2
Bone: final force	1.7	2.8	2.9	-1.7	1.7
Bone: final moment	1.4	2.2	2.2	-1.5	1.5
Bone: marrow area	1.5	3.1	3.7	-1.9	1.6
Bone: maximum diameter	2.2	4.0	4.6	-2.1	1.9
Bone: maximum force	1.3	2.3	2.4	-1.5	1.5
Bone: maximum moment	1.0	1.8	1.9	-1.4	1.3
Bone: minimum diameter	0.6	1.1	1.3	-1.2	1.0
Bone: periosteal estimation	2.0	4.1	4.7	-2.2	1.9
Bone: periosteal perimeter	2.2	3.7	4.2	-2.0	1.8
Bone: post-yield work	4.8	6.5	6.9	-2.6	2.5
Bone: stiffness	0.9	1.4	1.4	-1.2	1.2
Bone: tissue strength	0.1	0.1	0.1	0.3	-0.2
Bone: trabecular number	0.0	0.0	0.0	-0.0	0.2
Bone: trabecular spacing	0.3	0.4	0.5	-0.7	0.5
Bone: trabecular thickness	0.8	0.9	1.0	-1.0	0.9
Bone: trabecular tissue density	0.3	0.5	0.5	0.7	-0.7
Breakpoint value in progressive ratio session	4.9	5.5	5.5	2.3	-2.3
Distance traveled before self-admin	1.1	1.2	1.2	1.1	-1.1
Distance traveled after self-admin	0.0	0.0	0.0	0.0	-0.0
Delta time in closed arm before/after self-admin	0.2	0.2	0.2	0.4	-0.4
Delta time in open arm before/after self-admin	3.1	3.0	3.0	-1.7	1.7
Diff in mean of infusions in LGA sessions	0.5	0.6	0.6	0.8	-0.7
Extinction: sum of active levers before priming	0.3	0.3	0.3	0.6	-0.5
Active lever presses in extinction session 6	0.2	0.1	0.2	-0.4	0.4
Delta distance traveled before/after self-admin	1.0	1.1	1.1	-1.0	1.0
Delta ambulatory time before/after self-admin	0.5	0.6	0.6	-0.7	0.8
Time in closed arm before self-admin	0.7	0.8	0.8	-0.9	0.9
Time in closed arm after self-admin	0.7	0.7	0.7	0.8	-0.9
Time in open arm before self-admin	0.6	0.6	0.6	0.8	-0.8
Time in open arm after self-admin	2.3	2.6	2.6	-1.6	1.6
Sum of active levers in priming session hrs 5-6	0.0	0.0	0.0	-0.1	0.1
Time to tail flick, vehicle, before self-admin	0.7	0.7	0.7	-0.8	0.8
Time to tail flick, vehicle, after self-admin	0.7	0.8	0.8	0.9	-0.9
Time to tail flick, test, before self-admin	0.0	0.0	0.0	0.1	-0.1
Time to tail flick, test, after self-admin	0.0	0.0	0.0	-0.1	0.0
Delta time to tail flick, vehicle, before/after SA	0.1	0.1	0.1	0.3	-0.3
Delta time to tail flick, test, before/after SA	0.3	0.2	0.3	-0.5	0.5
Ambulatory time before self-admin	2.1	2.2	2.2	1.5	-1.5
Ambulatory time after self-admin	0.2	0.2	0.2	0.5	-0.4
Total heroin consumption	1.6	1.9	2.0	1.4	-1.4
Area under the delay curve	0.5	0.5	0.5	0.7	-0.7
Delay disc. indifference point, 0s delay	0.1	0.1	0.2	0.3	-0.4
Delay disc. indifference point, 16s delay	4.8	4.9	4.9	2.2	-2.2
Delay disc. indifference point, 2s delay	0.5	0.5	0.6	-0.8	0.7
Delay disc. indifference point, 24s delay	2.3	2.2	2.4	1.5	-1.5
Delay disc. indifference point, 4s delay	0.5	0.5	0.6	0.7	-0.8
Delay disc. indifference point, 8s delay	1.2	1.3	1.3	1.1	-1.1
Delay discount exponential model param	0.4	0.4	0.5	-0.6	0.7
Delay discount hyperbolic model param	0.3	0.3	0.3	-0.5	0.6
Fecal boli incidents, locomotor time 1	0.0	0.0	0.1	0.1	-0.2
Change in fecal boli incidents, locomotor task	0.0	0.0	0.0	0.1	-0.1
Time >=10cm from walls, locomotor time 1	0.8	0.8	0.9	0.9	-0.8
Bouts of movement, locomotor time 1	0.0	0.0	0.0	0.1	-0.1
Total resting periods, locomotor time 1	0.3	0.4	0.4	0.6	-0.6
Rest time, locomotor task time 1	4.3	4.7	5.0	2.2	-2.1
Distance moved, locomotor task time 1	2.2	2.4	2.4	-1.6	1.5
Vertical activity count, locomotor time 1	0.1	0.1	0.1	-0.4	0.3
Time >=10cm from walls, locomotor time 2	0.1	0.1	0.2	-0.3	0.4
Bouts of movement, locomotor time 2	0.4	0.5	0.5	-0.7	0.7
Total resting periods, locomotor time 2	0.7	0.7	0.7	-0.8	0.9
Rest time, locomotor task time 2	1.1	1.3	1.3	1.2	-1.1
Distance moved, locomotor task time 2	0.0	0.0	0.0	0.2	-0.1
Vertical activity count, locomotor time 2	0.8	0.9	0.9	0.9	-1.0
Weight adjusted by age	1.1	1.2	1.2	-1.1	1.1
Seeking ratio, delayed vs. immediate footshock	0.0	0.0	0.0	-0.1	0.1
Locomotion in novel chamber	5.3	6.6	6.7	-2.5	2.6
Locomotion in novel chamber post-restriction	0.3	0.4	0.4	-0.6	0.6
Progressive ratio	0.0	0.0	0.0	-0.1	-0.0
Food seeking constrained by brief footshock	0.5	0.6	0.7	0.7	-0.8
Seeking ratio, punishment vs. effort	0.0	0.0	0.0	-0.0	0.1
Run reversals in cocaine runway, females	1.9	1.9	2.2	-1.5	1.3
Run reversals in cocaine runway, males	2.6	2.5	2.7	1.6	-1.6
Latency to leave start box in cocaine runway	0.2	0.3	0.4	0.6	-0.3
Latency to leave start box in cocaine runway, F	0.1	0.1	0.1	0.1	0.3
Latency to leave start box in cocaine runway, M	2.3	2.2	2.2	1.5	-1.5
Cd content in liver	1.0	1.1	1.1	1.0	-1.0
Co content in liver	1.8	2.1	2.1	1.4	-1.5
Cu content in liver	0.1	0.2	0.2	-0.4	0.4
Fe content in liver	1.7	2.0	2.1	1.4	-1.4
K content in liver	1.6	1.5	1.6	-1.3	1.2
Mg content in liver	0.7	0.8	0.8	-0.9	0.9
Mn content in liver	1.0	1.1	1.1	-1.1	1.1
Na content in liver	1.6	1.7	1.7	-1.3	1.3
Rb content in liver	0.1	0.1	0.1	-0.3	0.3
Se content in liver	0.4	0.4	0.4	-0.7	0.7
Sr content in liver	2.4	2.2	2.2	-1.5	1.5
Zn content in liver	1.1	1.3	1.3	-1.1	1.1