Hub : Traits

Bone: trabecular tissue density

Tags: Physiology · Bone

Project: r01_doug_adams

6 significantly associated models · 3 unique genes

Significant Loci

# chr p0 p1 # assoc genes # joint models best TWAS P best SNP P cond SNP P % var exp joint genes
1 5 63138533 64537015 1 1 3.3e-07 3.3e-03 0.019 37 Acnat1
2 5 113826986 115224581 1 1 8.5e-08 2.9e-07 0.666 99 Itgb3bp
3 7 16845355 16970279 1 1 4.6e-22 NaN NA NA NA

p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.

Pleiotropic Associations

Trait chisq ratio # genes+ # genes++ % genes++ corr corr P genes
BMI without tail 106.7 1 1 33 0.00 1.0000 NA
Body weight 7.7 1 1 33 0.00 1.0000 NA
Epididymis fat weight 59.5 2 1 33 0.00 1.0000 Itgb3bp NA
Glucose 6.6 1 0 0 0.00 1.0000 NA
Heart weight 11.4 1 0 0 0.00 1.0000 NA
Left kidney weight 37.5 1 1 33 0.00 1.0000 NA
Right kidney weight 41.9 1 1 33 0.00 1.0000 NA
Tail length 58.1 1 1 33 0.00 1.0000 NA
Length with tail 2.8 2 0 0 0.00 1.0000 NA Acnat1
Length without tail 71.1 1 1 33 0.00 1.0000 NA
Liver weight, left 23.6 1 1 33 0.00 1.0000 NA
Liver weight, right 6.9 2 0 0 0.97 0.0261 Itgb3bp NA
Parametrial fat weight 9.5 2 1 33 0.11 0.8868 Itgb3bp NA
Retroperitoneal fat weight 3.2 2 0 0 0.00 1.0000 NA Acnat1
Intraocular pressure 19.0 1 1 33 0.00 1.0000 NA
Extensor digitorum longus weight 25.8 1 1 33 0.00 1.0000 NA
Soleus weight 13.7 1 1 33 0.00 1.0000 NA
Tibialis anterior weight 29.3 2 2 67 0.43 0.4679 Itgb3bp NA
Tibia length 3.8 2 0 0 -0.19 0.7645 Itgb3bp NA
Number of licking bursts 155.0 1 1 33 0.00 1.0000 NA
Food consumed during 24 hour testing period 17.5 1 0 0 0.00 1.0000 NA
Times rat made contact with spout 75.1 1 1 33 0.00 1.0000 NA
Mean time between licks in bursts 31.0 2 1 33 0.96 0.0367 Itgb3bp NA
Mean num. licks in bursts 164.2 1 1 33 0.00 1.0000 NA
Std. dev. time between licks in bursts 177.7 1 1 33 0.00 1.0000 NA
Indifference point 0 sec 12.7 2 1 33 -0.99 0.0011 Itgb3bp NA
Indifference point AUC 42.1 1 1 33 0.00 1.0000 NA
Delay discounting total patch changes 0 sec 12.0 2 1 33 -0.99 0.0012 Itgb3bp NA
Delay discounting total patch changes 12 sec 102.7 1 1 33 0.00 1.0000 NA
Delay discounting total patch changes 18 sec 175.3 1 1 33 0.00 1.0000 NA
Delay discounting total patch changes 24 sec 28.3 1 1 33 0.00 1.0000 NA
Delay discounting total patch changes 6 sec 51.7 2 1 33 -0.96 0.0431 Itgb3bp NA
Delay discounting water rate 0 sec 8.1 1 0 0 0.00 1.0000 NA
Delay discounting water rate 12 sec 19.0 2 1 33 0.00 1.0000 Itgb3bp NA
Delay discounting water rate 18 sec 10.5 1 0 0 0.00 1.0000 NA
Delay discounting water rate 24 sec 62.7 1 1 33 0.00 1.0000 NA
Delay discounting water rate 6 sec 44.2 1 1 33 0.00 1.0000 NA
Locomotor testing distance 11.5 1 0 0 0.00 1.0000 NA
Locomotor testing rearing 16.8 1 1 33 0.00 1.0000 NA
Light reinforcement 1 54.8 1 1 33 0.00 1.0000 NA
Reaction time number correct 9.4 1 0 0 0.00 1.0000 NA
Reaction time num false alarms 56.4 1 1 33 0.00 1.0000 NA
Reaction time num false alarms AUC 55.1 2 1 33 0.00 1.0000 NA Acnat1
Reaction time trials correct on left 9.4 1 0 0 0.00 1.0000 NA
Reaction time trials on left 10.3 1 0 0 0.00 1.0000 NA
Reaction time mean 41.3 1 1 33 0.00 1.0000 NA
Reaction time mean AUC 58.0 1 1 33 0.00 1.0000 NA
Median of all reaction times 51.2 1 1 33 0.00 1.0000 NA
Reaction time omissions 6.6 1 0 0 0.00 1.0000 Acnat1
Reaction time false alarm rate 44.1 2 1 33 0.00 1.0000 NA Acnat1
Reaction time premature initiation rate 32.1 1 1 33 0.00 1.0000 NA
Reaction time premature initiations 34.3 1 1 33 0.00 1.0000 NA
Std. dev. reaction times 17.4 1 1 33 0.00 1.0000 NA
Reaction time trials completed 10.3 1 0 0 0.00 1.0000 NA
Reaction time trials AUC 15.6 1 0 0 0.00 1.0000 NA
Social responses 51.8 2 1 33 0.00 1.0000 NA Acnat1
Social time 7.8 1 0 0 0.00 1.0000 NA
Cocaine response after cond. corrected 78.0 1 1 33 0.00 1.0000 NA
Cocaine response after cond. not corrected 102.3 1 1 33 0.00 1.0000 NA
Cocaine response before conditioning 17.4 1 1 33 0.00 1.0000 NA
Saline control response 30.3 1 1 33 0.00 1.0000 NA
Condit. Reinf. active minus inactive responses 29.4 1 1 33 0.00 1.0000 NA
Condit. Reinf. active-inactive response ratio 40.7 1 1 33 0.00 1.0000 NA
Condit. Reinf. active responses 11.1 1 0 0 0.00 1.0000 NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0000 NA
Pavlov. Cond. lever latency 36.3 1 1 33 0.00 1.0000 NA
Pavlov. Cond. magazine entry latency 104.9 1 1 33 0.00 1.0000 NA
Pavlov. Cond. change in total contacts 130.1 1 1 33 0.00 1.0000 NA
Pavlov. Cond. index score 62.2 1 1 33 0.00 1.0000 NA
Pavlov. Cond. latency score 67.1 1 1 33 0.00 1.0000 NA
Pavlov. Cond. lever contacts 29.4 1 1 33 0.00 1.0000 NA
Pavlov. Cond. magazine entry number 150.0 1 1 33 0.00 1.0000 NA
Pavlov. Cond. intertrial magazine entries 63.9 1 1 33 0.00 1.0000 NA
Pavlov. Cond. lever-magazine prob. diff. 55.1 1 1 33 0.00 1.0000 NA
Pavlov. Cond. response bias 30.8 1 1 33 0.00 1.0000 NA
Conditioned reinforcement - actives 13.0 1 0 0 0.00 1.0000 NA
Conditioned reinforcement - inactives 8.5 1 0 0 0.00 1.0000 Acnat1
Conditioned locomotion 9.9 1 0 0 0.00 1.0000 NA
Intermittent access intake day 1-15 change 61.5 1 1 33 0.00 1.0000 NA
Intermittent access intake escalation 82.5 1 1 33 0.00 1.0000 NA
Intermittent access intake escalation 2 42.5 1 1 33 0.00 1.0000 NA
Intermitt. access day 1 inactive lever presses 19.4 1 1 33 0.00 1.0000 NA
Intermitt. access escalation Index 9.2 1 0 0 0.00 1.0000 NA
Intermittent access day 1 total infusions 24.0 2 1 33 0.00 1.0000 NA Acnat1
Intermittent access day 1 locomotion 15.6 2 1 33 0.00 1.0000 NA Acnat1
Intermittent access total locomotion 7.3 1 0 0 0.00 1.0000 Acnat1
Post-drug Anxiety 13.7 1 0 0 0.00 1.0000 NA
Progressive ratio test 1 active lever presses 11.8 1 0 0 0.00 1.0000 NA
Progressive ratio test 1 breakpoint 10.4 1 0 0 0.00 1.0000 NA
Progressive ratio test 1 inactive lever presses 8.9 2 0 0 0.00 1.0000 NA Acnat1
Progressive ratio test 2 active lever presses 12.2 1 0 0 0.00 1.0000 NA
Progressive ratio test 2 breakpoint 38.7 1 1 33 0.00 1.0000 NA
Short access day 10 total inactive lever presses 12.2 1 0 0 0.00 1.0000 NA
Short access day 10 total infusions 24.0 1 1 33 0.00 1.0000 NA
Short access day 1 locomotion 17.2 1 0 0 0.00 1.0000 NA
Compulsive drug intake 28.2 1 1 33 0.00 1.0000 NA
One hour access (0.3 mA shock) 10.4 1 0 0 0.00 1.0000 NA
Context. condit. distance diff. score 149.8 1 1 33 0.00 1.0000 NA
Locomotion velocity, session 1 117.8 1 1 33 0.00 1.0000 NA
Locomotion distance, session 1 374.7 1 1 33 0.00 1.0000 NA
Locomotion velocity, session 2 82.2 1 1 33 0.00 1.0000 NA
Locomotion distance, session 2 776.0 1 1 33 0.00 1.0000 NA
Locomotion velocity, session 3 116.1 1 1 33 0.00 1.0000 NA
Locomotion distance, session 3 82.4 1 1 33 0.00 1.0000 NA
Stereotopy head waving bouts, day 3 8.8 1 0 0 0.00 1.0000 NA
Stereotopy head waving duration, day 3 25.6 1 1 33 0.00 1.0000 NA
Locomotion velocity, session 7 66.3 1 1 33 0.00 1.0000 NA
Locomotion distance, session 7 16.4 2 1 33 0.00 1.0000 NA Acnat1
Stereotopy head waving bouts, day 7 42.6 1 1 33 0.00 1.0000 NA
Stereotopy head waving duration, day 7 44.7 2 1 33 0.00 1.0000 NA Acnat1
Locomotion distance, session 8 102.8 1 1 33 0.00 1.0000 NA
Degree of sensitization distance 140.6 1 1 33 0.00 1.0000 NA
Degree of sensitization stereotypy 22.9 1 1 33 0.00 1.0000 NA
Condit. Reinf. active minus inactive responses 12.2 1 0 0 0.00 1.0000 Acnat1
Condit. Reinf. active-inactive response ratio 65.1 1 1 33 0.00 1.0000 NA
Condit. Reinf. active responses 17.1 2 0 0 0.00 1.0000 NA Acnat1
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.0000 NA
Incentive salience index mean 14.5 2 0 0 0.00 1.0000 NA Acnat1
Condit. Reinf. lever presses 15.7 2 1 33 0.00 1.0000 NA Acnat1
Time in familiar zone, hab. session 1 16.4 1 0 0 0.00 1.0000 NA
Time in novel zone, hab. session 1 12.9 1 0 0 0.00 1.0000 NA
Total zone transitions, hab. session 1 415.6 1 1 33 0.00 1.0000 NA
Total locomotion distance, hab. session 1 115.9 2 1 33 0.00 1.0000 NA Acnat1
Locomotion velocity, hab. session 1 218.6 1 1 33 0.00 1.0000 NA
Time in familiar zone, hab. session 2 28.0 1 1 33 0.00 1.0000 NA
Time in novel zone, hab. session 2 34.1 1 1 33 0.00 1.0000 NA
Total zone transitions, hab. session 2 106.5 2 1 33 -0.62 0.2612 Itgb3bp NA
Total locomotion distance, hab. session 2 133.1 1 1 33 0.00 1.0000 NA
Locomotion velocity, hab. session 2 139.4 1 1 33 0.00 1.0000 NA
Total zone transitions, NPP test 228.8 1 1 33 0.00 1.0000 NA
Total locomotion distance, NPP test 163.4 1 1 33 0.00 1.0000 NA
Locomotion velocity, NPP test 195.9 1 1 33 0.00 1.0000 NA
Pavlov. Cond. lever latency 8.6 1 0 0 0.00 1.0000 NA
Pavlov. Cond. magazine entry latency 56.4 1 1 33 0.00 1.0000 NA
Pavlov. Cond. change in total contacts 40.1 1 1 33 0.00 1.0000 NA
Pavlov. Cond. index score 28.9 1 1 33 0.00 1.0000 NA
Pavlov. Cond. latency score 16.6 1 0 0 0.00 1.0000 NA
Pavlov. Cond. lever contacts 13.3 1 0 0 0.00 1.0000 NA
Pavlov. Cond. magazine entry number 34.9 1 1 33 0.00 1.0000 NA
Pavlov. Cond. lever-magazine prob. diff. 50.5 1 1 33 0.00 1.0000 NA
Pavlov. Cond. response bias 29.4 1 1 33 0.00 1.0000 NA
Bone: apparent density 18.6 1 1 33 0.00 1.0000 NA
Bone surface 28.9 1 1 33 0.00 1.0000 NA
Bone volume 32.3 1 1 33 0.00 1.0000 NA
Bone: connectivity density 8.5 1 0 0 0.00 1.0000 NA
Bone: cortical apparent density 9.3 1 0 0 0.00 1.0000 Itgb3bp
Bone: cortical porosity 109.3 1 1 33 0.00 1.0000 NA
Bone: cortical porosity 91.2 1 1 33 0.00 1.0000 NA
Bone: cortical thickness 8.8 1 0 0 0.00 1.0000 NA
Bone: cortical thickness 17.9 1 0 0 0.00 1.0000 NA
Bone: cortical tissue density 9.2 1 0 0 0.00 1.0000 Itgb3bp
Bone: elastic displacement 17.3 1 1 33 0.00 1.0000 NA
Bone: endosteal estimation 12.7 1 1 33 0.00 1.0000 NA
Bone: final force 39.5 1 1 33 0.00 1.0000 NA
Bone: final moment 31.9 1 1 33 0.00 1.0000 NA
Bone: marrow area 10.6 1 1 33 0.00 1.0000 NA
Bone: maximum force 42.0 1 1 33 0.00 1.0000 NA
Bone: maximum moment 29.5 1 1 33 0.00 1.0000 NA
Bone: minimum diameter 57.3 1 1 33 0.00 1.0000 NA
Bone: periosteal estimation 7.8 1 0 0 0.00 1.0000 NA
Bone: periosteal perimeter 6.5 2 0 0 0.00 1.0000 NA Acnat1
Bone: post-yield work 82.8 1 1 33 0.00 1.0000 NA
Bone: stiffness 90.4 1 1 33 0.00 1.0000 NA
Bone: tissue strength 81.0 1 1 33 0.00 1.0000 NA
Bone: trabecular number 39.4 1 1 33 0.00 1.0000 NA
Bone: trabecular spacing 5.7 1 0 0 0.00 1.0000 NA
Bone: trabecular thickness 10.4 1 0 0 0.00 1.0000 NA
Distance traveled before self-admin 9.8 1 0 0 0.00 1.0000 NA
Delta time in open arm before/after self-admin 40.2 1 1 33 0.00 1.0000 NA
Extinction: sum of active levers before priming 12.2 1 0 0 0.00 1.0000 NA
Active lever presses in extinction session 6 9.2 1 0 0 0.00 1.0000 NA
Delta distance traveled before/after self-admin 11.3 1 0 0 0.00 1.0000 NA
Time in closed arm before self-admin 50.0 1 1 33 0.00 1.0000 NA
Time in closed arm after self-admin 25.8 1 1 33 0.00 1.0000 NA
Time in open arm after self-admin 31.3 1 1 33 0.00 1.0000 NA
Delta time to tail flick, vehicle, before/after SA 7.5 1 0 0 0.00 1.0000 NA
Delta time to tail flick, test, before/after SA 20.0 1 0 0 0.00 1.0000 NA
Fecal boli incidents, locomotor time 1 11.8 1 0 0 0.00 1.0000 NA
Change in fecal boli incidents, locomotor task 8.8 1 0 0 0.00 1.0000 NA
Time >=10cm from walls, locomotor time 1 19.5 1 0 0 0.00 1.0000 NA
Time >=10cm from walls, locomotor time 2 19.4 1 1 33 0.00 1.0000 NA
Rest time, locomotor task time 2 8.8 1 0 0 0.00 1.0000 NA
Distance moved, locomotor task time 2 13.1 1 0 0 0.00 1.0000 NA
Weight adjusted by age 16.7 1 1 33 0.00 1.0000 NA
Locomotion in novel chamber 10.2 1 0 0 0.00 1.0000 NA
Run reversals in cocaine runway, males 25.4 1 1 33 0.00 1.0000 NA
Latency to leave start box in cocaine runway 18.8 1 0 0 0.00 1.0000 NA
Cd content in liver 140.5 1 1 33 0.00 1.0000 NA
Co content in liver 83.2 1 1 33 0.00 1.0000 NA
Fe content in liver 10.3 1 0 0 0.00 1.0000 NA
K content in liver 62.6 1 1 33 0.00 1.0000 NA
Mn content in liver 130.2 1 1 33 0.00 1.0000 NA
Rb content in liver 14.7 2 1 33 0.00 1.0000 NA Acnat1
Se content in liver 47.0 1 1 33 0.00 1.0000 NA
Zn content in liver 27.1 2 1 33 0.00 1.0000 NA Acnat1

chisq ratio: Average Chi2 statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes+: Shared significant genes at Bonferroni correction. # genes++: Shared significant genes at transcriptome-wide significance. % genes++: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.

Associations by panel

tissue modality # hits % hits/tests avg chisq
Adipose alternative polyA 0 0.000 1.5
Adipose alternative TSS 0 0.000 1.3
Adipose gene expression 0 0.000 1.4
Adipose isoform ratio 0 0.000 1.4
Adipose intron excision ratio 0 0.000 1.4
Adipose mRNA stability 0 0.000 1.4
BLA alternative polyA 0 0.000 1.5
BLA alternative TSS 0 0.000 1.4
BLA gene expression 0 0.000 1.4
BLA isoform ratio 1 0.057 1.5
BLA intron excision ratio 0 0.000 1.4
BLA mRNA stability 0 0.000 1.4
Brain alternative polyA 0 0.000 1.4
Brain alternative TSS 0 0.000 1.3
Brain gene expression 0 0.000 1.4
Brain isoform ratio 1 0.032 1.4
Brain intron excision ratio 0 0.000 1.4
Brain mRNA stability 0 0.000 1.4
Eye alternative polyA 0 0.000 1.4
Eye alternative TSS 0 0.000 1.3
Eye gene expression 0 0.000 1.5
Eye isoform ratio 0 0.000 1.5
Eye intron excision ratio 0 0.000 1.5
Eye mRNA stability 0 0.000 1.6
IL alternative polyA 0 0.000 1.4
IL alternative TSS 0 0.000 1.4
IL gene expression 0 0.000 1.4
IL isoform ratio 0 0.000 1.3
IL intron excision ratio 0 0.000 1.3
IL mRNA stability 0 0.000 1.3
LHb alternative polyA 0 0.000 1.3
LHb alternative TSS 0 0.000 1.5
LHb gene expression 0 0.000 1.4
LHb isoform ratio 0 0.000 1.4
LHb intron excision ratio 0 0.000 1.3
LHb mRNA stability 0 0.000 1.4
Liver alternative polyA 0 0.000 1.5
Liver alternative TSS 0 0.000 1.3
Liver gene expression 0 0.000 1.3
Liver isoform ratio 1 0.042 1.4
Liver intron excision ratio 0 0.000 1.5
Liver mRNA stability 0 0.000 1.3
NAcc alternative polyA 0 0.000 1.4
NAcc alternative TSS 0 0.000 1.5
NAcc gene expression 0 0.000 1.4
NAcc isoform ratio 0 0.000 1.5
NAcc intron excision ratio 0 0.000 1.3
NAcc mRNA stability 0 0.000 1.4
OFC alternative polyA 0 0.000 1.4
OFC alternative TSS 0 0.000 1.4
OFC gene expression 0 0.000 1.4
OFC isoform ratio 0 0.000 1.3
OFC intron excision ratio 1 0.100 1.4
OFC mRNA stability 0 0.000 1.3
PL alternative polyA 0 0.000 1.5
PL alternative TSS 0 0.000 1.5
PL gene expression 0 0.000 1.4
PL isoform ratio 2 0.090 1.5
PL intron excision ratio 0 0.000 1.4
PL mRNA stability 0 0.000 1.4

avg chisq: Average Chi2 (squared Z-score) across all models in this panel for this trait.