Bone volume

Tags: Physiology · Bone

Project: r01_doug_adams

2 loci · 2 genes with independent associations · 2 total associated genes

Significant Loci

# Chr Start pos End pos # assoc genes # joint models Best TWAS P Best GWAS P Cond GWAS P Joint genes
1 5 137682119 138752373 1 1 4.81e-12 4.53e-02 7.25e-25 Stk40
2 7 16845355 16970279 1 1 2.76e-19 NaN NA ENSRNOG00000064438

Pleiotropic Associations

Trait Chi2 ratio # genes+ # genes++ % genes++ Corr Corr P Genes
BMI with tail 4.29 1 0 0 0 1e+00 Stk40
BMI without tail 72.67 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Body weight 6.44 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Epididymis fat weight 87.61 1 1 50 0 1e+00 ENSRNOG00000064438
Glucose 15.37 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Heart weight 11.41 1 0 0 0 1e+00 ENSRNOG00000064438
Left kidney weight 37.46 1 1 50 0 1e+00 ENSRNOG00000064438
Right kidney weight 41.88 1 1 50 0 1e+00 ENSRNOG00000064438
Tail length 39.87 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Length with tail 3.24 1 0 0 0 1e+00 ENSRNOG00000064438
Length without tail 71.11 1 1 50 0 1e+00 ENSRNOG00000064438
Liver weight, left 23.57 1 1 50 0 1e+00 ENSRNOG00000064438
Liver weight, right 9.6 1 0 0 0 1e+00 ENSRNOG00000064438
Parametrial fat weight 14.9 1 1 50 0 1e+00 ENSRNOG00000064438
Retroperitoneal fat weight 3.02 1 0 0 0 1e+00 ENSRNOG00000064438
Intraocular pressure 18.97 1 1 50 0 1e+00 ENSRNOG00000064438
Extensor digitorum longus weight 19.09 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Soleus weight 13.82 2 2 100 0 1e+00 Stk40 ENSRNOG00000064438
Tibialis anterior weight 40.54 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Tibia length 5.35 1 0 0 0 1e+00 ENSRNOG00000064438
Number of licking bursts 155.04 1 1 50 0 1e+00 ENSRNOG00000064438
Food consumed during 24 hour testing period 17.5 1 0 0 0 1e+00 ENSRNOG00000064438
Times rat made contact with spout 75.14 1 1 50 0 1e+00 ENSRNOG00000064438
Mean time between licks in bursts 54.91 1 1 50 0 1e+00 ENSRNOG00000064438
Mean num. licks in bursts 164.17 1 1 50 0 1e+00 ENSRNOG00000064438
Std. dev. time between licks in bursts 177.72 1 1 50 0 1e+00 ENSRNOG00000064438
Water consumed over 24 hours 5.74 1 0 0 0 1e+00 ENSRNOG00000064438
Indifference point 0 sec 18.72 1 1 50 0 1e+00 ENSRNOG00000064438
Indifference point AUC 30.17 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Indifference point function ln k 4.41 1 0 0 0 1e+00 ENSRNOG00000064438
Indifference point function log k 4.41 1 0 0 0 1e+00 ENSRNOG00000064438
Delay discounting total patch changes 0 sec 17.74 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting total patch changes 12 sec 102.69 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting total patch changes 18 sec 119.18 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Delay discounting total patch changes 24 sec 28.3 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting total patch changes 6 sec 98.45 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting water rate 0 sec 8.14 1 0 0 0 1e+00 ENSRNOG00000064438
Delay discounting water rate 12 sec 26.07 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting water rate 18 sec 10.52 1 0 0 0 1e+00 ENSRNOG00000064438
Delay discounting water rate 24 sec 62.69 1 1 50 0 1e+00 ENSRNOG00000064438
Delay discounting water rate 6 sec 44.17 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotor testing distance 11.51 1 0 0 0 1e+00 ENSRNOG00000064438
Locomotor testing rearing 16.22 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Light reinforcement 1 54.81 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time number correct 6.91 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time num false alarms 39.48 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time num false alarms AUC 56.81 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time trials correct on left 6.91 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time trials on left 7.52 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time mean 41.28 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time mean AUC 57.96 1 1 50 0 1e+00 ENSRNOG00000064438
Median of all reaction times 51.19 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time false alarm rate 63.39 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time premature initiation rate 32.14 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time premature initiations 24.29 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Std. dev. reaction times 17.36 1 1 50 0 1e+00 ENSRNOG00000064438
Reaction time trials completed 7.52 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Reaction time trials AUC 10.58 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Social responses 74.35 1 1 50 0 1e+00 ENSRNOG00000064438
Social time 7.75 1 0 0 0 1e+00 ENSRNOG00000064438
Conditioned locomotion 5.32 1 0 0 0 1e+00 Stk40
Cocaine response after cond. corrected 77.95 1 1 50 0 1e+00 ENSRNOG00000064438
Cocaine response after cond. not corrected 102.33 1 1 50 0 1e+00 ENSRNOG00000064438
Cocaine response before conditioning 13.79 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Saline control response 30.34 1 1 50 0 1e+00 ENSRNOG00000064438
Condit. Reinf. active minus inactive responses 29.4 1 1 50 0 1e+00 ENSRNOG00000064438
Condit. Reinf. active-inactive response ratio 40.66 1 1 50 0 1e+00 ENSRNOG00000064438
Condit. Reinf. active responses 11.07 1 0 0 0 1e+00 ENSRNOG00000064438
Condit. Reinf. inactive responses 20.59 1 0 0 0 1e+00 ENSRNOG00000064438
Condit. Reinf. lever presses 7.23 1 0 0 0 1e+00 Stk40
Pavlov. Cond. lever latency 36.27 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. magazine entry latency 104.88 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. change in total contacts 130.08 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. index score 62.19 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. latency score 67.08 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. lever contacts 17.16 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. magazine entry number 150.01 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. intertrial magazine entries 63.93 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. lever-magazine prob. diff. 55.11 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. response bias 30.81 1 1 50 0 1e+00 ENSRNOG00000064438
Conditioned reinforcement - actives 13.02 1 0 0 0 1e+00 ENSRNOG00000064438
Conditioned locomotion 9.86 1 0 0 0 1e+00 ENSRNOG00000064438
Intermittent access intake day 1-15 change 61.45 1 1 50 0 1e+00 ENSRNOG00000064438
Intermittent access intake escalation 82.51 1 1 50 0 1e+00 ENSRNOG00000064438
Intermittent access intake escalation 2 24.72 1 1 50 0 1e+00 ENSRNOG00000064438
Intermitt. access day 1 inactive lever presses 19.44 1 1 50 0 1e+00 ENSRNOG00000064438
Intermitt. access escalation Index 9.22 1 0 0 0 1e+00 ENSRNOG00000064438
Intermittent access day 1 total infusions 32.74 1 1 50 0 1e+00 ENSRNOG00000064438
Intermittent access day 1 locomotion 18.42 1 1 50 0 1e+00 ENSRNOG00000064438
Post-drug Anxiety 13.65 1 0 0 0 1e+00 ENSRNOG00000064438
Progressive ratio test 1 active lever presses 11.8 1 0 0 0 1e+00 ENSRNOG00000064438
Progressive ratio test 1 breakpoint 10.37 1 0 0 0 1e+00 ENSRNOG00000064438
Progressive ratio test 1 inactive lever presses 10.82 1 0 0 0 1e+00 ENSRNOG00000064438
Progressive ratio test 2 active lever presses 12.24 1 0 0 0 1e+00 ENSRNOG00000064438
Progressive ratio test 2 breakpoint 38.7 1 1 50 0 1e+00 ENSRNOG00000064438
Short access day 10 total inactive lever presses 8.14 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Short access day 10 total infusions 24.04 1 1 50 0 1e+00 ENSRNOG00000064438
Short access day 1 locomotion 11.36 1 0 0 0 1e+00 ENSRNOG00000064438
Compulsive drug intake 28.2 1 1 50 0 1e+00 ENSRNOG00000064438
One hour access (0.3 mA shock) 10.45 1 0 0 0 1e+00 ENSRNOG00000064438
Context. condit. distance diff. score 149.78 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, session 1 117.78 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion distance, session 1 374.74 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, session 2 82.2 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion distance, session 2 775.97 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, session 3 116.11 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion distance, session 3 82.39 1 1 50 0 1e+00 ENSRNOG00000064438
Stereotopy head waving bouts, day 3 8.83 1 0 0 0 1e+00 ENSRNOG00000064438
Stereotopy head waving duration, day 3 25.57 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, session 7 66.34 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion distance, session 7 21.3 1 1 50 0 1e+00 ENSRNOG00000064438
Stereotopy head waving bouts, day 7 42.65 1 1 50 0 1e+00 ENSRNOG00000064438
Stereotopy head waving duration, day 7 63.39 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion distance, session 8 102.75 1 1 50 0 1e+00 ENSRNOG00000064438
Degree of sensitization distance 140.58 1 1 50 0 1e+00 ENSRNOG00000064438
Degree of sensitization stereotypy 22.91 1 1 50 0 1e+00 ENSRNOG00000064438
Condit. Reinf. active minus inactive responses 10.13 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Condit. Reinf. active-inactive response ratio 46.37 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Condit. Reinf. active responses 14.11 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Condit. Reinf. inactive responses 17.25 1 0 0 0 1e+00 ENSRNOG00000064438
Incentive salience index mean 21.93 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Condit. Reinf. lever presses 21.81 2 2 100 0 1e+00 Stk40 ENSRNOG00000064438
Time in familiar zone, hab. session 1 16.37 1 0 0 0 1e+00 ENSRNOG00000064438
Time in novel zone, hab. session 1 12.91 1 0 0 0 1e+00 ENSRNOG00000064438
Total zone transitions, hab. session 1 415.63 1 1 50 0 1e+00 ENSRNOG00000064438
Total locomotion distance, hab. session 1 171.39 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, hab. session 1 218.59 1 1 50 0 1e+00 ENSRNOG00000064438
Time in familiar zone, hab. session 2 27.96 1 1 50 0 1e+00 ENSRNOG00000064438
Time in novel zone, hab. session 2 34.06 1 1 50 0 1e+00 ENSRNOG00000064438
Total zone transitions, hab. session 2 256.06 1 1 50 0 1e+00 ENSRNOG00000064438
Total locomotion distance, hab. session 2 133.05 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, hab. session 2 139.44 1 1 50 0 1e+00 ENSRNOG00000064438
Novelty place preference 5.87 1 0 0 0 1e+00 Stk40
Time in novel zone, NPP test 5.48 1 0 0 0 1e+00 Stk40
Total zone transitions, NPP test 228.75 1 1 50 0 1e+00 ENSRNOG00000064438
Total locomotion distance, NPP test 163.42 1 1 50 0 1e+00 ENSRNOG00000064438
Locomotion velocity, NPP test 195.87 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. lever latency 10.38 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. magazine entry latency 40.45 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. change in total contacts 18.38 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. index score 22.43 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. latency score 12.1 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. lever contacts 12.4 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. magazine entry number 34.9 1 1 50 0 1e+00 ENSRNOG00000064438
Pavlov. Cond. intertrial magazine entries 12.34 1 0 0 0 1e+00 Stk40
Pavlov. Cond. lever-magazine prob. diff. 37.35 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Pavlov. Cond. response bias 22.18 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone: apparent density 16.75 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone surface 25.55 2 2 100 0 1e+00 Stk40 ENSRNOG00000064438
Bone: connectivity density 7.98 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Bone: cortical porosity 109.3 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: cortical porosity 91.2 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: cortical thickness 8.79 1 0 0 0 1e+00 ENSRNOG00000064438
Bone: cortical thickness 17.92 1 0 0 0 1e+00 ENSRNOG00000064438
Bone: elastic displacement 17.29 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: endosteal estimation 10.65 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone: endosteal perimeter 3.03 1 0 0 0 1e+00 Stk40
Bone: final force 39.54 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: final moment 31.87 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: marrow area 9.15 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone: maximum force 41.95 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: maximum moment 29.46 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: minimum diameter 39.37 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone: periosteal estimation 6.39 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Bone: periosteal perimeter 6.62 2 0 0 0 1e+00 Stk40 ENSRNOG00000064438
Bone: post-yield work 82.77 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: stiffness 90.38 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: tissue strength 80.98 1 1 50 0 1e+00 ENSRNOG00000064438
Bone: trabecular number 28.59 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Bone: trabecular spacing 5.66 1 0 0 0 1e+00 ENSRNOG00000064438
Bone: trabecular thickness 10.38 1 0 0 0 1e+00 ENSRNOG00000064438
Bone: trabecular tissue density 30.07 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Distance traveled before self-admin 9.75 1 0 0 0 1e+00 ENSRNOG00000064438
Delta time in open arm before/after self-admin 23.55 1 1 50 0 1e+00 ENSRNOG00000064438
Extinction: sum of active levers before priming 12.19 1 0 0 0 1e+00 ENSRNOG00000064438
Active lever presses in extinction session 6 9.21 1 0 0 0 1e+00 ENSRNOG00000064438
Delta distance traveled before/after self-admin 8.72 1 0 0 0 1e+00 ENSRNOG00000064438
Time in closed arm before self-admin 50.04 1 1 50 0 1e+00 ENSRNOG00000064438
Time in closed arm after self-admin 25.79 1 1 50 0 1e+00 ENSRNOG00000064438
Time in open arm after self-admin 18.45 1 1 50 0 1e+00 ENSRNOG00000064438
Delta time to tail flick, vehicle, before/after SA 7.54 1 0 0 0 1e+00 ENSRNOG00000064438
Delta time to tail flick, test, before/after SA 20.03 1 0 0 0 1e+00 ENSRNOG00000064438
Ambulatory time before self-admin 5.66 1 0 0 0 1e+00 ENSRNOG00000064438
Fecal boli incidents, locomotor time 1 11.77 1 0 0 0 1e+00 ENSRNOG00000064438
Change in fecal boli incidents, locomotor task 8.82 1 0 0 0 1e+00 ENSRNOG00000064438
Time >=10cm from walls, locomotor time 1 19.54 1 0 0 0 1e+00 ENSRNOG00000064438
Rest time, locomotor task time 1 5.42 1 0 0 0 1e+00 Stk40
Time >=10cm from walls, locomotor time 2 19.42 1 1 50 0 1e+00 ENSRNOG00000064438
Total resting periods, locomotor time 2 6.01 1 0 0 0 1e+00 ENSRNOG00000064438
Rest time, locomotor task time 2 7 1 0 0 0 1e+00 ENSRNOG00000064438
Distance moved, locomotor task time 2 9.35 1 0 0 0 1e+00 ENSRNOG00000064438
Weight adjusted by age 16.68 1 1 50 0 1e+00 ENSRNOG00000064438
Seeking ratio, delayed vs. immediate footshock 5.34 1 0 0 0 1e+00 ENSRNOG00000064438
Locomotion in novel chamber 10.2 1 0 0 0 1e+00 ENSRNOG00000064438
Run reversals in cocaine runway, males 25.4 1 1 50 0 1e+00 ENSRNOG00000064438
Latency to leave start box in cocaine runway 18.78 1 0 0 0 1e+00 ENSRNOG00000064438
Cd content in liver 96.4 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Co content in liver 83.15 1 1 50 0 1e+00 ENSRNOG00000064438
Cu content in liver 4.78 1 0 0 0 1e+00 Stk40
Fe content in liver 10.34 1 0 0 0 1e+00 ENSRNOG00000064438
K content in liver 62.65 1 1 50 0 1e+00 ENSRNOG00000064438
Mg content in liver 13.66 1 0 0 0 1e+00 Stk40
Mn content in liver 130.23 1 1 50 0 1e+00 ENSRNOG00000064438
Rb content in liver 18.62 1 1 50 0 1e+00 ENSRNOG00000064438
Se content in liver 29.81 2 1 50 0 1e+00 Stk40 ENSRNOG00000064438
Sr content in liver 132.45 1 1 50 0 1e+00 Stk40
Zn content in liver 25.95 1 1 50 0 1e+00 ENSRNOG00000064438

Associations by panel

Tissue RNA modality # hits % hits/tests Avg chisq
Adipose alternative polyA 0 0 1.69
Adipose alternative TSS 0 0 1.73
Adipose gene expression 0 0 1.7
Adipose isoform ratio 0 0 1.63
Adipose intron excision ratio 0 0 1.65
Adipose mRNA stability 0 0 1.75
BLA alternative polyA 0 0 1.65
BLA alternative TSS 0 0 1.89
BLA gene expression 0 0 1.74
BLA isoform ratio 0 0 1.7
BLA intron excision ratio 0 0 1.62
BLA mRNA stability 0 0 1.74
Brain alternative polyA 0 0 1.73
Brain alternative TSS 0 0 1.86
Brain gene expression 0 0 1.7
Brain isoform ratio 0 0 1.61
Brain intron excision ratio 0 0 1.61
Brain mRNA stability 0 0 1.68
Eye alternative polyA 0 0 1.83
Eye alternative TSS 0 0 1.86
Eye gene expression 0 0 1.74
Eye isoform ratio 0 0 1.47
Eye intron excision ratio 0 0 1.6
Eye mRNA stability 0 0 1.87
IL alternative polyA 0 0 1.84
IL alternative TSS 0 0 1.98
IL gene expression 0 0 1.7
IL isoform ratio 0 0 1.62
IL intron excision ratio 0 0 1.65
IL mRNA stability 0 0 1.78
LHb alternative polyA 0 0 1.73
LHb alternative TSS 0 0 2.28
LHb gene expression 0 0 1.72
LHb isoform ratio 0 0 1.59
LHb intron excision ratio 0 0 1.49
LHb mRNA stability 0 0 1.75
Liver alternative polyA 0 0 1.5
Liver alternative TSS 0 0 1.79
Liver gene expression 0 0 1.7
Liver isoform ratio 0 0 1.66
Liver intron excision ratio 0 0 1.65
Liver mRNA stability 1 0 1.71
NAcc alternative polyA 0 0 1.64
NAcc alternative TSS 0 0 1.81
NAcc gene expression 0 0 1.74
NAcc isoform ratio 0 0 1.75
NAcc intron excision ratio 0 0 1.57
NAcc mRNA stability 0 0 1.75
OFC alternative polyA 0 0 1.67
OFC alternative TSS 0 0 1.7
OFC gene expression 0 0 1.71
OFC isoform ratio 0 0 1.59
OFC intron excision ratio 0 0 1.58
OFC mRNA stability 0 0 1.74
PL alternative polyA 0 0 1.66
PL alternative TSS 0 0 1.86
PL gene expression 0 0 1.73
PL isoform ratio 2 0.1 1.68
PL intron excision ratio 0 0 1.59
PL mRNA stability 0 0 1.75