Hub : Traits

Bone surface

Tags: Physiology · Bone

Project: r01_doug_adams

9 significantly associated models · 6 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 2 43366934 44763574 1 1 4.9e-08 1.7e-06 1.3e-01 90 Il6st
2 5 137682119 138752373 1 1 8.3e-09 3.1e-02 1.2e-13 -1083 Stk40
3 7 16845355 16970279 1 1 1.5e-17 NaN NA NA NA
4 10 90321052 91847115 2 1 1.7e-07 5.6e-06 7.7e-01 100 Map3k3
5 10 95263631 96660473 1 1 2.1e-07 1.8e-07 1.0e+00 100 Kcnj16

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 with tail 3.9 2 0 0 -0.51 4.9e-01 Kcnj16 Stk40
BMI without tail 72.7 2 1 20 0.00 1.0e+00 Stk40 NA
Body weight 5.0 4 2 40 0.62 1.8e-01 Kcnj16 Il6st Stk40 NA
Epididymis fat weight 87.6 1 1 20 0.00 1.0e+00 NA
Glucose 15.4 2 1 20 0.00 1.0e+00 Stk40 NA
Heart weight 11.4 1 0 0 0.00 1.0e+00 NA
Left kidney weight 37.5 1 1 20 0.00 1.0e+00 NA
Right kidney weight 41.9 1 1 20 0.00 1.0e+00 NA
Tail length 39.9 2 1 20 0.00 1.0e+00 Stk40 NA
Length with tail 4.0 4 1 20 0.95 1.2e-02 Ddx42 Il6st Map3k3 NA
Length without tail 53.8 2 2 40 0.00 1.0e+00 Il6st NA
Liver weight, left 23.6 1 1 20 0.00 1.0e+00 NA
Liver weight, right 9.6 1 0 0 0.00 1.0e+00 NA
Parametrial fat weight 26.4 1 1 20 0.00 1.0e+00 NA
Retroperitoneal fat weight 4.2 1 0 0 0.00 1.0e+00 NA
Intraocular pressure 19.0 1 1 20 0.00 1.0e+00 NA
Extensor digitorum longus weight 14.7 4 3 60 -0.81 9.5e-02 Ddx42 Stk40 Map3k3 NA
Soleus weight 13.8 2 2 40 0.00 1.0e+00 Stk40 NA
Tibialis anterior weight 59.9 1 1 20 0.00 1.0e+00 NA
Tibia length 5.3 2 0 0 0.00 1.0e+00 Il6st NA
Number of licking bursts 155.0 1 1 20 0.00 1.0e+00 NA
Food consumed during 24 hour testing period 17.5 1 0 0 0.00 1.0e+00 NA
Times rat made contact with spout 75.1 1 1 20 0.00 1.0e+00 NA
Mean time between licks in bursts 54.9 1 1 20 0.00 1.0e+00 NA
Mean num. licks in bursts 164.2 1 1 20 0.00 1.0e+00 NA
Std. dev. time between licks in bursts 177.7 1 1 20 0.00 1.0e+00 NA
Indifference point 0 sec 18.7 1 1 20 0.00 1.0e+00 NA
Indifference point AUC 42.1 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 0 sec 17.7 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 12 sec 102.7 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 119.2 2 1 20 0.00 1.0e+00 Stk40 NA
Delay discounting total patch changes 24 sec 28.3 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 98.5 1 1 20 0.00 1.0e+00 NA
Delay discounting water rate 0 sec 8.3 2 0 0 0.00 1.0e+00 Il6st NA
Delay discounting water rate 12 sec 26.1 1 1 20 0.00 1.0e+00 NA
Delay discounting water rate 18 sec 8.7 2 0 0 0.00 1.0e+00 Il6st NA
Delay discounting water rate 24 sec 62.7 1 1 20 0.00 1.0e+00 NA
Delay discounting water rate 6 sec 44.2 1 1 20 0.00 1.0e+00 NA
Locomotor testing distance 10.3 2 0 0 0.00 1.0e+00 Il6st NA
Locomotor testing rearing 11.5 3 1 20 -0.04 9.4e-01 Kcnj16 Stk40 NA
Light reinforcement 1 54.8 1 1 20 0.00 1.0e+00 NA
Reaction time number correct 9.4 1 0 0 0.00 1.0e+00 NA
Reaction time num false alarms 39.5 2 1 20 0.00 1.0e+00 Stk40 NA
Reaction time num false alarms AUC 56.8 2 1 20 0.00 1.0e+00 Stk40 NA
Reaction time trials correct on left 9.4 1 0 0 0.00 1.0e+00 NA
Reaction time trials on left 10.3 1 0 0 0.00 1.0e+00 NA
Reaction time mean 41.3 1 1 20 0.00 1.0e+00 NA
Reaction time mean AUC 58.0 1 1 20 0.00 1.0e+00 NA
Median of all reaction times 51.2 1 1 20 0.00 1.0e+00 NA
Reaction time false alarm rate 63.4 1 1 20 0.00 1.0e+00 NA
Reaction time premature initiation rate 32.1 1 1 20 0.00 1.0e+00 NA
Reaction time premature initiations 34.3 1 1 20 0.00 1.0e+00 NA
Std. dev. reaction times 17.4 1 1 20 0.00 1.0e+00 NA
Reaction time trials completed 10.3 1 0 0 0.00 1.0e+00 NA
Reaction time trials AUC 10.6 2 0 0 0.00 1.0e+00 Stk40 NA
Social responses 74.3 1 1 20 0.00 1.0e+00 NA
Social time 7.8 1 0 0 0.00 1.0e+00 NA
Cocaine response after cond. corrected 78.0 1 1 20 0.00 1.0e+00 NA
Cocaine response after cond. not corrected 102.3 1 1 20 0.00 1.0e+00 NA
Cocaine response before conditioning 17.6 2 1 20 0.00 1.0e+00 Stk40 NA
Saline control response 30.3 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 20.4 3 1 20 1.00 1.2e-04 Ddx42 Map3k3 NA
Condit. Reinf. active-inactive response ratio 22.2 4 1 20 0.98 2.6e-03 Ddx42 Il6st Map3k3 NA
Condit. Reinf. active responses 8.2 3 0 0 0.00 1.0e+00 Il6st Map3k3 NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. lever presses 7.2 1 0 0 0.00 1.0e+00 Stk40
Condit. Reinf. lever reinforcers received 6.5 2 0 0 0.00 1.0e+00 Il6st Map3k3
Pavlov. Cond. lever latency 36.3 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 72.4 2 1 20 0.00 1.0e+00 Il6st NA
Pavlov. Cond. change in total contacts 130.1 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. index score 62.2 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. latency score 67.1 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 29.4 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 102.2 2 1 20 0.00 1.0e+00 Il6st NA
Pavlov. Cond. intertrial magazine entries 63.9 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 55.1 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. response bias 30.8 1 1 20 0.00 1.0e+00 NA
Conditioned reinforcement - actives 18.5 1 0 0 0.00 1.0e+00 NA
Conditioned locomotion 9.9 1 0 0 0.00 1.0e+00 NA
Intermittent access intake day 1-15 change 61.5 1 1 20 0.00 1.0e+00 NA
Intermittent access intake escalation 82.5 1 1 20 0.00 1.0e+00 NA
Intermittent access intake escalation 2 42.5 1 1 20 0.00 1.0e+00 NA
Intermitt. access day 1 inactive lever presses 19.4 1 1 20 0.00 1.0e+00 NA
Intermitt. access escalation Index 9.2 1 0 0 0.00 1.0e+00 NA
Intermittent access day 1 total infusions 32.7 1 1 20 0.00 1.0e+00 NA
Intermittent access day 1 locomotion 18.4 1 1 20 0.00 1.0e+00 NA
Post-drug Anxiety 20.6 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 1 active lever presses 11.8 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 1 breakpoint 10.4 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 1 inactive lever presses 10.8 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 active lever presses 12.2 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 breakpoint 38.7 1 1 20 0.00 1.0e+00 NA
Short access day 10 total inactive lever presses 12.2 1 0 0 0.00 1.0e+00 NA
Short access day 10 total infusions 24.0 1 1 20 0.00 1.0e+00 NA
Short access day 1 locomotion 17.2 1 0 0 0.00 1.0e+00 NA
Compulsive drug intake 28.2 1 1 20 0.00 1.0e+00 NA
One hour access (0.3 mA shock) 10.4 1 0 0 0.00 1.0e+00 NA
Context. condit. distance diff. score 102.1 2 1 20 0.00 1.0e+00 Il6st NA
Locomotion velocity, session 1 117.8 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 1 374.7 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 2 82.2 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 2 776.0 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 3 116.1 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 3 82.4 1 1 20 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 3 8.8 1 0 0 0.00 1.0e+00 NA
Stereotopy head waving duration, day 3 25.6 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 7 66.3 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 7 21.3 1 1 20 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 7 42.6 1 1 20 0.00 1.0e+00 NA
Stereotopy head waving duration, day 7 63.4 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 8 102.8 1 1 20 0.00 1.0e+00 NA
Degree of sensitization distance 140.6 1 1 20 0.00 1.0e+00 NA
Degree of sensitization stereotypy 22.9 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 14.7 1 0 0 0.00 1.0e+00 Stk40
Condit. Reinf. active-inactive response ratio 46.4 2 1 20 0.00 1.0e+00 Stk40 NA
Condit. Reinf. active responses 14.1 2 0 0 0.00 1.0e+00 Stk40 NA
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.0e+00 NA
Incentive salience index mean 21.9 2 1 20 0.00 1.0e+00 Stk40 NA
Condit. Reinf. lever presses 29.9 2 2 40 0.00 1.0e+00 Stk40 NA
Time in familiar zone, hab. session 1 16.4 1 0 0 0.00 1.0e+00 NA
Time in novel zone, hab. session 1 12.9 1 0 0 0.00 1.0e+00 NA
Total zone transitions, hab. session 1 415.6 1 1 20 0.00 1.0e+00 NA
Total locomotion distance, hab. session 1 171.4 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, hab. session 1 218.6 1 1 20 0.00 1.0e+00 NA
Time in familiar zone, hab. session 2 48.9 1 1 20 0.00 1.0e+00 NA
Time in novel zone, hab. session 2 34.1 1 1 20 0.00 1.0e+00 NA
Total zone transitions, hab. session 2 256.1 1 1 20 0.00 1.0e+00 NA
Total locomotion distance, hab. session 2 133.1 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, hab. session 2 139.4 1 1 20 0.00 1.0e+00 NA
Total zone transitions, NPP test 228.8 1 1 20 0.00 1.0e+00 NA
Total locomotion distance, NPP test 163.4 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, NPP test 195.9 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. lever latency 10.4 2 0 0 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. magazine entry latency 40.5 2 1 20 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. change in total contacts 24.5 2 1 20 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. index score 22.4 2 1 20 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. latency score 12.1 2 0 0 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. lever contacts 12.4 2 0 0 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. magazine entry number 34.9 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 12.3 1 0 0 0.00 1.0e+00 Stk40
Pavlov. Cond. lever-magazine prob. diff. 37.4 2 1 20 0.00 1.0e+00 Stk40 NA
Pavlov. Cond. response bias 16.4 4 1 20 -0.75 1.5e-01 Ddx42 Stk40 Map3k3 NA
Bone: apparent density 9.8 6 1 20 0.23 5.5e-01 Kcnj16 Ddx42 Il6st Stk40 Map3k3 NA
Bone volume 18.3 6 2 40 0.99 1.1e-07 Kcnj16 Ddx42 Il6st Stk40 Map3k3 NA
Bone: connectivity density 7.4 6 0 0 0.64 9.0e-02 Kcnj16 Ddx42 Il6st Stk40 Map3k3 NA
Bone: cortical apparent density 6.7 1 0 0 0.00 1.0e+00 Kcnj16
Bone: cortical area 9.1 2 0 0 0.00 1.0e+00 Ddx42 Il6st
Bone: cortical porosity 52.2 4 1 20 -0.46 4.4e-01 Ddx42 Il6st Map3k3 NA
Bone: cortical porosity 43.6 4 1 20 -0.44 4.5e-01 Ddx42 Il6st Map3k3 NA
Bone: cortical thickness 11.6 3 0 0 -0.66 2.2e-01 Kcnj16 Il6st NA
Bone: cortical thickness 17.9 1 0 0 0.00 1.0e+00 NA
Bone: cortical tissue density 6.4 1 0 0 0.00 1.0e+00 Kcnj16
Bone: elastic displacement 28.2 1 1 20 0.00 1.0e+00 NA
Bone: endosteal estimation 12.7 6 2 40 0.96 3.2e-05 Kcnj16 Ddx42 Il6st Stk40 Map3k3 NA
Bone: endosteal perimeter 14.0 4 2 40 0.98 7.0e-04 Kcnj16 Ddx42 Il6st Map3k3
Bone: final force 23.5 3 1 20 0.97 2.8e-02 Ddx42 Il6st NA
Bone: final moment 17.0 4 1 20 0.98 3.4e-03 Ddx42 Il6st Map3k3 NA
Bone: marrow area 12.1 6 2 40 0.96 4.4e-05 Kcnj16 Ddx42 Il6st Stk40 Map3k3 NA
Bone: maximum diameter 8.7 4 0 0 1.00 1.1e-05 Kcnj16 Ddx42 Il6st Map3k3
Bone: maximum force 31.7 2 1 20 0.00 1.0e+00 Il6st NA
Bone: maximum moment 18.8 3 1 20 0.98 1.5e-02 Ddx42 Il6st NA
Bone: minimum diameter 21.2 5 1 20 0.95 2.6e-04 Kcnj16 Ddx42 Il6st Map3k3 NA
Bone: periosteal estimation 9.7 5 0 0 0.98 2.7e-05 Kcnj16 Ddx42 Il6st Map3k3 NA
Bone: periosteal perimeter 8.1 5 0 0 0.98 7.2e-05 Kcnj16 Ddx42 Stk40 Map3k3 NA
Bone: post-yield work 57.3 2 1 20 0.00 1.0e+00 Il6st NA
Bone: stiffness 62.5 2 1 20 0.00 1.0e+00 Il6st NA
Bone: tissue strength 81.0 1 1 20 0.00 1.0e+00 NA
Bone: trabecular number 15.1 5 1 20 -0.10 8.2e-01 Kcnj16 Ddx42 Stk40 Map3k3 NA
Bone: trabecular spacing 6.8 1 0 0 0.00 1.0e+00 Kcnj16
Bone: trabecular thickness 9.0 4 0 0 1.00 1.5e-04 Ddx42 Il6st Map3k3 NA
Bone: trabecular tissue density 43.1 1 1 20 0.00 1.0e+00 NA
Distance traveled before self-admin 12.6 1 0 0 0.00 1.0e+00 NA
Delta time in open arm before/after self-admin 40.2 1 1 20 0.00 1.0e+00 NA
Extinction: sum of active levers before priming 10.8 2 0 0 0.00 1.0e+00 Il6st NA
Active lever presses in extinction session 6 9.2 1 0 0 0.00 1.0e+00 NA
Delta distance traveled before/after self-admin 11.3 1 0 0 0.00 1.0e+00 NA
Time in closed arm before self-admin 50.0 1 1 20 0.00 1.0e+00 NA
Time in closed arm after self-admin 25.8 1 1 20 0.00 1.0e+00 NA
Time in open arm after self-admin 31.3 1 1 20 0.00 1.0e+00 NA
Time to tail flick, vehicle, before self-admin 9.6 1 0 0 0.00 1.0e+00 Il6st
Delta time to tail flick, vehicle, before/after SA 8.0 1 0 0 0.00 1.0e+00 Il6st
Delta time to tail flick, test, before/after SA 20.0 1 0 0 0.00 1.0e+00 NA
Fecal boli incidents, locomotor time 1 11.8 1 0 0 0.00 1.0e+00 NA
Change in fecal boli incidents, locomotor task 8.8 1 0 0 0.00 1.0e+00 NA
Time >=10cm from walls, locomotor time 1 19.5 1 0 0 0.00 1.0e+00 NA
Time >=10cm from walls, locomotor time 2 19.4 1 1 20 0.00 1.0e+00 NA
Rest time, locomotor task time 2 8.8 1 0 0 0.00 1.0e+00 NA
Distance moved, locomotor task time 2 13.1 1 0 0 0.00 1.0e+00 NA
Weight adjusted by age 16.7 1 1 20 0.00 1.0e+00 NA
Locomotion in novel chamber 10.2 1 0 0 0.00 1.0e+00 NA
Run reversals in cocaine runway, males 25.4 1 1 20 0.00 1.0e+00 NA
Latency to leave start box in cocaine runway 18.8 1 0 0 0.00 1.0e+00 NA
Cd content in liver 96.4 2 1 20 0.00 1.0e+00 Stk40 NA
Co content in liver 83.2 1 1 20 0.00 1.0e+00 NA
Fe content in liver 8.4 2 0 0 0.00 1.0e+00 Il6st NA
K content in liver 62.6 1 1 20 0.00 1.0e+00 NA
Mg content in liver 13.7 1 0 0 0.00 1.0e+00 Stk40
Mn content in liver 130.2 1 1 20 0.00 1.0e+00 NA
Rb content in liver 31.4 1 1 20 0.00 1.0e+00 NA
Se content in liver 29.8 2 1 20 0.00 1.0e+00 Stk40 NA
Sr content in liver 132.4 1 1 20 0.00 1.0e+00 Stk40
Zn content in liver 46.0 1 1 20 0.00 1.0e+00 NA

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 1.7
Adipose alternative TSS 0 0.000 1.9
Adipose gene expression 0 0.000 1.8
Adipose isoform ratio 0 0.000 1.7
Adipose intron excision ratio 0 0.000 1.7
Adipose mRNA stability 0 0.000 1.8
BLA alternative polyA 0 0.000 1.7
BLA alternative TSS 0 0.000 2.0
BLA gene expression 0 0.000 1.8
BLA isoform ratio 0 0.000 1.8
BLA intron excision ratio 0 0.000 1.7
BLA mRNA stability 0 0.000 1.8
Brain alternative polyA 0 0.000 1.8
Brain alternative TSS 0 0.000 2.0
Brain gene expression 1 0.011 1.8
Brain isoform ratio 1 0.032 1.7
Brain intron excision ratio 0 0.000 1.7
Brain mRNA stability 0 0.000 1.7
Eye alternative polyA 0 0.000 2.0
Eye alternative TSS 0 0.000 1.9
Eye gene expression 0 0.000 1.8
Eye isoform ratio 0 0.000 1.6
Eye intron excision ratio 0 0.000 1.6
Eye mRNA stability 0 0.000 2.0
IL alternative polyA 0 0.000 1.9
IL alternative TSS 0 0.000 2.2
IL gene expression 0 0.000 1.8
IL isoform ratio 0 0.000 1.7
IL intron excision ratio 0 0.000 1.8
IL mRNA stability 0 0.000 1.8
LHb alternative polyA 0 0.000 2.0
LHb alternative TSS 0 0.000 2.4
LHb gene expression 0 0.000 1.8
LHb isoform ratio 0 0.000 1.7
LHb intron excision ratio 0 0.000 1.6
LHb mRNA stability 0 0.000 1.8
Liver alternative polyA 0 0.000 1.7
Liver alternative TSS 0 0.000 1.8
Liver gene expression 2 0.028 1.8
Liver isoform ratio 0 0.000 1.7
Liver intron excision ratio 0 0.000 1.8
Liver mRNA stability 2 0.081 1.8
NAcc alternative polyA 0 0.000 1.7
NAcc alternative TSS 0 0.000 1.9
NAcc gene expression 0 0.000 1.8
NAcc isoform ratio 0 0.000 1.9
NAcc intron excision ratio 0 0.000 1.6
NAcc mRNA stability 0 0.000 1.8
OFC alternative polyA 0 0.000 1.8
OFC alternative TSS 0 0.000 1.8
OFC gene expression 0 0.000 1.8
OFC isoform ratio 0 0.000 1.7
OFC intron excision ratio 0 0.000 1.7
OFC mRNA stability 0 0.000 1.8
PL alternative polyA 0 0.000 1.7
PL alternative TSS 0 0.000 1.9
PL gene expression 1 0.014 1.8
PL isoform ratio 2 0.090 1.8
PL intron excision ratio 0 0.000 1.7
PL mRNA stability 0 0.000 1.8

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