Hub : Traits

Bone: minimum diameter

Tags: Physiology · Bone

Project: r01_doug_adams

165 significantly associated models · 43 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 1 234603337 236170162 2 1 1.8e-07 5.6e-08 8.7e-126 -1829 Exoc6
2 7 16845355 16970279 1 1 1.0e-36 NaN NA NA NA
3 10 89400319 96071622 40 7 2.6e-09 2.3e-08 1.0e+00 100 Wipi1 Ddx42 Ddx5 Bptf Snord104 Map3k3 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 11 0.00 1.0e+00 NA
Body weight 4.0 14 1 11 0.99 9.7e-19 Mettl2 Mrc2 Cyb561 Strada Ccdc47 Kpna2 Cep112 Ddx5 NA Map3k3 Ace NA NA NA
Epididymis fat weight 87.6 1 1 11 0.00 1.0e+00 NA
Heart weight 11.4 1 0 0 0.00 1.0e+00 NA
Left kidney weight 37.5 1 1 11 0.00 1.0e+00 NA
Right kidney weight 41.9 1 1 11 0.00 1.0e+00 NA
Tail length 58.1 1 1 11 0.00 1.0e+00 NA
Length with tail 3.8 2 0 0 0.00 1.0e+00 Mrc2 NA
Length without tail 71.1 1 1 11 0.00 1.0e+00 NA
Liver weight, left 23.6 1 1 11 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 11 0.00 1.0e+00 NA
Retroperitoneal fat weight 4.2 1 0 0 0.00 1.0e+00 NA
Intraocular pressure 29.4 1 1 11 0.00 1.0e+00 NA
Extensor digitorum longus weight 6.2 11 1 11 -0.99 2.1e-15 Taco1 Strada Ccdc47 Ddx42 Scn4a Kpna2 Dcaf7 NA Prr29 NA NA
Soleus weight 13.7 1 1 11 0.00 1.0e+00 NA
Tibialis anterior weight 59.9 1 1 11 0.00 1.0e+00 NA
Tibia length 7.4 1 0 0 0.00 1.0e+00 NA
Number of licking bursts 155.0 1 1 11 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 11 0.00 1.0e+00 NA
Mean time between licks in bursts 54.9 1 1 11 0.00 1.0e+00 NA
Mean num. licks in bursts 164.2 1 1 11 0.00 1.0e+00 NA
Std. dev. time between licks in bursts 177.7 1 1 11 0.00 1.0e+00 NA
Indifference point 0 sec 11.7 5 1 11 0.99 1.9e-05 Psmd12 NA NA NA NA
Indifference point AUC 42.1 1 1 11 0.00 1.0e+00 NA
Delay discounting total patch changes 0 sec 12.2 3 1 11 1.00 1.5e-05 NA NA NA
Delay discounting total patch changes 12 sec 102.7 1 1 11 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 175.3 1 1 11 0.00 1.0e+00 NA
Delay discounting total patch changes 24 sec 28.3 1 1 11 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 45.0 3 1 11 0.98 4.0e-03 Cep112 NA NA
Delay discounting water rate 0 sec 11.8 1 0 0 0.00 1.0e+00 NA
Delay discounting water rate 12 sec 44.2 1 1 11 0.00 1.0e+00 NA
Delay discounting water rate 18 sec 10.5 1 0 0 0.00 1.0e+00 NA
Delay discounting water rate 24 sec 62.7 1 1 11 0.00 1.0e+00 NA
Delay discounting water rate 6 sec 44.2 1 1 11 0.00 1.0e+00 NA
Locomotor testing distance 11.5 1 0 0 0.00 1.0e+00 NA
Locomotor testing rearing 16.8 1 1 11 0.00 1.0e+00 NA
Light reinforcement 1 54.8 1 1 11 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 56.4 1 1 11 0.00 1.0e+00 NA
Reaction time num false alarms AUC 79.5 1 1 11 0.00 1.0e+00 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 11 0.00 1.0e+00 NA
Reaction time mean AUC 58.0 1 1 11 0.00 1.0e+00 NA
Median of all reaction times 51.2 1 1 11 0.00 1.0e+00 NA
Reaction time false alarm rate 63.4 1 1 11 0.00 1.0e+00 NA
Reaction time premature initiation rate 32.1 1 1 11 0.00 1.0e+00 NA
Reaction time premature initiations 34.3 1 1 11 0.00 1.0e+00 NA
Std. dev. reaction times 27.0 1 1 11 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 15.6 1 0 0 0.00 1.0e+00 NA
Social responses 74.3 1 1 11 0.00 1.0e+00 NA
Cocaine response after cond. corrected 78.0 1 1 11 0.00 1.0e+00 NA
Cocaine response after cond. not corrected 102.3 1 1 11 0.00 1.0e+00 NA
Cocaine response before conditioning 28.6 1 1 11 0.00 1.0e+00 NA
Saline control response 30.3 1 1 11 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 14.0 8 1 11 0.99 2.4e-12 Strada Ccdc47 Kpna2 Dcaf7 NA Prr29 NA NA
Condit. Reinf. active-inactive response ratio 40.7 1 1 11 0.00 1.0e+00 NA
Condit. Reinf. active responses 10.4 8 0 0 0.96 1.2e-06 Wipi1 Fam20a Strada Scn4a Kpna2 Dcaf7 NA NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. lever reinforcers received 9.8 2 0 0 0.00 1.0e+00 Kpna2 NA
Pavlov. Cond. lever latency 36.3 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 104.9 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 130.1 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. index score 62.2 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. latency score 67.1 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 29.4 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 150.0 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 14.3 27 1 11 1.00 9.0e-126 Psmd12 Mettl2 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Polg2 Cep95 Kpna2 Icam2 Ddx5 Dcaf7 NA Bptf Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA NA
Pavlov. Cond. lever-magazine prob. diff. 55.1 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. response bias 30.8 1 1 11 0.00 1.0e+00 NA
Conditioned reinforcement - actives 18.5 1 0 0 0.00 1.0e+00 NA
Intermittent access intake day 1-15 change 61.5 1 1 11 0.00 1.0e+00 NA
Intermittent access intake escalation 82.5 1 1 11 0.00 1.0e+00 NA
Intermittent access intake escalation 2 42.5 1 1 11 0.00 1.0e+00 NA
Intermitt. access day 1 inactive lever presses 30.6 1 1 11 0.00 1.0e+00 NA
Intermittent access day 1 total infusions 32.7 1 1 11 0.00 1.0e+00 NA
Intermittent access day 1 locomotion 27.1 1 1 11 0.00 1.0e+00 NA
Intermittent access total locomotion 12.3 9 0 0 1.00 1.9e-28 Psmd12 Strada Scn4a Icam2 NA NA NA NA NA
Post-drug Anxiety 20.6 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 breakpoint 38.7 1 1 11 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 18.1 2 1 11 0.00 1.0e+00 NA NA
Short access day 1 locomotion 17.2 1 0 0 0.00 1.0e+00 NA
Short access day 10 total locomotion 13.2 17 0 0 1.00 1.1e-55 Psmd12 Taco1 Strada Ddx42 Scn4a Polg2 Kpna2 Icam2 Ddx5 NA Bptf AC133055.1 Snord104 Ace NA NA NA
Compulsive drug intake 45.4 1 1 11 0.00 1.0e+00 NA
One hour access (0.3 mA shock) 14.1 2 0 0 0.00 1.0e+00 Cyp26a1 Exoc6
Context. condit. distance diff. score 149.8 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, session 1 117.8 1 1 11 0.00 1.0e+00 NA
Locomotion distance, session 1 374.7 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, session 2 82.2 1 1 11 0.00 1.0e+00 NA
Locomotion distance, session 2 776.0 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, session 3 116.1 1 1 11 0.00 1.0e+00 NA
Locomotion distance, session 3 82.4 1 1 11 0.00 1.0e+00 NA
Stereotopy head waving duration, day 3 25.6 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, session 7 66.3 1 1 11 0.00 1.0e+00 NA
Locomotion distance, session 7 21.3 1 1 11 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 7 42.6 1 1 11 0.00 1.0e+00 NA
Stereotopy head waving duration, day 7 63.4 1 1 11 0.00 1.0e+00 NA
Locomotion distance, session 8 102.8 1 1 11 0.00 1.0e+00 NA
Degree of sensitization distance 140.6 1 1 11 0.00 1.0e+00 NA
Degree of sensitization stereotypy 37.5 1 1 11 0.00 1.0e+00 NA
Condit. Reinf. active-inactive response ratio 65.1 1 1 11 0.00 1.0e+00 NA
Condit. Reinf. active responses 20.0 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.0e+00 NA
Incentive salience index mean 15.6 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. lever presses 35.1 1 1 11 0.00 1.0e+00 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 17.4 1 0 0 0.00 1.0e+00 NA
Total zone transitions, hab. session 1 415.6 1 1 11 0.00 1.0e+00 NA
Total locomotion distance, hab. session 1 171.4 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, hab. session 1 218.6 1 1 11 0.00 1.0e+00 NA
Time in familiar zone, hab. session 2 48.9 1 1 11 0.00 1.0e+00 NA
Time in novel zone, hab. session 2 58.4 1 1 11 0.00 1.0e+00 NA
Total zone transitions, hab. session 2 256.1 1 1 11 0.00 1.0e+00 NA
Total locomotion distance, hab. session 2 133.1 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, hab. session 2 139.4 1 1 11 0.00 1.0e+00 NA
Total zone transitions, NPP test 228.8 1 1 11 0.00 1.0e+00 NA
Total locomotion distance, NPP test 163.4 1 1 11 0.00 1.0e+00 NA
Locomotion velocity, NPP test 195.9 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 56.4 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 40.1 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. index score 51.9 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. latency score 16.6 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 16.1 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 61.6 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 50.5 1 1 11 0.00 1.0e+00 NA
Pavlov. Cond. response bias 52.4 1 1 11 0.00 1.0e+00 NA
Bone: apparent density 19.9 2 1 11 0.00 1.0e+00 Exoc6 NA
Bone surface 10.1 23 1 11 1.00 1.6e-75 Psmd12 Arsg Mrc2 Cyb561 Taco1 Strada Ccdc47 Ddx42 Scn4a Cep95 Icam2 Ddx5 Exoc6 Dcaf7 NA Tanc2 Snord104 Prr29 Map3k3 Ace NA NA NA
Bone volume 10.0 15 1 11 1.00 6.4e-49 Arsg Mrc2 Taco1 Strada Ccdc47 Ddx42 Scn4a Icam2 Dcaf7 Tanc2 Prr29 Map3k3 Ace NA NA
Bone: connectivity density 8.5 1 0 0 0.00 1.0e+00 NA
Bone: cortical porosity 21.8 15 2 22 0.55 4.7e-04 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace NA NA
Bone: cortical porosity 28.8 7 1 11 -0.01 9.7e-01 Mrc2 Cyb561 Kcnh6 Taco1 Ddx42 NA NA
Bone: cortical thickness 9.4 7 0 0 -0.89 3.0e-03 Prkca Fam20a Map2k6 Cep95 AABR07030630.1 NA NA
Bone: cortical thickness 17.9 1 0 0 0.00 1.0e+00 NA
Bone: elastic displacement 28.2 1 1 11 0.00 1.0e+00 NA
Bone: endosteal estimation 17.3 43 40 444 0.99 3.1e-140 Psmd12 Cacng4 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Map2k6 Mettl2 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Polg2 Cep95 Kpna2 Cyp26a1 Cep112 Icam2 Ddx5 Exoc6 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA NA NA NA
Bone: endosteal perimeter 18.8 42 40 444 1.00 1.3e-197 Psmd12 Cacng4 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Map2k6 Mettl2 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Polg2 Cep95 Kpna2 Cyp26a1 Cep112 Icam2 Ddx5 Exoc6 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA NA NA
Bone: final force 39.5 1 1 11 0.00 1.0e+00 NA
Bone: final moment 31.9 1 1 11 0.00 1.0e+00 NA
Bone: marrow area 17.0 43 40 444 0.99 6.6e-142 Psmd12 Cacng4 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Map2k6 Mettl2 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Polg2 Cep95 Kpna2 Cyp26a1 Cep112 Icam2 Ddx5 Exoc6 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA NA NA NA
Bone: maximum diameter 8.3 26 0 0 1.00 6.0e-66 Psmd12 Cacng4 Prkca Fam20a Mrc2 Cyb561 Taco1 Strada Ccdc47 Ddx42 Scn4a Kpna2 Cyp26a1 Icam2 Exoc6 Dcaf7 NA AABR07030630.1 Tanc2 Prr29 Map3k3 Ace NA NA NA NA
Bone: maximum force 42.0 1 1 11 0.00 1.0e+00 NA
Bone: maximum moment 29.5 1 1 11 0.00 1.0e+00 NA
Bone: periosteal estimation 12.9 43 31 344 0.99 6.5e-148 Psmd12 Cacng4 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Map2k6 Mettl2 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Polg2 Cep95 Kpna2 Cyp26a1 Cep112 Icam2 Ddx5 Exoc6 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA NA NA NA
Bone: periosteal perimeter 9.8 29 0 0 0.98 5.0e-50 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Map2k6 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Kpna2 Cep112 Icam2 Dcaf7 NA Prkar1a AABR07030630.1 Tanc2 Prr29 Map3k3 Ace NA NA NA
Bone: post-yield work 82.8 1 1 11 0.00 1.0e+00 NA
Bone: stiffness 90.4 1 1 11 0.00 1.0e+00 NA
Bone: tissue strength 81.0 1 1 11 0.00 1.0e+00 NA
Bone: trabecular number 29.2 2 1 11 0.00 1.0e+00 Exoc6 NA
Bone: trabecular thickness 13.8 1 0 0 0.00 1.0e+00 NA
Bone: trabecular tissue density 43.1 1 1 11 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 11 0.00 1.0e+00 NA
Time in closed arm before self-admin 50.0 1 1 11 0.00 1.0e+00 NA
Time in closed arm after self-admin 40.2 1 1 11 0.00 1.0e+00 NA
Time in open arm after self-admin 31.3 1 1 11 0.00 1.0e+00 NA
Delta time to tail flick, test, before/after SA 20.0 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 27.2 1 1 11 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 25.0 1 1 11 0.00 1.0e+00 NA
Run reversals in cocaine runway, males 39.3 1 1 11 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 140.5 1 1 11 0.00 1.0e+00 NA
Co content in liver 83.2 1 1 11 0.00 1.0e+00 NA
K content in liver 62.6 1 1 11 0.00 1.0e+00 NA
Mn content in liver 130.2 1 1 11 0.00 1.0e+00 NA
Rb content in liver 31.4 1 1 11 0.00 1.0e+00 NA
Se content in liver 33.1 3 3 33 0.00 1.0e+00 Cyp26a1 Exoc6 NA
Zn content in liver 46.0 1 1 11 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 7 0.330 1.9
Adipose alternative TSS 0 0.000 1.6
Adipose gene expression 12 0.145 1.9
Adipose isoform ratio 4 0.142 1.7
Adipose intron excision ratio 2 0.069 2.0
Adipose mRNA stability 5 0.145 1.8
BLA alternative polyA 2 0.167 1.8
BLA alternative TSS 5 0.594 1.9
BLA gene expression 15 0.247 2.0
BLA isoform ratio 0 0.000 1.8
BLA intron excision ratio 1 0.033 1.8
BLA mRNA stability 4 0.198 1.9
Brain alternative polyA 4 0.199 1.8
Brain alternative TSS 4 0.233 1.9
Brain gene expression 12 0.133 1.9
Brain isoform ratio 3 0.095 1.8
Brain intron excision ratio 5 0.093 1.9
Brain mRNA stability 3 0.069 1.7
Eye alternative polyA 0 0.000 1.8
Eye alternative TSS 0 0.000 2.0
Eye gene expression 0 0.000 2.0
Eye isoform ratio 0 0.000 1.6
Eye intron excision ratio 0 0.000 1.7
Eye mRNA stability 0 0.000 1.8
IL alternative polyA 0 0.000 2.0
IL alternative TSS 0 0.000 1.5
IL gene expression 4 0.110 1.9
IL isoform ratio 0 0.000 1.9
IL intron excision ratio 0 0.000 1.7
IL mRNA stability 2 0.180 1.7
LHb alternative polyA 0 0.000 1.8
LHb alternative TSS 0 0.000 1.9
LHb gene expression 2 0.062 1.9
LHb isoform ratio 1 0.133 1.7
LHb intron excision ratio 0 0.000 1.7
LHb mRNA stability 4 0.386 1.9
Liver alternative polyA 2 0.133 1.7
Liver alternative TSS 0 0.000 1.8
Liver gene expression 10 0.139 1.9
Liver isoform ratio 1 0.042 1.7
Liver intron excision ratio 3 0.069 1.9
Liver mRNA stability 1 0.041 1.8
NAcc alternative polyA 4 0.305 1.9
NAcc alternative TSS 0 0.000 1.7
NAcc gene expression 9 0.143 1.9
NAcc isoform ratio 2 0.106 1.8
NAcc intron excision ratio 0 0.000 1.8
NAcc mRNA stability 4 0.177 2.0
OFC alternative polyA 0 0.000 2.0
OFC alternative TSS 0 0.000 1.7
OFC gene expression 4 0.108 1.9
OFC isoform ratio 0 0.000 1.8
OFC intron excision ratio 0 0.000 1.7
OFC mRNA stability 1 0.093 1.8
PL alternative polyA 1 0.070 1.8
PL alternative TSS 5 0.426 1.9
PL gene expression 10 0.135 1.9
PL isoform ratio 2 0.090 1.9
PL intron excision ratio 0 0.000 1.8
PL mRNA stability 5 0.171 1.9

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