Hub : Traits

Bone: endosteal estimation

Tags: Physiology · Bone

Project: r01_doug_adams

414 significantly associated models · 63 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 7 16845355 16970279 1 1 2.9e-10 NaN NA NA NA
2 10 89400319 96755402 62 7 4.7e-15 2.5e-13 NaN NaN Psmd12 Apoh Wipi1 Map2k6 Taco1 Kpna2 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 with tail 5.1 5 0 0 -1.00 2.6e-08 Cacng4 Prkca Cep112 AABR07030647.1 Prkar1a
BMI without tail 171.8 1 1 12 0.00 1.0e+00 NA
Body weight 4.3 13 1 12 0.99 3.5e-28 Amz2 Apoh Wipi1 Arsg Mettl2 Mrc2 NA Abca6 Prkar1a Ace NA NA NA
Epididymis fat weight 136.2 1 1 12 0.00 1.0e+00 NA
Heart weight 11.4 1 0 0 0.00 1.0e+00 NA
Left kidney weight 62.7 1 1 12 0.00 1.0e+00 NA
Right kidney weight 67.3 1 1 12 0.00 1.0e+00 NA
Tail length 91.1 1 1 12 0.00 1.0e+00 NA
Length without tail 120.2 1 1 12 0.00 1.0e+00 NA
Liver weight, left 23.6 1 1 12 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 12 0.00 1.0e+00 NA
Intraocular pressure 29.4 1 1 12 0.00 1.0e+00 NA
Extensor digitorum longus weight 7.2 11 1 12 -0.93 1.3e-06 Kcnh6 Ccdc47 Ddx42 Kpna2 Ddx5 Dcaf7 NA Bptf NA NA NA
Soleus weight 21.9 1 1 12 0.00 1.0e+00 NA
Tibialis anterior weight 96.0 1 1 12 0.00 1.0e+00 NA
Tibia length 7.4 1 0 0 0.00 1.0e+00 NA
Number of licking bursts 242.4 1 1 12 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 121.6 1 1 12 0.00 1.0e+00 NA
Mean time between licks in bursts 90.5 1 1 12 0.00 1.0e+00 NA
Mean num. licks in bursts 258.2 1 1 12 0.00 1.0e+00 NA
Std. dev. time between licks in bursts 291.0 1 1 12 0.00 1.0e+00 NA
Indifference point 0 sec 13.5 3 1 12 0.00 1.0e+00 NA NA NA
Indifference point AUC 66.7 1 1 12 0.00 1.0e+00 NA
Delay discounting total patch changes 0 sec 14.7 2 1 12 0.00 1.0e+00 NA NA
Delay discounting total patch changes 12 sec 156.9 1 1 12 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 277.7 1 1 12 0.00 1.0e+00 NA
Delay discounting total patch changes 24 sec 43.7 1 1 12 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 30.2 4 1 12 0.89 7.6e-03 Wipi1 Prkar1a 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 12 0.00 1.0e+00 NA
Delay discounting water rate 24 sec 100.9 1 1 12 0.00 1.0e+00 NA
Delay discounting water rate 6 sec 70.2 1 1 12 0.00 1.0e+00 NA
Locomotor testing distance 14.0 1 0 0 0.00 1.0e+00 NA
Locomotor testing rearing 23.9 1 1 12 0.00 1.0e+00 NA
Light reinforcement 1 84.1 1 1 12 0.00 1.0e+00 NA
Reaction time num false alarms 90.1 1 1 12 0.00 1.0e+00 NA
Reaction time num false alarms AUC 128.2 1 1 12 0.00 1.0e+00 NA
Reaction time mean 62.5 1 1 12 0.00 1.0e+00 NA
Reaction time mean AUC 89.1 1 1 12 0.00 1.0e+00 NA
Median of all reaction times 80.2 1 1 12 0.00 1.0e+00 NA
Reaction time false alarm rate 104.2 1 1 12 0.00 1.0e+00 NA
Reaction time premature initiation rate 47.3 1 1 12 0.00 1.0e+00 NA
Reaction time premature initiations 49.8 1 1 12 0.00 1.0e+00 NA
Std. dev. reaction times 27.0 1 1 12 0.00 1.0e+00 NA
Reaction time trials AUC 15.6 1 0 0 0.00 1.0e+00 NA
Social responses 108.6 1 1 12 0.00 1.0e+00 NA
Cocaine response after cond. corrected 135.7 1 1 12 0.00 1.0e+00 NA
Cocaine response after cond. not corrected 176.6 1 1 12 0.00 1.0e+00 NA
Cocaine response before conditioning 28.6 1 1 12 0.00 1.0e+00 NA
Saline control response 50.6 1 1 12 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 20.9 4 1 12 0.95 4.6e-02 Ccdc47 Kpna2 Dcaf7 NA
Condit. Reinf. active-inactive response ratio 68.7 1 1 12 0.00 1.0e+00 NA
Condit. Reinf. active responses 11.8 3 0 0 1.00 2.9e-03 Kpna2 NA NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. lever latency 60.5 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 173.4 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 216.7 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. index score 102.2 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. latency score 110.3 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 29.4 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 244.9 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 15.0 35 1 12 0.99 1.5e-132 Psmd12 Mettl2 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Icam2 Limd2 Ddx5 Dcaf7 NA Bptf Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA NA Pecam1 NA NA
Pavlov. Cond. lever-magazine prob. diff. 90.6 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. response bias 51.3 1 1 12 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 104.0 1 1 12 0.00 1.0e+00 NA
Intermittent access intake escalation 141.1 1 1 12 0.00 1.0e+00 NA
Intermittent access intake escalation 2 42.5 1 1 12 0.00 1.0e+00 NA
Intermitt. access day 1 inactive lever presses 30.6 1 1 12 0.00 1.0e+00 NA
Intermittent access day 1 total infusions 52.9 1 1 12 0.00 1.0e+00 NA
Intermittent access day 1 locomotion 27.1 1 1 12 0.00 1.0e+00 NA
Intermittent access total locomotion 14.2 6 0 0 0.39 4.5e-01 Psmd12 Helz NA NA NA NA
Post-drug Anxiety 20.6 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 breakpoint 61.6 1 1 12 0.00 1.0e+00 NA
Short access day 10 total infusions 24.0 1 1 12 0.00 1.0e+00 NA
Short access day 1 locomotion 17.2 1 0 0 0.00 1.0e+00 NA
Short access day 10 total locomotion 14.4 16 0 0 1.00 2.8e-26 Taco1 Strada Scn4a Kpna2 Icam2 Ddx5 Dcaf7 NA Bptf AC133055.1 Snord104 Ace NA NA Pecam1 NA
Compulsive drug intake 45.4 1 1 12 0.00 1.0e+00 NA
Context. condit. distance diff. score 240.2 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, session 1 190.8 1 1 12 0.00 1.0e+00 NA
Locomotion distance, session 1 609.6 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, session 2 139.6 1 1 12 0.00 1.0e+00 NA
Locomotion distance, session 2 1269.9 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, session 3 178.9 1 1 12 0.00 1.0e+00 NA
Locomotion distance, session 3 117.5 1 1 12 0.00 1.0e+00 NA
Stereotopy head waving duration, day 3 33.2 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, session 7 98.9 1 1 12 0.00 1.0e+00 NA
Locomotion distance, session 7 31.8 1 1 12 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 7 68.4 1 1 12 0.00 1.0e+00 NA
Stereotopy head waving duration, day 7 102.2 1 1 12 0.00 1.0e+00 NA
Locomotion distance, session 8 171.7 1 1 12 0.00 1.0e+00 NA
Degree of sensitization distance 198.5 1 1 12 0.00 1.0e+00 NA
Degree of sensitization stereotypy 37.5 1 1 12 0.00 1.0e+00 NA
Condit. Reinf. active-inactive response ratio 107.3 1 1 12 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 12 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 1 673.8 1 1 12 0.00 1.0e+00 NA
Total locomotion distance, hab. session 1 279.4 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, hab. session 1 349.5 1 1 12 0.00 1.0e+00 NA
Time in familiar zone, hab. session 2 48.9 1 1 12 0.00 1.0e+00 NA
Time in novel zone, hab. session 2 58.4 1 1 12 0.00 1.0e+00 NA
Total zone transitions, hab. session 2 421.2 1 1 12 0.00 1.0e+00 NA
Total locomotion distance, hab. session 2 214.3 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, hab. session 2 225.0 1 1 12 0.00 1.0e+00 NA
Total zone transitions, NPP test 376.1 1 1 12 0.00 1.0e+00 NA
Total locomotion distance, NPP test 269.3 1 1 12 0.00 1.0e+00 NA
Locomotion velocity, NPP test 317.8 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 95.9 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 40.1 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. index score 51.9 1 1 12 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 12 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 88.1 1 1 12 0.00 1.0e+00 NA
Pavlov. Cond. response bias 52.4 1 1 12 0.00 1.0e+00 NA
Bone: apparent density 31.2 1 1 12 0.00 1.0e+00 NA
Bone surface 10.8 29 2 25 0.99 5.9e-76 Psmd12 Wipi1 Arsg Fam20a Kcnj16 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Cep95 Icam2 Ddx5 Dcaf7 NA Prkar1a Tanc2 Abca9 Prr29 Map3k3 Ace Gna13 NA NA Kcnj2 NA
Bone volume 10.7 16 1 12 0.98 8.1e-33 Kcnj16 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Dcaf7 Prkar1a Tanc2 Abca9 Map3k3 Ace NA NA Kcnj2
Bone: cortical apparent density 11.9 1 0 0 0.00 1.0e+00 Marchf10
Bone: cortical porosity 23.1 15 5 62 0.75 4.8e-08 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace NA NA
Bone: cortical porosity 31.8 6 1 12 0.37 2.9e-01 Mrc2 Marchf10 Cyb561 Kcnh6 NA NA
Bone: cortical thickness 11.7 26 4 50 -0.99 1.4e-82 Psmd12 Helz Cacng4 Prkca Wipi1 Fam20a Abca8 Abca8a Map2k6 Kcnj16 Scn4a Tex2 Cep95 Smurf2 Icam2 Ddx5 NA Bptf Prkar1a Nol11 Abca9 Prr29 Kcnj2 NA Pecam1 Pitpnc1
Bone: cortical thickness 17.9 1 0 0 0.00 1.0e+00 NA
Bone: cortical tissue density 11.6 1 0 0 0.00 1.0e+00 Marchf10
Bone: elastic displacement 28.2 1 1 12 0.00 1.0e+00 NA
Bone: endosteal perimeter 16.9 62 61 762 1.00 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 AABR07030647.1 Dcaf7 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 Nol11 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA Kcnj2 NA Pecam1 NA NA Pitpnc1 NA
Bone: final force 57.4 1 1 12 0.00 1.0e+00 NA
Bone: final moment 45.6 1 1 12 0.00 1.0e+00 NA
Bone: marrow area 16.0 63 63 788 1.00 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 AABR07030647.1 Dcaf7 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 Nol11 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA NA Kcnj2 NA Pecam1 NA NA Pitpnc1 NA
Bone: maximum diameter 8.9 18 0 0 1.00 3.7e-41 Kcnj16 Mrc2 Cyb561 Taco1 Strada Ccdc47 Ddx42 Scn4a Kpna2 Dcaf7 NA AABR07030630.1 Prr29 Map3k3 Ace NA Kcnj2 NA
Bone: maximum force 60.3 1 1 12 0.00 1.0e+00 NA
Bone: maximum moment 41.2 1 1 12 0.00 1.0e+00 NA
Bone: minimum diameter 13.3 61 40 500 0.99 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 Dcaf7 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA NA Kcnj2 NA Pecam1 NA NA Pitpnc1 NA
Bone: periosteal estimation 11.1 62 35 438 1.00 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 AABR07030647.1 Dcaf7 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA NA Kcnj2 NA Pecam1 NA NA Pitpnc1 NA
Bone: periosteal perimeter 10.4 28 0 0 1.00 8.2e-51 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8a Map2k6 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Ccdc47 Ddx42 Scn4a Kpna2 Icam2 Dcaf7 Abca6 Prkar1a AABR07030630.1 Abca9 Prr29 Map3k3 Ace NA NA NA
Bone: post-yield work 124.3 1 1 12 0.00 1.0e+00 NA
Bone: stiffness 136.8 1 1 12 0.00 1.0e+00 NA
Bone: tissue strength 136.0 1 1 12 0.00 1.0e+00 NA
Bone: trabecular number 64.1 1 1 12 0.00 1.0e+00 NA
Bone: trabecular thickness 13.8 1 0 0 0.00 1.0e+00 NA
Bone: trabecular tissue density 66.6 1 1 12 0.00 1.0e+00 NA
Delta time in open arm before/after self-admin 40.2 1 1 12 0.00 1.0e+00 NA
Time in closed arm before self-admin 78.0 1 1 12 0.00 1.0e+00 NA
Time in closed arm after self-admin 40.2 1 1 12 0.00 1.0e+00 NA
Time in open arm after self-admin 31.3 1 1 12 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 12 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 12 0.00 1.0e+00 NA
Run reversals in cocaine runway, males 39.3 1 1 12 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
Latency to leave start box in cocaine runway, F 14.5 1 0 0 0.00 1.0e+00 Map2k6
Cd content in liver 239.3 1 1 12 0.00 1.0e+00 NA
Co content in liver 143.3 1 1 12 0.00 1.0e+00 NA
K content in liver 87.3 1 1 12 0.00 1.0e+00 NA
Mn content in liver 207.1 1 1 12 0.00 1.0e+00 NA
Rb content in liver 31.4 1 1 12 0.00 1.0e+00 NA
Se content in liver 47.0 1 1 12 0.00 1.0e+00 NA
Zn content in liver 46.0 1 1 12 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 14 0.660 2.3
Adipose alternative TSS 0 0.000 2.0
Adipose gene expression 22 0.265 2.1
Adipose isoform ratio 8 0.283 2.0
Adipose intron excision ratio 6 0.206 2.5
Adipose mRNA stability 12 0.348 2.1
BLA alternative polyA 4 0.334 2.2
BLA alternative TSS 8 0.950 2.5
BLA gene expression 24 0.396 2.2
BLA isoform ratio 5 0.284 2.1
BLA intron excision ratio 1 0.033 2.2
BLA mRNA stability 7 0.346 2.2
Brain alternative polyA 8 0.399 2.2
Brain alternative TSS 15 0.874 2.4
Brain gene expression 28 0.309 2.1
Brain isoform ratio 10 0.316 2.2
Brain intron excision ratio 8 0.148 2.2
Brain mRNA stability 9 0.206 2.0
Eye alternative polyA 0 0.000 2.2
Eye alternative TSS 0 0.000 2.2
Eye gene expression 2 0.178 2.3
Eye isoform ratio 0 0.000 1.8
Eye intron excision ratio 3 0.489 2.1
Eye mRNA stability 0 0.000 2.0
IL alternative polyA 0 0.000 2.3
IL alternative TSS 0 0.000 2.1
IL gene expression 10 0.274 2.2
IL isoform ratio 1 0.127 2.4
IL intron excision ratio 0 0.000 2.3
IL mRNA stability 2 0.180 2.0
LHb alternative polyA 0 0.000 2.4
LHb alternative TSS 3 0.857 2.8
LHb gene expression 7 0.218 2.2
LHb isoform ratio 1 0.133 2.2
LHb intron excision ratio 1 0.097 2.2
LHb mRNA stability 6 0.580 2.1
Liver alternative polyA 7 0.466 2.0
Liver alternative TSS 11 0.724 2.1
Liver gene expression 16 0.222 2.1
Liver isoform ratio 6 0.251 2.0
Liver intron excision ratio 14 0.320 2.2
Liver mRNA stability 5 0.204 2.0
NAcc alternative polyA 5 0.382 2.2
NAcc alternative TSS 1 0.108 2.1
NAcc gene expression 26 0.413 2.2
NAcc isoform ratio 4 0.212 2.1
NAcc intron excision ratio 1 0.033 2.2
NAcc mRNA stability 11 0.486 2.2
OFC alternative polyA 0 0.000 2.3
OFC alternative TSS 0 0.000 2.0
OFC gene expression 13 0.351 2.2
OFC isoform ratio 1 0.123 2.1
OFC intron excision ratio 0 0.000 2.4
OFC mRNA stability 3 0.278 2.2
PL alternative polyA 10 0.701 2.3
PL alternative TSS 7 0.596 2.3
PL gene expression 30 0.406 2.2
PL isoform ratio 3 0.136 2.0
PL intron excision ratio 1 0.028 2.2
PL mRNA stability 14 0.480 2.1

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