Hub : Traits

Bone: trabecular number

Tags: Physiology · Bone

Project: r01_doug_adams

9 significantly associated models · 8 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 144900859 146298381 1 1 2.9e-08 4.1e-07 6.1e-10 -49 Rap2b
2 2 147736101 148780607 1 1 1.6e-07 5.1e-07 1.0e+00 100 Gmps
3 2 150531618 152825152 5 2 5.5e-09 2.4e-07 4.3e-02 85 Schip1 Mfsd1
4 7 16845355 16970279 1 1 1.8e-23 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 171.8 1 1 20 0.00 1.0e+00 NA
Body weight 11.2 1 1 20 0.00 1.0e+00 NA
Epididymis fat weight 136.2 1 1 20 0.00 1.0e+00 NA
Glucose 6.6 1 0 0 0.00 1.0e+00 NA
Heart weight 11.4 1 0 0 0.00 1.0e+00 NA
Left kidney weight 32.9 2 1 20 0.00 1.0e+00 Gmps NA
Right kidney weight 67.3 1 1 20 0.00 1.0e+00 NA
Tail length 91.1 1 1 20 0.00 1.0e+00 NA
Length with tail 4.0 1 0 0 0.00 1.0e+00 NA
Length without tail 120.2 1 1 20 0.00 1.0e+00 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 29.4 1 1 20 0.00 1.0e+00 NA
Extensor digitorum longus weight 6.9 7 1 20 0.00 9.9e-01 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Soleus weight 21.9 1 1 20 0.00 1.0e+00 NA
Tibialis anterior weight 96.0 1 1 20 0.00 1.0e+00 NA
Tibia length 7.4 1 0 0 0.00 1.0e+00 NA
Number of licking bursts 125.0 2 1 20 0.00 1.0e+00 NA Rap2b
Food consumed during 24 hour testing period 17.5 1 0 0 0.00 1.0e+00 NA
Times rat made contact with spout 64.9 2 1 20 0.00 1.0e+00 NA Rap2b
Mean time between licks in bursts 19.1 7 1 20 0.06 8.9e-01 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Mean num. licks in bursts 258.2 1 1 20 0.00 1.0e+00 NA
Std. dev. time between licks in bursts 150.9 2 1 20 0.00 1.0e+00 NA Rap2b
Water consumed over 24 hours 7.5 1 0 0 0.00 1.0e+00 Rap2b
Indifference point 0 sec 21.3 1 1 20 0.00 1.0e+00 NA
Indifference point AUC 66.7 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 0 sec 20.1 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 12 sec 156.9 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 277.7 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 24 sec 43.7 1 1 20 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 145.0 1 1 20 0.00 1.0e+00 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 20 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 100.9 1 1 20 0.00 1.0e+00 NA
Delay discounting water rate 6 sec 70.2 1 1 20 0.00 1.0e+00 NA
Locomotor testing distance 9.7 2 0 0 0.00 1.0e+00 Gmps NA
Locomotor testing rearing 23.9 1 1 20 0.00 1.0e+00 NA
Light reinforcement 1 84.1 1 1 20 0.00 1.0e+00 NA
Reaction time number correct 7.0 3 0 0 0.00 1.0e+00 Mfsd1 Rsrc1 NA
Reaction time mean minus median 6.3 1 0 0 0.00 1.0e+00 Gmps
Reaction time mean minus median AUC 8.5 1 0 0 0.00 1.0e+00 Gmps
Reaction time num false alarms 48.1 2 1 20 0.00 1.0e+00 Schip1 NA
Reaction time num false alarms AUC 128.2 1 1 20 0.00 1.0e+00 NA
Reaction time trials correct on left 7.0 3 0 0 0.00 1.0e+00 Mfsd1 Rsrc1 NA
Reaction time trials on left 7.1 3 0 0 0.00 1.0e+00 Mfsd1 Rsrc1 NA
Reaction time mean 34.2 2 1 20 0.00 1.0e+00 Gmps NA
Reaction time mean AUC 48.3 2 1 20 0.00 1.0e+00 Gmps NA
Median of all reaction times 80.2 1 1 20 0.00 1.0e+00 NA
Reaction time omissions 9.1 1 0 0 0.00 1.0e+00 Gmps
Reaction time false alarm rate 104.2 1 1 20 0.00 1.0e+00 NA
Reaction time premature initiation rate 47.3 1 1 20 0.00 1.0e+00 NA
Reaction time premature initiations 49.8 1 1 20 0.00 1.0e+00 NA
Std. dev. reaction times 18.2 2 1 20 0.00 1.0e+00 Gmps NA
Reaction time trials completed 7.1 3 0 0 0.00 1.0e+00 Mfsd1 Rsrc1 NA
Reaction time trials AUC 15.6 1 0 0 0.00 1.0e+00 NA
Social responses 108.6 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 135.7 1 1 20 0.00 1.0e+00 NA
Cocaine response after cond. not corrected 176.6 1 1 20 0.00 1.0e+00 NA
Cocaine response before conditioning 28.6 1 1 20 0.00 1.0e+00 NA
Saline control response 50.6 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 46.4 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active-inactive response ratio 68.7 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active responses 11.1 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. lever presses 5.8 1 0 0 0.00 1.0e+00 Rap2b
Pavlov. Cond. lever latency 60.5 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 173.4 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 216.7 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. index score 102.2 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. latency score 110.3 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 244.9 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 106.2 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 90.6 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. response bias 51.3 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 104.0 1 1 20 0.00 1.0e+00 NA
Intermittent access intake escalation 141.1 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 30.6 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 52.9 1 1 20 0.00 1.0e+00 NA
Intermittent access day 1 locomotion 27.1 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 61.6 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 45.4 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 125.9 2 1 20 0.00 1.0e+00 NA Rap2b
Locomotion velocity, session 1 190.8 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 1 609.6 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 2 139.6 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 2 1269.9 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 3 178.9 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 3 117.5 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 33.2 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, session 7 98.9 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 7 31.8 1 1 20 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 7 68.4 1 1 20 0.00 1.0e+00 NA
Stereotopy head waving duration, day 7 102.2 1 1 20 0.00 1.0e+00 NA
Locomotion distance, session 8 171.7 1 1 20 0.00 1.0e+00 NA
Degree of sensitization distance 103.9 2 1 20 0.00 1.0e+00 Schip1 NA
Degree of sensitization stereotypy 37.5 1 1 20 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 17.9 1 0 0 0.00 1.0e+00 Rap2b
Condit. Reinf. active-inactive response ratio 63.1 2 1 20 0.00 1.0e+00 NA Rap2b
Condit. Reinf. active responses 14.0 3 0 0 0.00 1.0e+00 Gmps NA Rap2b
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.0e+00 NA
Incentive salience index mean 19.1 2 1 20 0.00 1.0e+00 NA Rap2b
Condit. Reinf. lever presses 21.7 2 1 20 0.00 1.0e+00 NA Rap2b
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 20 0.00 1.0e+00 NA
Total locomotion distance, hab. session 1 143.2 2 1 20 0.00 1.0e+00 NA Rap2b
Locomotion velocity, hab. session 1 179.8 2 1 20 0.00 1.0e+00 NA Rap2b
Time in familiar zone, hab. session 2 15.3 6 1 20 -1.00 2.2e-05 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA
Time in novel zone, hab. session 2 58.4 1 1 20 0.00 1.0e+00 NA
Total zone transitions, hab. session 2 421.2 1 1 20 0.00 1.0e+00 NA
Total locomotion distance, hab. session 2 214.3 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, hab. session 2 225.0 1 1 20 0.00 1.0e+00 NA
Total zone transitions, NPP test 376.1 1 1 20 0.00 1.0e+00 NA
Total locomotion distance, NPP test 269.3 1 1 20 0.00 1.0e+00 NA
Locomotion velocity, NPP test 161.8 2 1 20 0.00 1.0e+00 Mfsd1 NA
Pavlov. Cond. lever latency 9.3 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 95.9 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 40.1 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. index score 51.9 1 1 20 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 20 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 6.9 1 0 0 0.00 1.0e+00 Mlf1
Pavlov. Cond. lever-magazine prob. diff. 88.1 1 1 20 0.00 1.0e+00 NA
Pavlov. Cond. response bias 52.4 1 1 20 0.00 1.0e+00 NA
Bone: apparent density 16.5 8 2 40 0.99 1.2e-07 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Bone surface 10.2 8 1 20 0.22 5.7e-01 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Bone volume 14.4 8 1 20 0.28 4.7e-01 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Bone: connectivity density 8.8 8 0 0 0.96 3.9e-05 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Bone: cortical porosity 98.6 2 1 20 0.00 1.0e+00 NA Rap2b
Bone: cortical porosity 155.8 1 1 20 0.00 1.0e+00 NA
Bone: cortical thickness 8.8 1 0 0 0.00 1.0e+00 NA
Bone: cortical thickness 9.7 4 0 0 1.00 1.5e-03 Schip1 Mlf1 Mfsd1 NA
Bone: elastic displacement 28.2 1 1 20 0.00 1.0e+00 NA
Bone: endosteal estimation 18.4 1 1 20 0.00 1.0e+00 NA
Bone: final force 57.4 1 1 20 0.00 1.0e+00 NA
Bone: final moment 45.6 1 1 20 0.00 1.0e+00 NA
Bone: marrow area 15.3 1 1 20 0.00 1.0e+00 NA
Bone: maximum force 60.3 1 1 20 0.00 1.0e+00 NA
Bone: maximum moment 41.2 1 1 20 0.00 1.0e+00 NA
Bone: minimum diameter 86.7 1 1 20 0.00 1.0e+00 NA
Bone: periosteal estimation 10.0 1 0 0 0.00 1.0e+00 NA
Bone: periosteal perimeter 8.8 1 0 0 0.00 1.0e+00 NA
Bone: post-yield work 124.3 1 1 20 0.00 1.0e+00 NA
Bone: stiffness 136.8 1 1 20 0.00 1.0e+00 NA
Bone: tissue strength 136.0 1 1 20 0.00 1.0e+00 NA
Bone: trabecular spacing 11.3 7 0 0 -1.00 1.8e-08 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 Rap2b
Bone: trabecular thickness 17.9 8 1 20 0.59 9.3e-02 Schip1 Mlf1 Gfm1 Mfsd1 Gmps Rsrc1 NA Rap2b
Bone: trabecular tissue density 66.6 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 12.2 1 0 0 0.00 1.0e+00 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 78.0 1 1 20 0.00 1.0e+00 NA
Time in closed arm after self-admin 40.2 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, after self-admin 9.4 1 0 0 0.00 1.0e+00 Rap2b
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 27.2 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 25.0 1 1 20 0.00 1.0e+00 NA
Locomotion in novel chamber 10.2 1 0 0 0.00 1.0e+00 NA
Seeking ratio, punishment vs. effort 6.5 1 0 0 0.00 1.0e+00 Rap2b
Run reversals in cocaine runway, males 39.3 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 239.3 1 1 20 0.00 1.0e+00 NA
Co content in liver 75.2 2 1 20 0.00 1.0e+00 NA Rap2b
Fe content in liver 10.3 1 0 0 0.00 1.0e+00 NA
K content in liver 87.3 1 1 20 0.00 1.0e+00 NA
Mn content in liver 207.1 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 26.8 2 1 20 0.00 1.0e+00 NA Rap2b
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 1.5
Adipose alternative TSS 0 0.000 1.6
Adipose gene expression 1 0.012 1.6
Adipose isoform ratio 0 0.000 1.5
Adipose intron excision ratio 0 0.000 1.5
Adipose mRNA stability 1 0.029 1.6
BLA alternative polyA 0 0.000 1.4
BLA alternative TSS 0 0.000 1.7
BLA gene expression 1 0.016 1.6
BLA isoform ratio 1 0.057 1.5
BLA intron excision ratio 0 0.000 1.6
BLA mRNA stability 0 0.000 1.5
Brain alternative polyA 0 0.000 1.5
Brain alternative TSS 0 0.000 1.6
Brain gene expression 0 0.000 1.6
Brain isoform ratio 0 0.000 1.5
Brain intron excision ratio 0 0.000 1.6
Brain mRNA stability 0 0.000 1.5
Eye alternative polyA 0 0.000 1.7
Eye alternative TSS 0 0.000 1.6
Eye gene expression 0 0.000 1.6
Eye isoform ratio 0 0.000 1.5
Eye intron excision ratio 0 0.000 1.7
Eye mRNA stability 0 0.000 1.6
IL alternative polyA 0 0.000 1.4
IL alternative TSS 0 0.000 1.5
IL gene expression 0 0.000 1.6
IL isoform ratio 0 0.000 1.6
IL intron excision ratio 0 0.000 1.7
IL mRNA stability 0 0.000 1.5
LHb alternative polyA 0 0.000 1.6
LHb alternative TSS 0 0.000 1.9
LHb gene expression 0 0.000 1.6
LHb isoform ratio 0 0.000 1.5
LHb intron excision ratio 0 0.000 1.7
LHb mRNA stability 0 0.000 1.6
Liver alternative polyA 0 0.000 1.4
Liver alternative TSS 0 0.000 1.5
Liver gene expression 1 0.014 1.5
Liver isoform ratio 0 0.000 1.5
Liver intron excision ratio 0 0.000 1.4
Liver mRNA stability 0 0.000 1.5
NAcc alternative polyA 0 0.000 1.5
NAcc alternative TSS 0 0.000 1.5
NAcc gene expression 1 0.016 1.6
NAcc isoform ratio 0 0.000 1.6
NAcc intron excision ratio 0 0.000 1.6
NAcc mRNA stability 0 0.000 1.6
OFC alternative polyA 0 0.000 1.5
OFC alternative TSS 1 0.313 1.4
OFC gene expression 0 0.000 1.6
OFC isoform ratio 1 0.123 1.5
OFC intron excision ratio 0 0.000 1.7
OFC mRNA stability 0 0.000 1.6
PL alternative polyA 0 0.000 1.5
PL alternative TSS 0 0.000 1.6
PL gene expression 0 0.000 1.6
PL isoform ratio 1 0.045 1.6
PL intron excision ratio 0 0.000 1.6
PL mRNA stability 0 0.000 1.5

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