Hub : Traits

Bone: trabecular thickness

Tags: Physiology · Bone

Project: r01_doug_adams

1 significantly associated model · 1 unique gene

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 2.3e-08 6.7e-05 0.0031 45 Rap2b

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
Left kidney weight 1.6 1 0 0 0 1 Rap2b
Extensor digitorum longus weight 2.5 1 0 0 0 1 Rap2b
Number of licking bursts 7.6 1 0 0 0 1 Rap2b
Times rat made contact with spout 8.1 1 0 0 0 1 Rap2b
Mean time between licks in bursts 11.1 1 0 0 0 1 Rap2b
Std. dev. time between licks in bursts 10.8 1 0 0 0 1 Rap2b
Water consumed over 24 hours 7.5 1 0 0 0 1 Rap2b
Locomotor testing distance 3.7 1 0 0 0 1 Rap2b
Reaction time mean minus median 3.2 1 0 0 0 1 Rap2b
Reaction time mean minus median AUC 4.4 1 0 0 0 1 Rap2b
Reaction time mean 3.5 1 0 0 0 1 Rap2b
Reaction time mean AUC 4.7 1 0 0 0 1 Rap2b
Reaction time omissions 4.8 1 0 0 0 1 Rap2b
Std. dev. reaction times 5.2 1 0 0 0 1 Rap2b
Condit. Reinf. lever presses 5.8 1 0 0 0 1 Rap2b
Baseline Anxiety 4.3 1 0 0 0 1 Rap2b
Context. condit. distance diff. score 11.6 1 0 0 0 1 Rap2b
Locomotion distance, session 1 3.1 1 0 0 0 1 Rap2b
Locomotion distance, session 2 3.9 1 0 0 0 1 Rap2b
Locomotion distance, session 3 5.1 1 0 0 0 1 Rap2b
Condit. Reinf. active minus inactive responses 17.9 1 0 0 0 1 Rap2b
Condit. Reinf. active-inactive response ratio 18.9 1 0 0 0 1 Rap2b
Condit. Reinf. active responses 13.7 1 0 0 0 1 Rap2b
Incentive salience index mean 22.6 1 1 100 0 1 Rap2b
Condit. Reinf. lever presses 8.2 1 0 0 0 1 Rap2b
Total zone transitions, hab. session 1 4.7 1 0 0 0 1 Rap2b
Total locomotion distance, hab. session 1 7.0 1 0 0 0 1 Rap2b
Locomotion velocity, hab. session 1 10.1 1 0 0 0 1 Rap2b
Novelty place preference 3.9 1 0 0 0 1 Rap2b
Total locomotion distance, NPP test 3.1 1 0 0 0 1 Rap2b
Locomotion velocity, NPP test 4.1 1 0 0 0 1 Rap2b
Pavlov. Cond. lever latency 4.7 1 0 0 0 1 Rap2b
Pavlov. Cond. intertrial magazine entries 6.2 1 0 0 0 1 Rap2b
Bone: apparent density 14.4 1 0 0 0 1 Rap2b
Bone surface 4.8 1 0 0 0 1 Rap2b
Bone volume 7.5 1 0 0 0 1 Rap2b
Bone: connectivity density 10.6 1 0 0 0 1 Rap2b
Bone: cortical apparent density 4.3 1 0 0 0 1 Rap2b
Bone: cortical porosity 8.7 1 0 0 0 1 Rap2b
Bone: cortical porosity 6.3 1 0 0 0 1 Rap2b
Bone: cortical tissue density 4.9 1 0 0 0 1 Rap2b
Bone: maximum diameter 3.8 1 0 0 0 1 Rap2b
Bone: post-yield work 3.8 1 0 0 0 1 Rap2b
Bone: trabecular number 19.8 1 1 100 0 1 Rap2b
Bone: trabecular spacing 14.0 1 0 0 0 1 Rap2b
Extinction: sum of active levers before priming 6.6 1 0 0 0 1 Rap2b
Time to tail flick, vehicle, after self-admin 9.4 1 0 0 0 1 Rap2b
Seeking ratio, delayed vs. immediate footshock 4.3 1 0 0 0 1 Rap2b
Seeking ratio, punishment vs. effort 6.5 1 0 0 0 1 Rap2b
Co content in liver 7.0 1 0 0 0 1 Rap2b
Fe content in liver 6.1 1 0 0 0 1 Rap2b
Se content in liver 6.7 1 0 0 0 1 Rap2b

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 1.32
Adipose alternative TSS 0 0.000 1.27
Adipose gene expression 0 0.000 1.27
Adipose isoform ratio 0 0.000 1.24
Adipose intron excision ratio 0 0.000 1.22
Adipose mRNA stability 0 0.000 1.27
BLA alternative polyA 0 0.000 1.19
BLA alternative TSS 0 0.000 1.23
BLA gene expression 0 0.000 1.21
BLA isoform ratio 0 0.000 1.21
BLA intron excision ratio 0 0.000 1.18
BLA mRNA stability 0 0.000 1.23
Brain alternative polyA 0 0.000 1.31
Brain alternative TSS 0 0.000 1.20
Brain gene expression 0 0.000 1.19
Brain isoform ratio 0 0.000 1.19
Brain intron excision ratio 0 0.000 1.15
Brain mRNA stability 0 0.000 1.22
Eye alternative polyA 0 0.000 1.24
Eye alternative TSS 0 0.000 0.98
Eye gene expression 0 0.000 1.23
Eye isoform ratio 0 0.000 1.26
Eye intron excision ratio 0 0.000 1.29
Eye mRNA stability 0 0.000 1.15
IL alternative polyA 0 0.000 1.12
IL alternative TSS 0 0.000 1.39
IL gene expression 0 0.000 1.16
IL isoform ratio 0 0.000 1.13
IL intron excision ratio 0 0.000 1.07
IL mRNA stability 0 0.000 1.23
LHb alternative polyA 0 0.000 1.32
LHb alternative TSS 0 0.000 1.45
LHb gene expression 0 0.000 1.19
LHb isoform ratio 0 0.000 1.18
LHb intron excision ratio 0 0.000 1.09
LHb mRNA stability 0 0.000 1.28
Liver alternative polyA 0 0.000 1.21
Liver alternative TSS 0 0.000 1.25
Liver gene expression 1 0.014 1.27
Liver isoform ratio 0 0.000 1.23
Liver intron excision ratio 0 0.000 1.14
Liver mRNA stability 0 0.000 1.26
NAcc alternative polyA 0 0.000 1.23
NAcc alternative TSS 0 0.000 1.20
NAcc gene expression 0 0.000 1.21
NAcc isoform ratio 0 0.000 1.28
NAcc intron excision ratio 0 0.000 1.14
NAcc mRNA stability 0 0.000 1.24
OFC alternative polyA 0 0.000 1.17
OFC alternative TSS 0 0.000 1.26
OFC gene expression 0 0.000 1.22
OFC isoform ratio 0 0.000 1.23
OFC intron excision ratio 0 0.000 1.17
OFC mRNA stability 0 0.000 1.21
PL alternative polyA 0 0.000 1.20
PL alternative TSS 0 0.000 1.22
PL gene expression 0 0.000 1.21
PL isoform ratio 0 0.000 1.19
PL intron excision ratio 0 0.000 1.12
PL mRNA stability 0 0.000 1.21

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