Hub : Traits

Bone: periosteal perimeter

Tags: Physiology · Bone

Project: r01_doug_adams

4 significantly associated models · 3 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 254889979 256760534 2 1 1.2e-07 3.3e-07 1.000 100 Afap1l2
2 5 59640609 61037099 1 1 6.0e-08 6.3e-06 0.012 69 Tmod1

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 10.3 2 2 100 0.00 1.00000 Afap1l2 Dclre1a
BMI without tail 4.3 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Body weight 11.2 2 2 100 0.00 1.00000 Afap1l2 Dclre1a
Epididymis fat weight 17.3 2 2 100 0.00 1.00000 Afap1l2 Dclre1a
Glucose 5.6 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Left kidney weight 3.8 1 0 0 0.00 1.00000 Dclre1a
Right kidney weight 5.5 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Length with tail 2.6 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Length without tail 6.6 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Liver weight, left 5.2 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Liver weight, right 8.9 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Parametrial fat weight 11.5 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Retroperitoneal fat weight 15.2 2 2 100 0.00 1.00000 Afap1l2 Dclre1a
Intraocular pressure 5.9 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Soleus weight 4.3 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Tibia length 2.3 1 0 0 0.00 1.00000 Dclre1a
Indifference point 0 sec 5.1 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Delay discounting total patch changes 0 sec 5.1 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Delay discounting total patch changes 18 sec 7.1 1 0 0 0.00 1.00000 Afap1l2
Delay discounting total patch changes 24 sec 5.1 1 0 0 0.00 1.00000 Afap1l2
Delay discounting total patch changes 6 sec 7.4 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Social responses 6.9 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Condit. Reinf. active responses 6.0 1 0 0 0.00 1.00000 Afap1l2
Cocaine induced anxiety 7.8 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Baseline Anxiety 8.6 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Total sessions with >9 infusions 7.8 1 0 0 0.00 1.00000 Dclre1a
Short access day 10 total locomotion 6.9 1 0 0 0.00 1.00000 Tmod1
Degree of sensitization stereotypy 6.3 1 0 0 0.00 1.00000 Tmod1
Condit. Reinf. active responses 5.8 1 0 0 0.00 1.00000 Tmod1
Incentive salience index mean 7.5 1 0 0 0.00 1.00000 Tmod1
Condit. Reinf. lever presses 5.4 1 0 0 0.00 1.00000 Tmod1
Bone volume 4.0 1 0 0 0.00 1.00000 Afap1l2
Bone: cortical area 11.6 3 0 0 0.99 0.00731 Tmod1 Afap1l2 Dclre1a
Bone: cortical porosity 8.6 1 0 0 0.00 1.00000 Tmod1
Bone: cortical thickness 6.6 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Bone: endosteal perimeter 7.3 3 0 0 1.00 0.00023 Tmod1 Afap1l2 Dclre1a
Bone: final force 5.0 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Bone: final moment 5.0 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Bone: maximum diameter 13.1 3 1 50 1.00 0.00048 Tmod1 Afap1l2 Dclre1a
Bone: maximum force 4.3 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Bone: maximum moment 4.3 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Bone: minimum diameter 5.7 3 0 0 1.00 0.00044 Tmod1 Afap1l2 Dclre1a
Bone: periosteal estimation 6.9 3 0 0 0.99 0.00708 Tmod1 Afap1l2 Dclre1a
Bone: trabecular thickness 7.2 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Delay disc. indifference point, 8s delay 6.8 1 0 0 0.00 1.00000 Afap1l2
Weight adjusted by age 8.7 2 0 0 0.00 1.00000 Afap1l2 Dclre1a
Zn content in liver 6.4 1 0 0 0.00 1.00000 Tmod1

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 0.00 1.7
Adipose alternative TSS 0 0.00 1.5
Adipose gene expression 0 0.00 1.6
Adipose isoform ratio 0 0.00 1.6
Adipose intron excision ratio 0 0.00 1.7
Adipose mRNA stability 0 0.00 1.7
BLA alternative polyA 0 0.00 1.6
BLA alternative TSS 0 0.00 1.7
BLA gene expression 0 0.00 1.7
BLA isoform ratio 0 0.00 1.6
BLA intron excision ratio 0 0.00 1.6
BLA mRNA stability 0 0.00 1.7
Brain alternative polyA 0 0.00 1.7
Brain alternative TSS 0 0.00 1.7
Brain gene expression 0 0.00 1.7
Brain isoform ratio 0 0.00 1.6
Brain intron excision ratio 0 0.00 1.7
Brain mRNA stability 0 0.00 1.6
Eye alternative polyA 0 0.00 1.7
Eye alternative TSS 0 0.00 1.5
Eye gene expression 0 0.00 1.9
Eye isoform ratio 0 0.00 1.5
Eye intron excision ratio 0 0.00 1.8
Eye mRNA stability 0 0.00 1.6
IL alternative polyA 0 0.00 1.8
IL alternative TSS 0 0.00 1.4
IL gene expression 0 0.00 1.7
IL isoform ratio 0 0.00 1.7
IL intron excision ratio 0 0.00 1.6
IL mRNA stability 0 0.00 1.7
LHb alternative polyA 0 0.00 1.8
LHb alternative TSS 0 0.00 1.6
LHb gene expression 0 0.00 1.7
LHb isoform ratio 0 0.00 1.6
LHb intron excision ratio 0 0.00 1.7
LHb mRNA stability 0 0.00 1.7
Liver alternative polyA 2 0.13 1.6
Liver alternative TSS 0 0.00 1.7
Liver gene expression 0 0.00 1.7
Liver isoform ratio 0 0.00 1.6
Liver intron excision ratio 0 0.00 1.7
Liver mRNA stability 0 0.00 1.6
NAcc alternative polyA 0 0.00 1.7
NAcc alternative TSS 0 0.00 1.6
NAcc gene expression 0 0.00 1.7
NAcc isoform ratio 0 0.00 1.6
NAcc intron excision ratio 0 0.00 1.6
NAcc mRNA stability 0 0.00 1.7
OFC alternative polyA 0 0.00 1.8
OFC alternative TSS 0 0.00 1.7
OFC gene expression 0 0.00 1.8
OFC isoform ratio 0 0.00 1.6
OFC intron excision ratio 0 0.00 1.6
OFC mRNA stability 2 0.19 1.7
PL alternative polyA 0 0.00 1.7
PL alternative TSS 0 0.00 1.6
PL gene expression 0 0.00 1.7
PL isoform ratio 0 0.00 1.6
PL intron excision ratio 0 0.00 1.6
PL mRNA stability 0 0.00 1.7

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