Hub : Traits

Bone: maximum diameter

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 5 59640609 61037099 1 1 1.9e-07 1e-05 0.012 68 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
Social time 4.1 1 0 0 0 1 Tmod1
Intermittent access intake day 1-15 change 4.4 1 0 0 0 1 Tmod1
Progressive ratio test 2 active lever presses 4.5 1 0 0 0 1 Tmod1
Progressive ratio test 2 breakpoint 5.1 1 0 0 0 1 Tmod1
Short access day 10 total locomotion 7.0 1 0 0 0 1 Tmod1
Stereotopy head waving bouts, day 7 3.9 1 0 0 0 1 Tmod1
Stereotopy head waving duration, day 7 3.7 1 0 0 0 1 Tmod1
Degree of sensitization stereotypy 6.3 1 0 0 0 1 Tmod1
Condit. Reinf. active minus inactive responses 4.2 1 0 0 0 1 Tmod1
Condit. Reinf. active responses 5.1 1 0 0 0 1 Tmod1
Incentive salience index mean 7.1 1 0 0 0 1 Tmod1
Condit. Reinf. lever presses 5.3 1 0 0 0 1 Tmod1
Pavlov. Cond. lever latency 3.3 1 0 0 0 1 Tmod1
Pavlov. Cond. lever contacts 4.1 1 0 0 0 1 Tmod1
Bone: cortical area 9.6 1 0 0 0 1 Tmod1
Bone: cortical porosity 5.0 1 0 0 0 1 Tmod1
Bone: cortical porosity 8.5 1 0 0 0 1 Tmod1
Bone: elastic work 3.0 1 0 0 0 1 Tmod1
Bone: endosteal perimeter 7.4 1 0 0 0 1 Tmod1
Bone: minimum diameter 6.2 1 0 0 0 1 Tmod1
Bone: periosteal estimation 5.7 1 0 0 0 1 Tmod1
Bone: periosteal perimeter 17.7 1 1 100 0 1 Tmod1
Bone: trabecular tissue density 3.0 1 0 0 0 1 Tmod1
Zn content in liver 6.7 1 0 0 0 1 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 0.000 1.9
Adipose alternative TSS 0 0.000 1.8
Adipose gene expression 0 0.000 1.8
Adipose isoform ratio 0 0.000 1.8
Adipose intron excision ratio 0 0.000 2.0
Adipose mRNA stability 0 0.000 1.8
BLA alternative polyA 0 0.000 1.7
BLA alternative TSS 0 0.000 1.7
BLA gene expression 0 0.000 1.9
BLA isoform ratio 0 0.000 1.7
BLA intron excision ratio 0 0.000 1.8
BLA mRNA stability 0 0.000 1.9
Brain alternative polyA 0 0.000 1.8
Brain alternative TSS 0 0.000 1.9
Brain gene expression 0 0.000 1.8
Brain isoform ratio 0 0.000 1.8
Brain intron excision ratio 0 0.000 1.8
Brain mRNA stability 0 0.000 1.8
Eye alternative polyA 0 0.000 1.7
Eye alternative TSS 0 0.000 1.7
Eye gene expression 0 0.000 2.1
Eye isoform ratio 0 0.000 1.7
Eye intron excision ratio 0 0.000 1.8
Eye mRNA stability 0 0.000 1.7
IL alternative polyA 0 0.000 1.7
IL alternative TSS 0 0.000 1.6
IL gene expression 0 0.000 1.9
IL isoform ratio 0 0.000 1.8
IL intron excision ratio 0 0.000 1.8
IL mRNA stability 0 0.000 1.8
LHb alternative polyA 0 0.000 1.8
LHb alternative TSS 0 0.000 2.0
LHb gene expression 0 0.000 1.9
LHb isoform ratio 0 0.000 1.8
LHb intron excision ratio 0 0.000 1.9
LHb mRNA stability 0 0.000 1.9
Liver alternative polyA 1 0.067 1.8
Liver alternative TSS 0 0.000 1.8
Liver gene expression 0 0.000 1.8
Liver isoform ratio 0 0.000 1.7
Liver intron excision ratio 0 0.000 1.9
Liver mRNA stability 0 0.000 1.8
NAcc alternative polyA 0 0.000 1.8
NAcc alternative TSS 0 0.000 1.8
NAcc gene expression 0 0.000 1.8
NAcc isoform ratio 0 0.000 1.8
NAcc intron excision ratio 0 0.000 1.8
NAcc mRNA stability 0 0.000 1.9
OFC alternative polyA 0 0.000 1.7
OFC alternative TSS 0 0.000 1.7
OFC gene expression 0 0.000 1.9
OFC isoform ratio 0 0.000 1.8
OFC intron excision ratio 0 0.000 1.9
OFC mRNA stability 0 0.000 2.0
PL alternative polyA 0 0.000 1.8
PL alternative TSS 0 0.000 1.8
PL gene expression 0 0.000 1.9
PL isoform ratio 0 0.000 1.7
PL intron excision ratio 0 0.000 1.8
PL mRNA stability 0 0.000 1.9

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