Hub : Traits

Trabecular tissue density

Project: r01_doug_adams

5 significantly associated models · 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 113826986 115224581 1 1 8.5e-08 2.9e-07 0.63 99 Itgb3bp

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
Tibia length in mm 2.7 1 0 0 -0.47 0.53 Itgb3bp
TA weight in grams 9.0 1 1 100 -0.11 0.86 Itgb3bp
Average time between licks in bursts 6.4 1 0 0 0.56 0.44 Itgb3bp
tautz: manual_spc15 5.4 1 0 0 0.00 1.00 Itgb3bp
tautz: manual_spc24 5.2 1 0 0 0.00 1.00 Itgb3bp
tautz: manual_spc13 6.6 1 0 0 -0.51 0.49 Itgb3bp
tautz: manual_mpc6 5.8 1 0 0 0.00 1.00 Itgb3bp
punishment 5.5 1 0 0 0.00 1.00 Itgb3bp

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 1.3
Adipose gene expression 0 0.000 1.4
Adipose isoform ratio 0 0.000 1.4
Adipose intron excision ratio 0 0.000 1.4
Adipose mRNA stability 0 0.000 1.4
BLA alternative polyA 0 0.000 1.5
BLA alternative TSS 0 0.000 1.4
BLA gene expression 0 0.000 1.4
BLA isoform ratio 0 0.000 1.5
BLA intron excision ratio 0 0.000 1.4
BLA mRNA stability 0 0.000 1.4
Brain alternative polyA 0 0.000 1.4
Brain alternative TSS 0 0.000 1.3
Brain gene expression 0 0.000 1.4
Brain isoform ratio 1 0.032 1.4
Brain intron excision ratio 0 0.000 1.4
Brain mRNA stability 0 0.000 1.4
Eye alternative polyA 0 0.000 1.4
Eye alternative TSS 0 0.000 1.3
Eye gene expression 0 0.000 1.5
Eye isoform ratio 0 0.000 1.5
Eye intron excision ratio 0 0.000 1.5
Eye mRNA stability 0 0.000 1.6
IL alternative polyA 0 0.000 1.4
IL alternative TSS 0 0.000 1.4
IL gene expression 0 0.000 1.4
IL isoform ratio 0 0.000 1.3
IL intron excision ratio 0 0.000 1.3
IL mRNA stability 0 0.000 1.3
LHb alternative polyA 0 0.000 1.3
LHb alternative TSS 0 0.000 1.5
LHb gene expression 0 0.000 1.4
LHb isoform ratio 0 0.000 1.4
LHb intron excision ratio 0 0.000 1.3
LHb mRNA stability 0 0.000 1.4
Liver alternative polyA 0 0.000 1.5
Liver alternative TSS 0 0.000 1.3
Liver gene expression 0 0.000 1.3
Liver isoform ratio 0 0.000 1.4
Liver intron excision ratio 0 0.000 1.5
Liver mRNA stability 0 0.000 1.3
NAcc alternative polyA 0 0.000 1.3
NAcc alternative TSS 0 0.000 1.3
NAcc gene expression 1 0.030 1.4
NAcc isoform ratio 0 0.000 1.5
NAcc intron excision ratio 1 0.105 1.3
NAcc mRNA stability 0 0.000 1.4
NAcc2 alternative polyA 0 0.000 1.4
NAcc2 alternative TSS 0 0.000 1.5
NAcc2 gene expression 0 0.000 1.4
NAcc2 isoform ratio 0 0.000 1.5
NAcc2 intron excision ratio 1 0.038 1.4
NAcc2 mRNA stability 0 0.000 1.4
OFC alternative polyA 0 0.000 1.4
OFC alternative TSS 0 0.000 1.4
OFC gene expression 0 0.000 1.4
OFC isoform ratio 0 0.000 1.3
OFC intron excision ratio 1 0.100 1.4
OFC mRNA stability 0 0.000 1.3
PL alternative polyA 0 0.000 1.4
PL alternative TSS 0 0.000 1.4
PL gene expression 0 0.000 1.4
PL isoform ratio 0 0.000 1.4
PL intron excision ratio 0 0.000 1.5
PL mRNA stability 0 0.000 1.4
PL2 alternative polyA 0 0.000 1.4
PL2 alternative TSS 0 0.000 1.6
PL2 gene expression 0 0.000 1.4
PL2 isoform ratio 0 0.000 1.5
PL2 intron excision ratio 0 0.000 1.4
PL2 mRNA stability 0 0.000 1.4

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