Hub : Traits

Bone: cortical area

Tags: Physiology · Bone

Project: r01_doug_adams

5 significantly associated models · 4 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 10 105499327 107195627 4 1 9.1e-14 1.5e-09 0.015 84 Ccdc57

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 6.1 2 1 100 0.00 1.0e+00 Ccdc57 NA
BMI without tail 5.8 2 0 0 0.00 1.0e+00 Ccdc57 B3gntl1
Body weight 8.2 4 1 100 1.00 9.4e-05 Tbcd Ccdc57 B3gntl1 NA
Heart weight 5.2 2 0 0 0.00 1.0e+00 Ccdc57 NA
Left kidney weight 3.6 2 0 0 0.00 1.0e+00 Ccdc57 NA
Right kidney weight 3.4 2 0 0 0.00 1.0e+00 Ccdc57 NA
Tail length 3.1 1 0 0 0.00 1.0e+00 B3gntl1
Length with tail 2.7 4 0 0 0.99 6.0e-04 Tbcd Ccdc57 B3gntl1 NA
Length without tail 4.3 1 0 0 0.00 1.0e+00 NA
Retroperitoneal fat weight 2.6 3 0 0 0.00 1.0e+00 Tbcd Ccdc57 B3gntl1
Tibia length 20.4 4 4 400 0.99 1.2e-03 Tbcd Ccdc57 B3gntl1 NA
Delay discounting water rate 12 sec 5.5 1 0 0 0.00 1.0e+00 Ccdc57
Delay discounting water rate 24 sec 8.6 1 0 0 0.00 1.0e+00 Ccdc57
Delay discounting water rate 6 sec 6.9 1 0 0 0.00 1.0e+00 Ccdc57
Conditioned locomotion 5.9 1 0 0 0.00 1.0e+00 B3gntl1
Condit. Reinf. active minus inactive responses 6.7 1 0 0 0.00 1.0e+00 B3gntl1
Condit. Reinf. active-inactive response ratio 6.8 3 0 0 0.00 1.0e+00 Tbcd B3gntl1 NA
Locomotion distance, session 7 5.3 1 0 0 0.00 1.0e+00 NA
Bone: cortical thickness 26.0 4 3 300 1.00 1.7e-04 Tbcd Ccdc57 B3gntl1 NA
Bone: cortical thickness 16.9 2 0 0 0.00 1.0e+00 Ccdc57 NA
Bone: cortical tissue density 5.6 1 0 0 0.00 1.0e+00 B3gntl1
Bone: elastic work 12.2 4 0 0 0.99 9.4e-04 Tbcd Ccdc57 B3gntl1 NA
Bone: final force 20.8 4 1 100 1.00 2.2e-05 Tbcd Ccdc57 B3gntl1 NA
Bone: final moment 21.6 4 1 100 1.00 8.2e-08 Tbcd Ccdc57 B3gntl1 NA
Bone: maximum diameter 6.1 4 0 0 1.00 3.1e-04 Tbcd Ccdc57 B3gntl1 NA
Bone: maximum force 21.2 4 3 300 1.00 1.4e-06 Tbcd Ccdc57 B3gntl1 NA
Bone: maximum moment 21.8 4 4 400 1.00 9.5e-06 Tbcd Ccdc57 B3gntl1 NA
Bone: minimum diameter 6.4 4 0 0 0.99 1.4e-03 Tbcd Ccdc57 B3gntl1 NA
Bone: periosteal estimation 7.6 4 0 0 0.99 6.2e-04 Tbcd Ccdc57 B3gntl1 NA
Bone: periosteal perimeter 8.5 4 0 0 0.98 4.3e-03 Tbcd Ccdc57 B3gntl1 NA
Bone: stiffness 12.6 2 0 0 0.00 1.0e+00 Ccdc57 NA
Bone: tissue strength 9.8 1 0 0 0.00 1.0e+00 Ccdc57
Delta ambulatory time before/after self-admin 6.3 1 0 0 0.00 1.0e+00 Tbcd

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 1.6
Adipose alternative TSS 0 0.000 1.5
Adipose gene expression 0 0.000 1.5
Adipose isoform ratio 0 0.000 1.6
Adipose intron excision ratio 0 0.000 1.5
Adipose mRNA stability 1 0.029 1.5
BLA alternative polyA 0 0.000 1.3
BLA alternative TSS 0 0.000 1.4
BLA gene expression 0 0.000 1.6
BLA isoform ratio 0 0.000 1.5
BLA intron excision ratio 0 0.000 1.5
BLA mRNA stability 1 0.049 1.5
Brain alternative polyA 0 0.000 1.5
Brain alternative TSS 0 0.000 1.6
Brain gene expression 0 0.000 1.5
Brain isoform ratio 0 0.000 1.5
Brain intron excision ratio 0 0.000 1.5
Brain mRNA stability 0 0.000 1.5
Eye alternative polyA 0 0.000 1.9
Eye alternative TSS 0 0.000 1.7
Eye gene expression 0 0.000 1.7
Eye isoform ratio 0 0.000 1.5
Eye intron excision ratio 0 0.000 1.6
Eye mRNA stability 0 0.000 1.6
IL alternative polyA 0 0.000 1.6
IL alternative TSS 0 0.000 1.3
IL gene expression 0 0.000 1.5
IL isoform ratio 0 0.000 1.6
IL intron excision ratio 0 0.000 1.6
IL mRNA stability 0 0.000 1.5
LHb alternative polyA 0 0.000 1.5
LHb alternative TSS 0 0.000 1.6
LHb gene expression 0 0.000 1.6
LHb isoform ratio 0 0.000 1.6
LHb intron excision ratio 0 0.000 1.4
LHb mRNA stability 1 0.097 1.5
Liver alternative polyA 0 0.000 1.4
Liver alternative TSS 0 0.000 1.5
Liver gene expression 0 0.000 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 1.4
NAcc alternative TSS 2 0.216 1.7
NAcc gene expression 0 0.000 1.5
NAcc isoform ratio 0 0.000 1.5
NAcc intron excision ratio 0 0.000 1.5
NAcc mRNA stability 0 0.000 1.5
OFC alternative polyA 0 0.000 1.6
OFC alternative TSS 0 0.000 1.5
OFC gene expression 0 0.000 1.6
OFC isoform ratio 0 0.000 1.6
OFC intron excision ratio 0 0.000 1.5
OFC mRNA stability 0 0.000 1.5
PL alternative polyA 0 0.000 1.4
PL alternative TSS 0 0.000 1.6
PL gene expression 0 0.000 1.5
PL isoform ratio 0 0.000 1.5
PL intron excision ratio 0 0.000 1.5
PL mRNA stability 0 0.000 1.5

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