Hub : Traits

Liver weight, right

Tags: Physiology · Liver · Weight

Project: dissection

17 significantly associated models · 9 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 258394596 260518987 4 1 1.5e-08 9.7e-09 1 100 Cacul1
2 20 5086090 7380732 5 4 5.8e-08 3.4e-08 1 100 Spdef Taf11 Ilrun NA

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 40.9 4 4 80 1.00 5.0e-15 Rab11fip2 Prlhr Cacul1 Sfxn4
BMI without tail 26.8 4 4 80 1.00 1.2e-13 Rab11fip2 Prlhr Cacul1 Sfxn4
Body weight 34.6 5 4 80 0.98 7.0e-09 Srpk1 Rab11fip2 Prlhr Cacul1 Sfxn4
Epididymis fat weight 44.5 8 7 140 0.69 3.0e-03 Spdef Rab11fip2 Prlhr Cacul1 Taf11 Sfxn4 Ilrun NA
Glucose 7.6 2 0 0 1.00 4.1e-04 Cacul1 Taf11
Heart weight 9.5 4 0 0 1.00 1.9e-11 Rab11fip2 Prlhr Cacul1 Sfxn4
Left kidney weight 13.6 4 4 80 0.99 2.5e-10 Rab11fip2 Prlhr Cacul1 Sfxn4
Right kidney weight 12.8 5 4 80 0.98 1.2e-09 Srpk1 Rab11fip2 Prlhr Cacul1 Sfxn4
Tail length 7.8 5 2 40 1.00 4.7e-05 Spdef Srpk1 Taf11 Ilrun NA
Length with tail 4.3 9 0 0 0.99 3.2e-15 Spdef Srpk1 Rab11fip2 Prlhr Cacul1 Taf11 Sfxn4 Ilrun NA
Length without tail 7.1 4 0 0 1.00 9.0e-14 Rab11fip2 Prlhr Cacul1 Sfxn4
Liver weight, left 9.0 9 0 0 1.00 1.7e-17 Spdef Srpk1 Rab11fip2 Prlhr Cacul1 Taf11 Sfxn4 Ilrun NA
Parametrial fat weight 36.0 4 4 80 1.00 4.9e-18 Rab11fip2 Prlhr Cacul1 Sfxn4
Retroperitoneal fat weight 61.5 4 4 80 1.00 8.3e-17 Rab11fip2 Prlhr Cacul1 Sfxn4
Extensor digitorum longus weight 2.7 4 0 0 1.00 5.4e-11 Rab11fip2 Prlhr Cacul1 Sfxn4
Soleus weight 6.1 7 3 60 0.98 4.7e-06 Spdef Srpk1 Rab11fip2 Cacul1 Taf11 Ilrun NA
Tibia length 3.6 4 0 0 1.00 5.1e-04 Spdef Srpk1 Ilrun NA
Mean time between licks in bursts 8.1 3 0 0 0.00 1.0e+00 Spdef Taf11 NA
Indifference point 0 sec 6.9 3 0 0 1.00 1.4e-15 Rab11fip2 Cacul1 Sfxn4
Delay discounting total patch changes 0 sec 8.0 4 0 0 1.00 1.4e-15 Rab11fip2 Prlhr Cacul1 Sfxn4
Delay discounting total patch changes 6 sec 6.2 1 0 0 0.00 1.0e+00 Cacul1
Delay discounting water rate 24 sec 6.6 1 0 0 0.00 1.0e+00 Rab11fip2
Reaction time mean minus median 10.4 4 0 0 1.00 2.8e-04 Spdef Taf11 Ilrun NA
Reaction time mean minus median AUC 9.2 3 0 0 0.00 1.0e+00 Spdef Taf11 NA
Std. dev. reaction times 10.9 4 0 0 1.00 2.2e-04 Spdef Taf11 Ilrun NA
Cocaine response after cond. not corrected 8.5 1 0 0 0.00 1.0e+00 Cacul1
Conditioned reinforcement - actives 9.7 1 0 0 0.00 1.0e+00 Cacul1
Locomotion velocity, session 8 8.2 1 0 0 0.00 1.0e+00 Taf11
Condit. Reinf. inactive responses 8.7 1 0 0 0.00 1.0e+00 Cacul1
Bone: apparent density 6.8 4 0 0 1.00 3.8e-13 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone surface 5.6 4 0 0 1.00 2.9e-11 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone volume 8.5 4 0 0 1.00 2.1e-13 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: cortical apparent density 9.0 4 0 0 -1.00 4.7e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: cortical area 15.3 4 0 0 1.00 4.0e-16 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: cortical thickness 8.4 8 0 0 0.55 2.8e-02 Spdef Rab11fip2 Prlhr Cacul1 Taf11 Sfxn4 Ilrun NA
Bone: cortical tissue density 9.9 4 0 0 -1.00 2.9e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: endosteal estimation 7.0 5 0 0 1.00 4.0e-05 Spdef Srpk1 Taf11 Ilrun NA
Bone: endosteal perimeter 5.1 4 0 0 1.00 4.9e-04 Spdef Srpk1 Ilrun NA
Bone: final force 9.3 4 0 0 1.00 1.7e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: final moment 10.2 4 0 0 1.00 3.0e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: marrow area 6.9 5 0 0 1.00 5.0e-05 Spdef Srpk1 Taf11 Ilrun NA
Bone: maximum diameter 7.9 4 0 0 1.00 1.8e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: maximum force 9.0 4 0 0 1.00 1.7e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: maximum moment 9.6 4 0 0 1.00 4.6e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: minimum diameter 7.2 4 0 0 1.00 1.4e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: periosteal estimation 10.0 4 0 0 1.00 1.6e-14 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: periosteal perimeter 9.9 4 0 0 1.00 3.3e-12 Rab11fip2 Prlhr Cacul1 Sfxn4
Bone: trabecular thickness 13.7 4 0 0 1.00 2.1e-13 Rab11fip2 Prlhr Cacul1 Sfxn4
Seeking ratio, delayed vs. immediate footshock 8.5 1 0 0 0.00 1.0e+00 Cacul1
Food seeking constrained by brief footshock 8.5 2 0 0 -0.99 6.4e-05 Cacul1 Sfxn4
Cu content in liver 7.6 1 0 0 0.00 1.0e+00 Ilrun
Mn content in liver 11.3 4 0 0 1.00 6.8e-04 Spdef Taf11 Ilrun NA
Se content in liver 8.9 3 0 0 0.00 1.0e+00 Spdef Taf11 NA

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 1.7
Adipose alternative TSS 0 0.000 1.5
Adipose gene expression 1 0.012 1.6
Adipose isoform ratio 0 0.000 1.6
Adipose intron excision ratio 0 0.000 1.9
Adipose mRNA stability 0 0.000 1.6
BLA alternative polyA 0 0.000 1.5
BLA alternative TSS 0 0.000 1.7
BLA gene expression 1 0.017 1.7
BLA isoform ratio 0 0.000 1.5
BLA intron excision ratio 0 0.000 1.7
BLA mRNA stability 0 0.000 1.7
Brain alternative polyA 0 0.000 1.6
Brain alternative TSS 0 0.000 1.8
Brain gene expression 0 0.000 1.7
Brain isoform ratio 1 0.032 1.6
Brain intron excision ratio 1 0.018 1.7
Brain mRNA stability 0 0.000 1.6
Eye alternative polyA 0 0.000 2.0
Eye alternative TSS 0 0.000 1.9
Eye gene expression 0 0.000 1.7
Eye isoform ratio 0 0.000 1.8
Eye intron excision ratio 0 0.000 1.8
Eye mRNA stability 0 0.000 1.5
IL alternative polyA 0 0.000 1.3
IL alternative TSS 0 0.000 1.8
IL gene expression 0 0.000 1.7
IL isoform ratio 0 0.000 1.7
IL intron excision ratio 0 0.000 1.5
IL mRNA stability 0 0.000 1.7
LHb alternative polyA 0 0.000 1.7
LHb alternative TSS 0 0.000 1.6
LHb gene expression 0 0.000 1.7
LHb isoform ratio 0 0.000 1.7
LHb intron excision ratio 0 0.000 1.7
LHb mRNA stability 0 0.000 1.7
Liver alternative polyA 0 0.000 1.6
Liver alternative TSS 0 0.000 1.6
Liver gene expression 1 0.014 1.6
Liver isoform ratio 1 0.042 1.7
Liver intron excision ratio 0 0.000 1.7
Liver mRNA stability 1 0.041 1.7
NAcc alternative polyA 0 0.000 1.6
NAcc alternative TSS 0 0.000 1.9
NAcc gene expression 2 0.032 1.7
NAcc isoform ratio 2 0.106 1.7
NAcc intron excision ratio 0 0.000 1.8
NAcc mRNA stability 0 0.000 1.6
OFC alternative polyA 0 0.000 1.5
OFC alternative TSS 0 0.000 1.8
OFC gene expression 2 0.054 1.7
OFC isoform ratio 0 0.000 1.6
OFC intron excision ratio 1 0.100 1.9
OFC mRNA stability 1 0.093 1.8
PL alternative polyA 0 0.000 1.6
PL alternative TSS 0 0.000 1.7
PL gene expression 1 0.014 1.7
PL isoform ratio 1 0.045 1.6
PL intron excision ratio 0 0.000 1.7
PL mRNA stability 0 0.000 1.6

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