Hub : Traits

dissection: PC 3 of all traits

Project: dissection

179 significantly associated models · 48 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 260424315 2 1 7.0e-08 4.8e-08 1.00 100 Cacul1
2 2 90636696 92031287 1 1 3.9e-11 6.9e-02 0.05 -16 Snx16
3 8 56566379 57963728 1 1 1.6e-07 3.9e-05 0.01 61 Cspg4
4 9 54177385 57420165 6 1 6.4e-08 2.0e-08 1.00 100 Coq10b
5 10 79556862 83433454 37 6 9.0e-13 8.6e-13 1.00 100 Phospho1 Hoxb9 Kpnb1 Mrpl45 Zfp652 Cdk5rap3

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
dissection: UMAP 1 of all traits 58.7 2 2 20 -1.00 1.6e-03 Rab11fip2 Cacul1
retroperitoneal_fat_g 59.0 2 2 20 1.00 2.2e-03 Rab11fip2 Cacul1
body_g 27.8 3 2 20 0.75 1.4e-01 Rab11fip2 Snx16 Cacul1
dissection: UMAP 3 of all traits 9.6 44 26 260 0.98 1.3e-129 Spop Ttll6 Phospho1 Abi3 Gip Snf8 Ube2z Atp5mc1 Hoxb9 Hoxb4 Hoxb3 NA Snx11 Cbx1 Nfe2l1 Copz2 Kpnb1 Tbkbp1 Osbpl7 Mrpl10 Lrrc46 Scrn2 Sp2 Mrpl45 Slc39a10 Pip4k2b Pgap1 Coq10b Hspd1 Zfp652 Kat7 Npepps Sp6 Skap1 Pnpo Phb Cdk5rap3 Prr15l Psmb3 NA NA B4galnt2 Atp5mc1 NA
kidney_right_g 15.1 2 2 20 1.00 6.5e-04 Rab11fip2 Cacul1
dissection: PC 2 of all traits 9.8 45 26 260 -0.99 1.9e-156 Spop Ttll6 Phospho1 Abi3 Gip Snf8 Ube2z Atp5mc1 Hoxb9 Hoxb4 Hoxb3 NA Snx11 Cbx1 Nfe2l1 Copz2 Kpnb1 Tbkbp1 Osbpl7 Rab11fip2 Mrpl10 Lrrc46 Cacul1 Scrn2 Sp2 Mrpl45 Slc39a10 Pip4k2b Pgap1 Coq10b Hspd1 Zfp652 Kat7 Npepps Sp6 Skap1 Pnpo Phb Cdk5rap3 Prr15l Psmb3 NA B4galnt2 Atp5mc1 NA
EDL weight in grams 5.9 2 1 10 0.00 1.0e+00 Snx16 Cspg4
Tibia length in mm 7.1 6 0 0 -1.00 2.4e-11 Slc39a10 Pgap1 Coq10b Hspd1 NA NA
TA weight in grams 8.2 1 1 10 0.00 1.0e+00 Snx16
tb_th_sd 13.4 2 0 0 0.00 1.0e+00 Rab11fip2 Cacul1
tautz: manual_mpc4 14.1 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_mpc14 28.2 1 1 10 0.00 1.0e+00 Snx16
tautz: manual_spc24 10.1 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_spc4 13.8 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_spc20 14.7 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_mpc13 10.2 1 0 0 0.00 1.0e+00 Gip
tautz: manual_spc3 18.0 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_mpc6 15.8 1 0 0 0.00 1.0e+00 Snx16
tautz: manual_mpc11 14.4 1 0 0 0.00 1.0e+00 Snx16
punishment 16.8 1 0 0 0.00 1.0e+00 Snx16
Weight adjusted by age 50.2 1 1 10 0.00 1.0e+00 Snx16

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 9 0.424 2.5
Adipose alternative TSS 1 0.062 2.5
Adipose gene expression 18 0.217 2.4
Adipose isoform ratio 5 0.177 2.3
Adipose intron excision ratio 1 0.034 2.6
Adipose mRNA stability 5 0.145 2.4
BLA alternative polyA 0 0.000 2.3
BLA alternative TSS 0 0.000 2.5
BLA gene expression 8 0.132 2.4
BLA isoform ratio 1 0.057 2.5
BLA intron excision ratio 1 0.034 2.5
BLA mRNA stability 4 0.198 2.5
Brain alternative polyA 2 0.100 2.4
Brain alternative TSS 2 0.116 2.4
Brain gene expression 8 0.088 2.4
Brain isoform ratio 2 0.063 2.4
Brain intron excision ratio 2 0.037 2.6
Brain mRNA stability 2 0.046 2.3
Eye alternative polyA 2 1.117 2.4
Eye alternative TSS 0 0.000 2.1
Eye gene expression 3 0.267 2.3
Eye isoform ratio 0 0.000 2.4
Eye intron excision ratio 1 0.163 2.5
Eye mRNA stability 0 0.000 2.9
IL alternative polyA 0 0.000 2.6
IL alternative TSS 0 0.000 2.5
IL gene expression 4 0.110 2.4
IL isoform ratio 1 0.127 2.6
IL intron excision ratio 2 0.207 2.3
IL mRNA stability 1 0.090 2.4
LHb alternative polyA 0 0.000 2.5
LHb alternative TSS 0 0.000 2.1
LHb gene expression 5 0.156 2.4
LHb isoform ratio 0 0.000 2.3
LHb intron excision ratio 0 0.000 2.2
LHb mRNA stability 1 0.097 2.4
Liver alternative polyA 4 0.266 2.3
Liver alternative TSS 3 0.198 2.3
Liver gene expression 17 0.236 2.4
Liver isoform ratio 2 0.084 2.3
Liver intron excision ratio 6 0.137 2.5
Liver mRNA stability 4 0.163 2.4
NAcc alternative polyA 0 0.000 2.8
NAcc alternative TSS 0 0.000 2.3
NAcc gene expression 6 0.183 2.5
NAcc isoform ratio 0 0.000 2.5
NAcc intron excision ratio 1 0.105 2.4
NAcc mRNA stability 1 0.092 2.4
NAcc2 alternative polyA 0 0.000 2.4
NAcc2 alternative TSS 0 0.000 2.4
NAcc2 gene expression 6 0.112 2.4
NAcc2 isoform ratio 3 0.194 2.6
NAcc2 intron excision ratio 1 0.038 2.4
NAcc2 mRNA stability 0 0.000 2.4
OFC alternative polyA 0 0.000 2.5
OFC alternative TSS 1 0.313 2.6
OFC gene expression 6 0.162 2.4
OFC isoform ratio 2 0.245 2.6
OFC intron excision ratio 4 0.398 2.5
OFC mRNA stability 1 0.093 2.5
PL alternative polyA 0 0.000 2.5
PL alternative TSS 0 0.000 2.6
PL gene expression 4 0.108 2.4
PL isoform ratio 0 0.000 2.5
PL intron excision ratio 2 0.192 2.4
PL mRNA stability 0 0.000 2.4
PL2 alternative polyA 0 0.000 2.6
PL2 alternative TSS 0 0.000 2.7
PL2 gene expression 10 0.156 2.4
PL2 isoform ratio 1 0.054 2.5
PL2 intron excision ratio 2 0.063 2.5
PL2 mRNA stability 1 0.041 2.4

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