Hub : Traits

Total cortical area

Project: r01_doug_adams

390 significantly associated models · 68 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 3 126323673 128206530 4 1 6.4e-08 5.7e-08 1.0e-01 91 Esf1
2 10 89561948 96755402 56 8 1.6e-16 3.4e-18 NaN NaN Slc16a6 Cacng4 Wipi1 Map2k6 Kcnj16 Abca6 Ace Pecam1
3 10 97108442 99310778 2 1 1.6e-08 8.4e-17 7.6e-12 32 Sox9
4 10 102999385 104353671 5 3 2.9e-10 3.8e-09 1.0e+00 100 Cant1 Usp36 Cep295nl
5 20 5176396 6575423 1 1 1.3e-07 1.2e-06 1.0e+00 100 Ilrun

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 6.5 4 3 21.4 -1.00 8.0e-44 Tasp1 Esf1 Ndufaf5 Ism1
retroperitoneal_fat_g 5.4 4 0 0.0 1.00 4.9e-43 Tasp1 Esf1 Ndufaf5 Ism1
body_g 5.4 8 2 14.3 0.88 8.5e-15 Map2k6 Tasp1 Esf1 Ndufaf5 Usp36 Abca6 Ace Ism1
dissection: UMAP 3 of all traits 6.9 1 0 0.0 0.00 1.0e+00 Ilrun
dissection: PC 2 of all traits 7.7 1 0 0.0 0.00 1.0e+00 Cacng4
EDL weight in grams 4.1 6 0 0.0 0.04 9.3e-01 Ddx5 Dcaf7 NA Prr29 NA NA
Tibia length in mm 6.2 6 1 7.1 0.85 5.1e-04 Tasp1 Esf1 Ndufaf5 Usp36 Ilrun Ism1
sol weight in grams 7.0 1 0 0.0 0.00 1.0e+00 Ilrun
ccp_trial_3_saline_dist_mm 12.7 1 0 0.0 0.00 1.0e+00 Map2k6
pavca_ny_d5_magazine_ncs 12.1 12 0 0.0 -1.00 8.3e-30 Strada Scn4a Tex2 Smurf2 Icam2 Dcaf7 Bptf Snord104 Prr29 Ace NA Pecam1
Cortical porosity 17.1 9 1 7.1 -0.99 1.6e-09 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Dcaf7 Prr29 Ace NA
tautz: manual_spc15 13.8 49 15 107.1 0.99 1.4e-170 Slc16a6 Psmd12 Helz Cacng4 Prkca Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 Dcaf7 Abca6 Bptf Prkar1a AABR07030630.1 Nol11 Snord104 Abca9 Prr29 Ace NA Gna13 Kcnj2 NA Pecam1 NA NA
tautz: manual_spc9 10.6 1 0 0.0 0.00 1.0e+00 Slc39a11
tautz: manual_mpc3 9.9 1 0 0.0 0.00 1.0e+00 Slc39a11
tautz: manual_spc17 11.5 1 0 0.0 0.00 1.0e+00 Ilrun
tautz: manual_spc20 11.5 1 0 0.0 -1.00 1.2e-08 Kcnj16

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 16 0.754 2.1
Adipose alternative TSS 0 0.000 1.8
Adipose gene expression 18 0.217 1.8
Adipose isoform ratio 9 0.319 1.9
Adipose intron excision ratio 10 0.343 2.3
Adipose mRNA stability 8 0.232 1.9
BLA alternative polyA 4 0.334 1.9
BLA alternative TSS 6 0.713 2.0
BLA gene expression 22 0.363 1.9
BLA isoform ratio 5 0.284 1.9
BLA intron excision ratio 3 0.100 1.9
BLA mRNA stability 8 0.395 1.9
Brain alternative polyA 3 0.150 2.0
Brain alternative TSS 12 0.699 2.1
Brain gene expression 19 0.210 1.9
Brain isoform ratio 10 0.316 2.1
Brain intron excision ratio 10 0.185 2.0
Brain mRNA stability 11 0.252 1.9
Eye alternative polyA 0 0.000 1.8
Eye alternative TSS 0 0.000 1.7
Eye gene expression 2 0.178 2.0
Eye isoform ratio 0 0.000 1.6
Eye intron excision ratio 3 0.489 1.8
Eye mRNA stability 0 0.000 1.8
IL alternative polyA 0 0.000 1.9
IL alternative TSS 1 0.346 1.8
IL gene expression 7 0.192 1.9
IL isoform ratio 0 0.000 2.1
IL intron excision ratio 3 0.311 1.9
IL mRNA stability 1 0.090 1.8
LHb alternative polyA 0 0.000 2.0
LHb alternative TSS 3 0.857 2.5
LHb gene expression 5 0.156 1.9
LHb isoform ratio 1 0.133 2.1
LHb intron excision ratio 3 0.292 1.8
LHb mRNA stability 3 0.290 1.9
Liver alternative polyA 6 0.399 1.8
Liver alternative TSS 7 0.461 1.8
Liver gene expression 17 0.236 1.9
Liver isoform ratio 7 0.293 1.8
Liver intron excision ratio 11 0.251 2.0
Liver mRNA stability 6 0.244 1.9
NAcc alternative polyA 0 0.000 2.0
NAcc alternative TSS 0 0.000 1.8
NAcc gene expression 12 0.366 2.0
NAcc isoform ratio 0 0.000 1.7
NAcc intron excision ratio 3 0.314 1.7
NAcc mRNA stability 4 0.369 1.9
NAcc2 alternative polyA 1 0.090 1.8
NAcc2 alternative TSS 2 0.273 1.8
NAcc2 gene expression 19 0.356 1.9
NAcc2 isoform ratio 1 0.065 1.9
NAcc2 intron excision ratio 5 0.189 1.9
NAcc2 mRNA stability 4 0.224 1.9
OFC alternative polyA 0 0.000 2.0
OFC alternative TSS 0 0.000 1.6
OFC gene expression 8 0.216 1.9
OFC isoform ratio 1 0.123 2.0
OFC intron excision ratio 2 0.199 2.3
OFC mRNA stability 3 0.278 1.9
PL alternative polyA 0 0.000 2.0
PL alternative TSS 1 0.324 1.9
PL gene expression 10 0.269 1.9
PL isoform ratio 1 0.115 2.1
PL intron excision ratio 2 0.192 1.9
PL mRNA stability 3 0.261 1.8
PL2 alternative polyA 2 0.159 2.2
PL2 alternative TSS 6 0.639 2.0
PL2 gene expression 22 0.344 1.9
PL2 isoform ratio 3 0.163 1.9
PL2 intron excision ratio 5 0.159 2.0
PL2 mRNA stability 10 0.410 1.9

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