Hub : Traits

Bone: periosteal estimation

Tags: Physiology · Bone

Project: r01_doug_adams

179 significantly associated models · 62 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 7 128200675 130977246 22 4 4.0e-08 1.3e-07 1.0e+00 100 Asb8 Tuba1b Hdac7 Fkbp11
2 10 89561948 96071622 36 5 6.1e-09 2.0e-08 NaN NaN Psmd12 Apoh Dcaf7 AABR07030630.1 Map3k3
3 16 558324 2117247 3 1 1.7e-07 1.9e-07 1.2e-133 -2131 Ppif
4 16 2999353 4396663 1 1 2.6e-07 6.9e-10 4.4e-04 68 Wnt5a

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 4.8 21 0 0 1.00 4.4e-46 Asb8 Tuba1c Zfp641 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Body weight 6.3 28 19 173 0.99 1.8e-45 Ccdc47 Asb8 Kpna2 Tuba1c Cep112 Zfp641 NA Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Map3k3 Kmt2d NA NA NA NA NA Fkbp11
Length without tail 7.7 22 0 0 1.00 1.2e-57 Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Intraocular pressure 11.2 4 0 0 -1.00 1.9e-07 Zfp641 Tmem106c Hdac7 Pfkm
Extensor digitorum longus weight 4.6 32 2 18 0.39 1.8e-03 Kcnh6 Taco1 Ccdc47 Ddx42 Asb8 Smarcd2 Kpna2 Tuba1c Zfp641 Dcaf7 NA Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Kmt2d NA NA NA NA NA Fkbp11
Tibia length 7.7 22 4 36 1.00 1.2e-54 Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Indifference point 0 sec 8.8 4 0 0 1.00 7.8e-07 Psmd12 NA NA NA
Delay discounting total patch changes 0 sec 8.7 2 0 0 0.00 1.0e+00 NA NA
Delay discounting total patch changes 6 sec 9.3 2 0 0 0.00 1.0e+00 Cep112 NA
Reaction time mean minus median 10.5 1 0 0 0.00 1.0e+00 Fkbp11
Reaction time omissions 10.5 19 0 0 -1.00 6.9e-51 Asb8 Tuba1c Zfp641 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Hdac7 Pfkm Ccdc65 Rapgef3 Kmt2d NA NA NA NA Fkbp11
Condit. Reinf. active minus inactive responses 11.7 5 0 0 1.00 1.7e-08 Ccdc47 Kpna2 Dcaf7 NA NA
Condit. Reinf. active responses 10.8 5 0 0 1.00 8.9e-08 Wipi1 Fam20a Kpna2 Dcaf7 NA
Condit. Reinf. lever reinforcers received 9.8 2 0 0 0.00 1.0e+00 Kpna2 NA
Pavlov. Cond. intertrial magazine entries 13.0 19 0 0 1.00 3.6e-81 Psmd12 Mrc2 Taco1 Strada Ccdc47 Ddx42 Scn4a Icam2 Ddx5 Dcaf7 NA Bptf Tanc2 Prr29 Map3k3 Ace NA NA NA
Intermittent access total locomotion 12.9 8 0 0 1.00 4.4e-22 Psmd12 Helz Cacng5 Icam2 NA NA NA NA
Short access day 10 total infusions 12.2 1 0 0 0.00 1.0e+00 NA
Short access day 10 total locomotion 13.1 7 0 0 1.00 2.8e-21 Psmd12 Taco1 Icam2 Ddx5 NA Bptf NA
Locomotion velocity, session 8 15.3 1 0 0 0.00 1.0e+00 Wnt5a
Bone: apparent density 10.5 22 0 0 1.00 2.1e-56 Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone surface 11.3 41 0 0 1.00 7.5e-98 Psmd12 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Tuba1c Icam2 Ddx5 Zfp641 Dcaf7 NA Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA NA Fkbp11
Bone volume 9.3 35 0 0 1.00 3.8e-94 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Tuba1c Icam2 Zfp641 Dcaf7 Spats2 Tanc2 Prph Slc48a1 Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA Fkbp11
Bone: connectivity density 8.8 5 0 0 1.00 1.1e-06 Tuba1b Adcy6 Hdac7 Ccdc65 NA
Bone: cortical apparent density 11.0 1 0 0 0.00 1.0e+00 Cacng4
Bone: cortical area 10.9 26 0 0 1.00 7.7e-89 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: cortical porosity 17.1 12 2 18 1.00 3.6e-28 Mrc2 Kcnh6 Taco1 Ccdc47 Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace NA
Bone: cortical porosity 14.9 6 0 0 1.00 1.5e-05 Mrc2 Kcnh6 Taco1 Ccdc47 Ddx42 NA
Bone: cortical thickness 9.1 5 0 0 -1.00 7.7e-08 Psmd12 Cacng4 Prkca Map2k6 AABR07030630.1
Bone: cortical tissue density 10.5 1 0 0 0.00 1.0e+00 Cacng4
Bone: endosteal estimation 14.8 62 35 318 0.98 1.5e-134 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA NA NA NA Fkbp11
Bone: endosteal perimeter 15.7 58 36 327 0.99 2.2e-127 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Smurf2 Kpna2 Tuba1c Cep112 Icam2 Ddx5 Zfp641 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA NA NA NA Fkbp11
Bone: final force 10.4 26 0 0 1.00 3.1e-79 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: final moment 10.4 26 0 0 1.00 3.2e-75 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: marrow area 14.4 62 35 318 0.98 1.7e-134 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA NA NA NA Fkbp11
Bone: maximum diameter 8.3 23 0 0 1.00 5.3e-67 Psmd12 Prkca Fam20a Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Kpna2 Icam2 Dcaf7 NA AABR07030630.1 Tanc2 Prr29 Map3k3 Ace NA NA NA
Bone: maximum force 14.3 26 5 46 1.00 3.3e-79 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: maximum moment 14.2 26 7 64 1.00 8.8e-72 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: minimum diameter 13.6 62 31 282 1.00 8.4e-183 Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 NA Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA NA NA NA Fkbp11
Bone: periosteal perimeter 10.5 47 0 0 1.00 4.8e-106 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Kpna2 Tuba1c Icam2 Zfp641 Dcaf7 NA Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d NA Ace NA NA NA NA Fkbp11
Bone: post-yield work 10.0 3 0 0 1.00 1.0e-04 Tuba1b NA Fkbp11
Bone: stiffness 16.4 26 22 200 1.00 1.2e-62 Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d NA NA NA NA Fkbp11
Bone: trabecular thickness 11.4 1 0 0 0.00 1.0e+00 Ddx42

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 7 0.330 2.2
Adipose alternative TSS 0 0.000 1.9
Adipose gene expression 16 0.193 2.0
Adipose isoform ratio 2 0.071 2.0
Adipose intron excision ratio 1 0.034 2.1
Adipose mRNA stability 8 0.232 2.0
BLA alternative polyA 2 0.167 2.0
BLA alternative TSS 4 0.475 2.2
BLA gene expression 15 0.247 2.1
BLA isoform ratio 4 0.227 2.0
BLA intron excision ratio 2 0.067 2.0
BLA mRNA stability 2 0.099 2.1
Brain alternative polyA 3 0.150 2.0
Brain alternative TSS 4 0.233 2.3
Brain gene expression 14 0.155 2.0
Brain isoform ratio 5 0.158 2.0
Brain intron excision ratio 4 0.074 2.0
Brain mRNA stability 6 0.138 1.9
Eye alternative polyA 0 0.000 2.2
Eye alternative TSS 0 0.000 2.2
Eye gene expression 0 0.000 2.2
Eye isoform ratio 0 0.000 1.8
Eye intron excision ratio 0 0.000 2.1
Eye mRNA stability 0 0.000 2.0
IL alternative polyA 0 0.000 2.2
IL alternative TSS 1 0.346 1.9
IL gene expression 1 0.027 2.1
IL isoform ratio 0 0.000 2.1
IL intron excision ratio 0 0.000 2.1
IL mRNA stability 1 0.090 2.0
LHb alternative polyA 0 0.000 2.2
LHb alternative TSS 2 0.571 2.4
LHb gene expression 5 0.156 2.1
LHb isoform ratio 0 0.000 2.0
LHb intron excision ratio 0 0.000 2.1
LHb mRNA stability 2 0.193 2.0
Liver alternative polyA 2 0.133 1.9
Liver alternative TSS 0 0.000 2.1
Liver gene expression 9 0.125 2.0
Liver isoform ratio 0 0.000 1.9
Liver intron excision ratio 3 0.069 2.0
Liver mRNA stability 4 0.163 2.0
NAcc alternative polyA 3 0.229 2.0
NAcc alternative TSS 0 0.000 2.0
NAcc gene expression 12 0.190 2.0
NAcc isoform ratio 3 0.159 2.0
NAcc intron excision ratio 0 0.000 2.0
NAcc mRNA stability 6 0.265 2.1
OFC alternative polyA 0 0.000 2.1
OFC alternative TSS 0 0.000 2.0
OFC gene expression 3 0.081 2.1
OFC isoform ratio 0 0.000 2.0
OFC intron excision ratio 0 0.000 2.1
OFC mRNA stability 0 0.000 2.1
PL alternative polyA 2 0.140 2.0
PL alternative TSS 5 0.426 2.1
PL gene expression 9 0.122 2.1
PL isoform ratio 0 0.000 1.9
PL intron excision ratio 1 0.028 2.1
PL mRNA stability 6 0.206 2.1

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