Hub : Traits

Bone: endosteal perimeter

Tags: Physiology · Bone

Project: r01_doug_adams

471 significantly associated models · 69 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 87823507 96755402 67 7 8.9e-13 1.3e-11 NaN NaN Cacng5 Wipi1 Map2k6 Marchf10 Strada Cep95 Prkar1a
2 10 99794956 101075728 1 1 8.7e-08 2.1e-06 7.3e-47 -818 Cd300lf
3 10 102999385 104282175 1 1 2.2e-07 2.5e-05 6.0e-02 80 Cep295nl

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 5.2 6 0 0 -1.00 1.1e-09 Slc16a6 Cacng4 Prkca Cep112 AABR07030647.1 Prkar1a
Body weight 4.4 15 0 0 1.00 1.5e-47 Amz2 Apoh Wipi1 Arsg Mettl2 Mrc2 Marchf10 Cyb561 NA Abca6 Prkar1a Abca9 Map3k3 NA NA
Epididymis fat weight 7.2 1 0 0 0.00 1.0e+00 Slc16a6
Extensor digitorum longus weight 5.0 12 1 11 -0.99 1.2e-13 Kcnh6 Ccdc47 Ddx42 Smarcd2 Tex2 Kpna2 Dcaf7 NA Bptf NA NA Pecam1
Indifference point 0 sec 10.0 1 0 0 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 11.3 2 0 0 1.00 2.9e-05 Wipi1 Prkar1a
Condit. Reinf. active minus inactive responses 12.6 2 0 0 0.00 1.0e+00 Ccdc47 Dcaf7
Condit. Reinf. active responses 11.6 4 0 0 1.00 1.4e-04 Kpna2 NA Gna13 Pecam1
Pavlov. Cond. intertrial magazine entries 14.6 33 0 0 0.99 1.4e-160 Psmd12 Mettl2 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Icam2 Limd2 Ddx5 Dcaf7 NA Bptf Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace NA NA Pecam1 NA
Intermittent access total locomotion 14.2 6 0 0 0.14 7.9e-01 Psmd12 Helz NA NA NA NA
Short access day 10 total locomotion 14.7 13 0 0 1.00 3.1e-22 Strada Scn4a Kpna2 Icam2 Ddx5 Dcaf7 NA AC133055.1 Ace NA NA Pecam1 NA
Bone surface 10.6 28 2 22 0.99 1.9e-79 Slc16a6 Arsg Fam20a Kcnj16 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Cep95 Icam2 Ddx5 Dcaf7 NA Prkar1a Tanc2 Abca9 Prr29 Map3k3 Ace Gna13 NA Kcnj2 NA
Bone volume 10.1 14 0 0 1.00 3.0e-44 Kcnj16 Kcnh6 Taco1 Ccdc47 Ddx42 Smarcd2 Scn4a Dcaf7 Prkar1a Abca9 Map3k3 Ace NA Kcnj2
Bone: cortical apparent density 11.9 1 0 0 0.00 1.0e+00 Marchf10
Bone: cortical porosity 20.8 18 5 56 0.99 2.8e-49 Lyzl6 Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace NA NA
Bone: cortical porosity 19.5 9 0 0 1.00 7.5e-32 Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Strada Ccdc47 Ddx42 NA
Bone: cortical thickness 11.9 25 4 44 -0.99 6.6e-73 Psmd12 Helz Cacng4 Prkca Wipi1 Fam20a Abca8 Abca8a Map2k6 Kcnj16 Scn4a Tex2 Cep95 Smurf2 Icam2 Ddx5 Cep295nl Bptf Prkar1a Abca9 Prr29 Kcnj2 NA Pecam1 Pitpnc1
Bone: cortical tissue density 11.6 1 0 0 0.00 1.0e+00 Marchf10
Bone: endosteal estimation 15.5 69 61 678 1.00 0.0e+00 Slc16a6 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cd300lf Cep112 Icam2 Limd2 Ddx5 Cep295nl AABR07030647.1 Dcaf7 Prp2l1 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA Kcnj2 NA Pecam1 NA NA NA Pitpnc1 NA
Bone: marrow area 15.1 69 61 678 1.00 0.0e+00 Slc16a6 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cd300lf Cep112 Icam2 Limd2 Ddx5 Cep295nl AABR07030647.1 Dcaf7 Prp2l1 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA Kcnj2 NA Pecam1 NA NA NA Pitpnc1 NA
Bone: maximum diameter 8.9 20 0 0 1.00 5.0e-57 Kcnj16 Mrc2 Marchf10 Cyb561 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Kpna2 Dcaf7 NA AABR07030630.1 Prr29 Map3k3 Ace NA Kcnj2 NA
Bone: minimum diameter 13.0 65 40 444 1.00 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 Dcaf7 Prp2l1 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA Kcnj2 NA Pecam1 NA NA NA Pitpnc1 NA
Bone: periosteal estimation 11.1 64 36 400 1.00 0.0e+00 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 AABR07030647.1 Dcaf7 NA Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace NA Gna13 NA Kcnj2 NA Pecam1 NA NA Pitpnc1 NA
Bone: periosteal perimeter 11.0 30 0 0 0.99 1.5e-78 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Tex2 Kpna2 Dcaf7 Abca6 Prkar1a AABR07030630.1 Abca9 Map3k3 Ace NA NA NA
Latency to leave start box in cocaine runway, F 14.5 1 0 0 0.00 1.0e+00 Map2k6

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 14 0.660 2.1
Adipose alternative TSS 0 0.000 1.8
Adipose gene expression 26 0.313 2.0
Adipose isoform ratio 7 0.248 2.0
Adipose intron excision ratio 6 0.206 2.2
Adipose mRNA stability 13 0.377 2.1
BLA alternative polyA 5 0.417 2.1
BLA alternative TSS 8 0.950 2.2
BLA gene expression 30 0.495 2.2
BLA isoform ratio 5 0.284 2.0
BLA intron excision ratio 5 0.167 2.0
BLA mRNA stability 8 0.395 2.1
Brain alternative polyA 8 0.399 2.0
Brain alternative TSS 15 0.874 2.2
Brain gene expression 29 0.320 2.0
Brain isoform ratio 12 0.380 2.1
Brain intron excision ratio 14 0.259 2.1
Brain mRNA stability 8 0.183 2.0
Eye alternative polyA 0 0.000 2.0
Eye alternative TSS 0 0.000 1.8
Eye gene expression 5 0.444 2.3
Eye isoform ratio 0 0.000 1.8
Eye intron excision ratio 3 0.489 2.0
Eye mRNA stability 0 0.000 2.0
IL alternative polyA 0 0.000 2.1
IL alternative TSS 1 0.346 2.0
IL gene expression 12 0.329 2.1
IL isoform ratio 1 0.127 2.1
IL intron excision ratio 1 0.104 2.0
IL mRNA stability 3 0.270 2.0
LHb alternative polyA 0 0.000 2.0
LHb alternative TSS 3 0.857 2.2
LHb gene expression 8 0.250 2.1
LHb isoform ratio 1 0.133 2.0
LHb intron excision ratio 1 0.097 2.0
LHb mRNA stability 7 0.676 2.1
Liver alternative polyA 5 0.333 1.9
Liver alternative TSS 11 0.724 2.0
Liver gene expression 21 0.292 2.0
Liver isoform ratio 6 0.251 1.9
Liver intron excision ratio 16 0.366 2.2
Liver mRNA stability 7 0.285 2.0
NAcc alternative polyA 6 0.458 2.1
NAcc alternative TSS 1 0.108 1.8
NAcc gene expression 28 0.444 2.1
NAcc isoform ratio 2 0.106 1.9
NAcc intron excision ratio 4 0.131 2.0
NAcc mRNA stability 13 0.575 2.1
OFC alternative polyA 2 0.342 2.1
OFC alternative TSS 0 0.000 1.7
OFC gene expression 13 0.351 2.2
OFC isoform ratio 2 0.245 2.0
OFC intron excision ratio 0 0.000 2.2
OFC mRNA stability 4 0.370 2.1
PL alternative polyA 8 0.561 2.2
PL alternative TSS 7 0.596 2.0
PL gene expression 34 0.460 2.1
PL isoform ratio 2 0.090 1.9
PL intron excision ratio 6 0.167 2.0
PL mRNA stability 14 0.480 2.1

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