Bone: cortical thickness

Tags: Physiology · Bone

Project: r01_doug_adams

5 loci · 17 genes with independent associations · 76 total associated genes

Significant Loci

# Chr Start pos End pos # assoc genes # joint models Best TWAS P Best GWAS P Cond GWAS P Joint genes
1 chr3 126160536 128206530 42 5 3.96e-09 5.49e-09 1.00e+00 Esf1 Ndufaf5 Tasp1
2 chr10 94609547 96755402 7 1 1.65e-08 7.78e-11 2.56e-06 Map2k6
3 chr10 97108442 98722043 3 1 1.50e-09 2.01e-10 2.34e-03 LOC102549521
4 chr10 102999385 104405337 10 3 4.14e-08 7.18e-08 NaN Afmid C1qtnf1 Usp36
5 chr10 105295338 107195627 14 7 3.22e-12 2.68e-10 NaN B3gntl1 Dus1l Foxk2 Lrrc45 Rab40b Sectm1a

Pleiotropic Associations

Trait Chi2 ratio # genes+ # genes++ % genes++ Corr Corr P Genes
BMI with tail 5.67 8 0 0 1 1.30e-23 Afmid C1qtnf1 Cep295nl Esf1 Sptlc3 Tasp1 Timp2 Usp36
Body weight 5.64 7 5 29.4 0.99 1.22e-81 B3gntl1 Esf1 Ism1 Lrrc45 Ndufaf5 Sptlc3 Tasp1
Epididymis fat weight 7.13 3 0 0 1 8.65e-07 Ndufaf5 Sptlc3 Tasp1
Left kidney weight 5.94 2 0 0 0 1.00e+00 B3gntl1 Foxk2
Right kidney weight 5.26 2 0 0 0 1.00e+00 B3gntl1 Foxk2
Tail length 4.78 1 0 0 0 1.00e+00 Foxk2
Length with tail 3.85 2 0 0 0.89 4.14e-02 Lrrc45 Tasp1
Length without tail 8.22 8 0 0 1 8.75e-11 Afmid B3gntl1 Dus1l Fn3k Foxk2 Rab40b Sectm1a Wdr45b
Retroperitoneal fat weight 5.84 5 3 17.6 0.99 2.54e-78 Esf1 Ism1 Ndufaf5 Sptlc3 Tasp1
Tibia length 6.24 15 6 35.3 0.98 8.00e-66 Afmid B3gntl1 Dus1l Esf1 Fn3k Foxk2 Ism1 Lrrc45 Narf Ndufaf5 Rab40b Sectm1a Sptlc3 Tasp1 Wdr45b
Patch foraging indifference point 0 sec 8.58 1 0 0 0 1.00e+00 Abca5
Patch foraging total patch changes 0 sec 8.97 1 0 0 0 1.00e+00 Abca5
Patch foraging total patch changes 18 sec 10.06 1 0 0 0 1.00e+00 Sptlc3
Locomotor testing rearing 9.49 2 0 0 0 1.00e+00 Abca5 LOC120095206
Intermitt. access day 1 inactive lever presses 12.3 1 0 0 0 1.00e+00 LOC102549521
Bone surface 12.37 4 1 5.9 -0.99 1.56e-05 Abca5 Kcnj16 LOC120095206 Usp36
Bone volume 10.26 2 0 0 -1 1.62e-04 Abca5 Kcnj16
Bone: cortical apparent density 11.33 1 0 0 0 1.00e+00 LOC120095206
Bone: cortical area 10.42 13 3 17.6 1 7.26e-105 B3gntl1 Dus1l Esf1 Fn3k Foxk2 Ism1 Lrrc45 Narf Ndufaf5 Rab40b Sectm1a Tasp1 Wdr45b
Bone: cortical thickness 12.35 6 0 0 1 9.18e-10 B3gntl1 Dus1l Foxk2 Rab40b Usp36 Wdr45b
Bone: cortical tissue density 11.01 1 0 0 0 1.00e+00 LOC120095206
Bone: elastic work 13.12 6 0 0 0.99 1.08e-06 B3gntl1 Dus1l Lrrc45 Narf Rab40b Sox9
Bone: endosteal estimation 10.74 11 4 23.5 -0.96 7.74e-14 Abca5 Afmid C1qtnf1 Cep295nl Kcnj16 LOC102549521 LOC120095206 Map2k6 Sox9 Timp2 Usp36
Bone: endosteal perimeter 10.71 11 4 23.5 -0.98 7.22e-18 Abca5 Afmid C1qtnf1 Cep295nl Kcnj16 LOC102549521 LOC120095206 Map2k6 Sox9 Timp2 Usp36
Bone: final force 11.87 8 1 5.9 0.99 1.45e-11 B3gntl1 Dus1l Fn3k Foxk2 Lrrc45 Narf Rab40b Wdr45b
Bone: final moment 12.82 8 1 5.9 0.99 6.00e-11 B3gntl1 Dus1l Fn3k Foxk2 Lrrc45 Narf Rab40b Wdr45b
Bone: marrow area 10.6 11 4 23.5 -0.96 4.28e-14 Abca5 Afmid C1qtnf1 Cep295nl Kcnj16 LOC102549521 LOC120095206 Map2k6 Sox9 Timp2 Usp36
Bone: maximum diameter 8.78 2 0 0 0 1.00e+00 Kcnj16 LOC120095206
Bone: maximum force 11.11 7 1 5.9 0.99 6.24e-10 B3gntl1 Dus1l Foxk2 Lrrc45 Narf Rab40b Wdr45b
Bone: maximum moment 11.92 7 1 5.9 0.99 2.04e-09 B3gntl1 Dus1l Foxk2 Lrrc45 Narf Rab40b Wdr45b
Bone: minimum diameter 9.37 3 0 0 -1 1.56e-03 Abca5 Kcnj16 LOC120095206
Bone: periosteal estimation 9.66 3 0 0 -1 2.91e-04 Abca5 Kcnj16 LOC120095206
Bone: periosteal perimeter 8.53 1 0 0 0 1.00e+00 B3gntl1
Bone: stiffness 9.83 1 0 0 0 1.00e+00 B3gntl1

Associations by panel

Tissue RNA modality # hits % hits/tests Avg chisq
Adipose alternative polyA 4 0.1 1.73
Adipose alternative TSS 7 0.2 1.74
Adipose gene expression 4 0 1.61
Adipose isoform ratio 3 0.1 1.68
Adipose intron excision ratio 2 0.1 1.68
Adipose mRNA stability 1 0 1.67
BLA alternative polyA 0 0 1.61
BLA alternative TSS 4 0.2 1.7
BLA gene expression 2 0 1.64
BLA isoform ratio 4 0.1 1.65
BLA intron excision ratio 2 0.1 1.68
BLA mRNA stability 1 0 1.62
Brain alternative polyA 0 0 1.6
Brain alternative TSS 4 0.1 1.65
Brain gene expression 6 0.1 1.64
Brain isoform ratio 7 0.1 1.69
Brain intron excision ratio 5 0.1 1.7
Brain mRNA stability 4 0.1 1.65
Eye alternative polyA 0 0 1.73
Eye alternative TSS 0 0 1.49
Eye gene expression 2 0.2 1.73
Eye isoform ratio 0 0 1.68
Eye intron excision ratio 0 0 1.49
Eye mRNA stability 0 0 1.68
IL alternative polyA 0 0 1.65
IL alternative TSS 0 0 1.69
IL gene expression 2 0 1.67
IL isoform ratio 0 0 1.67
IL intron excision ratio 0 0 1.63
IL mRNA stability 1 0.1 1.64
LHb alternative polyA 0 0 1.65
LHb alternative TSS 1 0.2 1.55
LHb gene expression 3 0.1 1.7
LHb isoform ratio 0 0 1.52
LHb intron excision ratio 2 0.2 1.51
LHb mRNA stability 0 0 1.61
Liver alternative polyA 0 0 1.65
Liver alternative TSS 0 0 1.58
Liver gene expression 2 0 1.61
Liver isoform ratio 1 0 1.71
Liver intron excision ratio 1 0 1.57
Liver mRNA stability 1 0 1.61
NAcc alternative polyA 1 0 1.61
NAcc alternative TSS 4 0.1 1.61
NAcc gene expression 2 0 1.64
NAcc isoform ratio 5 0.1 1.67
NAcc intron excision ratio 5 0.1 1.65
NAcc mRNA stability 1 0 1.62
OFC alternative polyA 0 0 1.7
OFC alternative TSS 0 0 1.61
OFC gene expression 5 0.1 1.66
OFC isoform ratio 0 0 1.56
OFC intron excision ratio 2 0.2 1.73
OFC mRNA stability 0 0 1.55
PL alternative polyA 0 0 1.61
PL alternative TSS 4 0.1 1.63
PL gene expression 3 0 1.64
PL isoform ratio 5 0.1 1.72
PL intron excision ratio 3 0.1 1.63
PL mRNA stability 0 0 1.6
pVTA alternative polyA 1 0.1 1.65
pVTA alternative TSS 5 0.4 1.54
pVTA gene expression 3 0.1 1.65
pVTA isoform ratio 3 0.1 1.69
pVTA intron excision ratio 3 0.1 1.62
pVTA mRNA stability 1 0.1 1.64
RMTg alternative polyA 0 0 1.61
RMTg alternative TSS 0 0 1.55
RMTg gene expression 0 0 1.64
RMTg isoform ratio 0 0 1.53
RMTg intron excision ratio 0 0 1.55
RMTg mRNA stability 1 0.2 1.88