Hub : Traits

Bone: cortical thickness

Tags: Physiology · Bone

Project: r01_doug_adams

74 significantly associated models · 23 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 128419948 5 1 5.1e-09 5.5e-09 1.7e-01 94 Ndufaf5
2 10 91442275 92841363 1 1 1.4e-07 1.4e-06 1.0e-01 89 Nol11
3 10 94609547 96660473 3 1 6.5e-09 7.8e-11 3.3e-04 69 NA
4 10 97108442 98504204 1 1 3.5e-09 2.0e-10 3.3e-03 79 Sox9
5 10 102999385 104353671 5 3 7.3e-08 7.2e-08 8.9e-16 -123 Lgals3bp Cep295nl Afmid
6 10 105499327 107195627 8 3 7.7e-17 2.7e-10 2.0e-05 54 Wdr45b Znf750 Ccdc57

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 5.4 10 1 10 0.99 6.8e-20 Lgals3bp C1qtnf1 Tasp1 Esf1 Ndufaf5 Usp36 Cep295nl Ccdc57 Afmid Nol11
BMI without tail 6.8 1 0 0 0.00 1.0e+00 Ccdc57
Body weight 6.1 9 4 40 0.99 1.0e-44 Tasp1 Esf1 Ndufaf5 Tbcd Znf750 Ccdc57 AABR07054000.1 Ism1 NA
Epididymis fat weight 6.1 3 0 0 1.00 2.1e-05 Tasp1 Ndufaf5 Ism1
Glucose 7.7 2 0 0 0.00 1.0e+00 Wdr45b Narf
Left kidney weight 4.4 1 0 0 0.00 1.0e+00 NA
Tail length 4.0 1 0 0 0.00 1.0e+00 Wdr45b
Length with tail 3.3 3 0 0 1.00 6.5e-06 Tasp1 Esf1 Ndufaf5
Length without tail 8.6 4 0 0 0.99 1.7e-03 Fn3k Wdr45b Narf Sectm1a
Retroperitoneal fat weight 6.0 5 3 30 0.99 5.5e-38 Tasp1 Esf1 Ndufaf5 AABR07054000.1 Ism1
Tibia length 6.8 14 4 40 0.98 1.7e-34 Tasp1 Esf1 Ndufaf5 Cep295nl Tbcd Fn3k Wdr45b Narf Sectm1a Znf750 Ccdc57 AABR07054000.1 Ism1 NA
Delay discounting total patch changes 0 sec 7.1 1 0 0 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 9.5 1 0 0 0.00 1.0e+00 Ndufaf5
Delay discounting water rate 24 sec 8.6 1 0 0 0.00 1.0e+00 Ccdc57
Locomotor testing rearing 8.3 2 0 0 1.00 1.6e-04 Kcnj16 NA
Intermitt. access day 1 inactive lever presses 11.5 1 0 0 0.00 1.0e+00 Sox9
Bone surface 8.9 7 0 0 -0.99 5.7e-13 Lgals3bp C1qtnf1 Kcnj16 Usp36 Cep295nl Afmid NA
Bone volume 9.3 2 0 0 -1.00 2.4e-04 Kcnj16 NA
Bone: cortical apparent density 9.5 3 0 0 1.00 1.2e-06 Kcnj16 Nol11 NA
Bone: cortical area 11.1 13 3 30 0.99 3.1e-47 Tasp1 Esf1 Ndufaf5 Tbcd Fn3k Wdr45b Narf Sectm1a Znf750 Ccdc57 AABR07054000.1 Ism1 NA
Bone: cortical thickness 12.8 7 0 0 1.00 1.3e-10 Lgals3bp Usp36 Cep295nl Wdr45b Narf Ccdc57 Afmid
Bone: cortical tissue density 9.1 2 0 0 1.00 7.4e-04 Kcnj16 Nol11
Bone: elastic work 12.2 5 0 0 0.98 1.1e-05 Sox9 Tbcd Znf750 Ccdc57 NA
Bone: endosteal estimation 11.6 9 4 40 -0.96 2.4e-10 Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 NA
Bone: endosteal perimeter 11.9 10 4 40 -0.98 1.1e-12 Sox9 Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 NA
Bone: final force 18.5 5 1 10 1.00 2.8e-05 Tbcd Wdr45b Znf750 Ccdc57 NA
Bone: final moment 16.1 6 1 10 0.99 1.8e-06 Sox9 Tbcd Wdr45b Znf750 Ccdc57 NA
Bone: marrow area 11.5 9 4 40 -0.96 1.7e-10 Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 NA
Bone: maximum diameter 8.8 2 0 0 -0.19 7.1e-01 Kcnj16 Ccdc57
Bone: maximum force 18.2 5 2 20 0.99 6.9e-05 Tbcd Wdr45b Znf750 Ccdc57 NA
Bone: maximum moment 18.7 5 3 30 0.99 8.1e-05 Tbcd Wdr45b Znf750 Ccdc57 NA
Bone: minimum diameter 8.7 3 0 0 -0.12 8.0e-01 Kcnj16 Tbcd Ccdc57
Bone: periosteal estimation 9.1 4 0 0 0.03 9.4e-01 Kcnj16 Tbcd Ccdc57 NA
Bone: periosteal perimeter 8.3 4 0 0 0.70 1.9e-01 Kcnj16 Tbcd Ccdc57 NA
Bone: stiffness 15.5 1 0 0 0.00 1.0e+00 Ccdc57
Latency to leave start box in cocaine runway 10.6 1 0 0 0.00 1.0e+00 Ndufaf5

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 0 0.000 1.7
Adipose alternative TSS 0 0.000 1.6
Adipose gene expression 3 0.036 1.6
Adipose isoform ratio 1 0.035 1.7
Adipose intron excision ratio 2 0.069 1.7
Adipose mRNA stability 3 0.087 1.7
BLA alternative polyA 0 0.000 1.5
BLA alternative TSS 0 0.000 1.6
BLA gene expression 3 0.049 1.7
BLA isoform ratio 0 0.000 1.7
BLA intron excision ratio 2 0.067 1.7
BLA mRNA stability 1 0.049 1.6
Brain alternative polyA 0 0.000 1.7
Brain alternative TSS 4 0.233 1.8
Brain gene expression 6 0.066 1.6
Brain isoform ratio 0 0.000 1.8
Brain intron excision ratio 6 0.111 1.7
Brain mRNA stability 4 0.092 1.7
Eye alternative polyA 0 0.000 1.9
Eye alternative TSS 0 0.000 1.6
Eye gene expression 0 0.000 1.8
Eye isoform ratio 0 0.000 1.7
Eye intron excision ratio 0 0.000 1.6
Eye mRNA stability 1 0.429 1.8
IL alternative polyA 0 0.000 1.5
IL alternative TSS 0 0.000 1.5
IL gene expression 2 0.055 1.6
IL isoform ratio 0 0.000 1.7
IL intron excision ratio 3 0.311 1.7
IL mRNA stability 0 0.000 1.7
LHb alternative polyA 0 0.000 1.6
LHb alternative TSS 0 0.000 1.9
LHb gene expression 2 0.062 1.7
LHb isoform ratio 0 0.000 1.8
LHb intron excision ratio 2 0.194 1.5
LHb mRNA stability 1 0.097 1.6
Liver alternative polyA 0 0.000 1.5
Liver alternative TSS 0 0.000 1.6
Liver gene expression 3 0.042 1.6
Liver isoform ratio 0 0.000 1.6
Liver intron excision ratio 0 0.000 1.6
Liver mRNA stability 0 0.000 1.6
NAcc alternative polyA 0 0.000 1.6
NAcc alternative TSS 2 0.216 1.9
NAcc gene expression 2 0.032 1.7
NAcc isoform ratio 0 0.000 1.7
NAcc intron excision ratio 5 0.163 1.7
NAcc mRNA stability 1 0.044 1.6
OFC alternative polyA 0 0.000 1.7
OFC alternative TSS 0 0.000 1.4
OFC gene expression 3 0.081 1.7
OFC isoform ratio 0 0.000 1.8
OFC intron excision ratio 2 0.199 1.8
OFC mRNA stability 0 0.000 1.6
PL alternative polyA 0 0.000 1.6
PL alternative TSS 0 0.000 1.7
PL gene expression 5 0.068 1.7
PL isoform ratio 1 0.045 1.7
PL intron excision ratio 3 0.084 1.7
PL mRNA stability 1 0.034 1.6

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