Hub : Traits

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