Hub : Traits

Bone: cortical area

Tags: Physiology · Bone

Project: r01_doug_adams

2 loci · 5 genes with independent associations · 6 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	chr1	254086596	255485810	1	1	1.7e-07	2.40e-06	1.35e-04	Tcf7l2
2	chr10	105364159	107195627	5	4	8.4e-09	1.54e-09	1.16e-03	B3gntl1 Dus1l Foxk2

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	3.39	3	0	0	0	1.00e+00	B3gntl1 Foxk2 Tcf7l2
Body weight	3.98	3	0	0	0.98	2.50e-03	B3gntl1 Dus1l Tcf7l2
Epididymis fat weight	9.86	1	0	0	0	1.00e+00	Tcf7l2
Heart weight	5.71	2	0	0	0	1.00e+00	B3gntl1 Foxk2
Left kidney weight	5.13	3	0	0	0	1.00e+00	B3gntl1 Dus1l Foxk2
Right kidney weight	4.46	3	0	0	0	1.00e+00	B3gntl1 Dus1l Foxk2
Tail length	4.78	1	0	0	0	1.00e+00	Foxk2
Length with tail	2.04	1	0	0	0	1.00e+00	B3gntl1
Length without tail	8.78	3	0	0	0	1.00e+00	B3gntl1 Dus1l Foxk2
Parametrial fat weight	6.13	1	0	0	0	1.00e+00	Tcf7l2
Retroperitoneal fat weight	6.95	1	0	0	0	1.00e+00	Tcf7l2
Intraocular pressure	5.48	1	0	0	0	1.00e+00	Tcf7l2
Tibia length	16.32	3	3	60	-0.19	7.65e-01	B3gntl1 Dus1l Foxk2
Condit. Reinf. active minus inactive responses	12.75	1	0	0	0	1.00e+00	Tcf7l2
Condit. Reinf. active-inactive response ratio	8.21	2	0	0	0	1.00e+00	B3gntl1 Tcf7l2
Condit. Reinf. active responses	12.11	1	0	0	0	1.00e+00	Tcf7l2
Condit. Reinf. lever presses	6.33	1	0	0	0	1.00e+00	Tcf7l2
Condit. Reinf. lever reinforcers received	10.57	1	0	0	0	1.00e+00	Tcf7l2
Intermittent access intake day 1-15 change	8.79	1	0	0	0	1.00e+00	Foxk2
Intermittent access intake escalation	11.8	1	0	0	0	1.00e+00	Foxk2
Baseline Anxiety	8.74	1	0	0	0	1.00e+00	Tcf7l2
One hour access (0.3 mA shock)	6.59	1	0	0	0	1.00e+00	Tcf7l2
Bone volume	4.82	1	0	0	0	1.00e+00	Tcf7l2
Bone: cortical thickness	22.31	4	3	60	0.99	6.81e-05	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: cortical thickness	11.45	3	0	0	0.56	3.30e-01	B3gntl1 Dus1l Foxk2
Bone: elastic work	13	3	0	0	-0.5	3.94e-01	B3gntl1 Dus1l Foxk2
Bone: endosteal estimation	3.56	1	0	0	0	1.00e+00	Tcf7l2
Bone: endosteal perimeter	9.97	1	0	0	0	1.00e+00	Tcf7l2
Bone: final force	13.51	4	1	20	1	3.84e-06	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: final moment	14.62	4	1	20	1	9.18e-06	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: marrow area	3.53	1	0	0	0	1.00e+00	Tcf7l2
Bone: maximum diameter	6.58	3	1	20	1	3.89e-06	B3gntl1 Foxk2 Tcf7l2
Bone: maximum force	12.85	4	1	20	1	1.64e-05	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: maximum moment	13.78	4	1	20	0.99	4.36e-05	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: minimum diameter	6.36	2	0	0	0	1.00e+00	B3gntl1 Tcf7l2
Bone: periosteal estimation	5.42	4	0	0	1	1.18e-05	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: periosteal perimeter	9.32	4	1	20	1	2.05e-05	B3gntl1 Dus1l Foxk2 Tcf7l2
Bone: stiffness	7.32	3	0	0	0.7	3.00e-01	B3gntl1 Dus1l Foxk2
Bone: trabecular thickness	7.22	1	0	0	0	1.00e+00	Tcf7l2
Distance traveled after self-admin	7.98	2	0	0	0	1.00e+00	B3gntl1 Foxk2
Delta ambulatory time before/after self-admin	7.34	2	0	0	0	1.00e+00	B3gntl1 Foxk2
Total heroin consumption	7.5	2	0	0	0	1.00e+00	B3gntl1 Dus1l
Co content in liver	6.33	1	0	0	0	1.00e+00	Tcf7l2
Mg content in liver	7.93	1	0	0	0	1.00e+00	B3gntl1

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	2	0.1	1.63
Adipose	alternative TSS	1	0	1.56
Adipose	gene expression	0	0	1.51
Adipose	isoform ratio	0	0	1.53
Adipose	intron excision ratio	0	0	1.45
Adipose	mRNA stability	0	0	1.53
BLA	alternative polyA	0	0	1.55
BLA	alternative TSS	0	0	1.55
BLA	gene expression	0	0	1.55
BLA	isoform ratio	0	0	1.44
BLA	intron excision ratio	0	0	1.43
BLA	mRNA stability	0	0	1.52
Brain	alternative polyA	0	0	1.56
Brain	alternative TSS	0	0	1.47
Brain	gene expression	0	0	1.51
Brain	isoform ratio	0	0	1.54
Brain	intron excision ratio	0	0	1.45
Brain	mRNA stability	0	0	1.52
Eye	alternative polyA	0	0	1.61
Eye	alternative TSS	0	0	1.04
Eye	gene expression	0	0	1.49
Eye	isoform ratio	0	0	1.66
Eye	intron excision ratio	0	0	1.33
Eye	mRNA stability	0	0	1.36
IL	alternative polyA	0	0	1.44
IL	alternative TSS	0	0	1.53
IL	gene expression	0	0	1.58
IL	isoform ratio	0	0	1.45
IL	intron excision ratio	0	0	1.44
IL	mRNA stability	0	0	1.63
LHb	alternative polyA	0	0	1.49
LHb	alternative TSS	1	0.2	1.29
LHb	gene expression	0	0	1.54
LHb	isoform ratio	0	0	1.41
LHb	intron excision ratio	0	0	1.35
LHb	mRNA stability	0	0	1.53
Liver	alternative polyA	0	0	1.52
Liver	alternative TSS	0	0	1.39
Liver	gene expression	0	0	1.52
Liver	isoform ratio	0	0	1.52
Liver	intron excision ratio	1	0	1.44
Liver	mRNA stability	0	0	1.5
NAcc	alternative polyA	0	0	1.48
NAcc	alternative TSS	0	0	1.55
NAcc	gene expression	0	0	1.53
NAcc	isoform ratio	0	0	1.53
NAcc	intron excision ratio	0	0	1.46
NAcc	mRNA stability	0	0	1.54
OFC	alternative polyA	0	0	1.53
OFC	alternative TSS	0	0	1.49
OFC	gene expression	0	0	1.56
OFC	isoform ratio	0	0	1.4
OFC	intron excision ratio	0	0	1.44
OFC	mRNA stability	0	0	1.58
PL	alternative polyA	0	0	1.53
PL	alternative TSS	0	0	1.51
PL	gene expression	0	0	1.57
PL	isoform ratio	0	0	1.56
PL	intron excision ratio	0	0	1.45
PL	mRNA stability	0	0	1.53
pVTA	alternative polyA	0	0	1.58
pVTA	alternative TSS	0	0	1.35
pVTA	gene expression	0	0	1.55
pVTA	isoform ratio	1	0	1.51
pVTA	intron excision ratio	0	0	1.46
pVTA	mRNA stability	0	0	1.56
RMTg	alternative polyA	0	0	1.37
RMTg	alternative TSS	0	0	1.63
RMTg	gene expression	0	0	1.48
RMTg	isoform ratio	0	0	1.46
RMTg	intron excision ratio	0	0	1.26
RMTg	mRNA stability	0	0	1.59