Hub : Traits

Bone: maximum force

Tags: Physiology · Bone

Project: r01_doug_adams

7 loci · 8 genes with independent associations · 51 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	chr2	175255218	176649376	1	1	7.17e-11	3.51e-01	1.33e-32	Ilf2
2	chr3	44152620	45549784	1	1	1.95e-09	5.92e-03	4.29e-05	Ly75
3	chr7	129232833	131872914	44	2	3.03e-08	1.34e-07	1.00e+00	LOC102546778 Tuba1b
4	chr9	87238851	88635740	1	1	1.67e-07	3.45e-06	8.05e-02	Efhd1
5	chr10	106235924	107195627	1	1	1.18e-07	4.58e-09	1.60e-06	B3gntl1
6	chr16	2113611	4396663	2	1	3.29e-08	7.49e-09	2.74e-54	Erc2
7	chr16	17477182	18874041	1	1	2.26e-07	4.57e-05	3.98e-02	Gtpbp3

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	4.5	23	0	0	1	3.22e-132	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Body weight	5.96	25	5	62.5	1	6.14e-116	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Gtpbp3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Left kidney weight	5.75	1	0	0	0	1.00e+00	B3gntl1
Right kidney weight	4.8	1	0	0	0	1.00e+00	B3gntl1
Length without tail	7.42	24	0	0	1	1.48e-110	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Retroperitoneal fat weight	8.85	1	1	12.5	0	1.00e+00	Ly75
Extensor digitorum longus weight	4.23	22	0	0	1	9.87e-110	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Tibialis anterior weight	3.75	1	0	0	0	1.00e+00	Ly75
Tibia length	6.65	25	1	12.5	1	8.71e-95	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Efhd1 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Food consumed during 24 hour testing period	11.76	1	0	0	0	1.00e+00	Ly75
Water consumed over 24 hours	19.18	1	0	0	0	1.00e+00	Ly75
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1.00e+00	Ly75
Reaction time mean minus median	9.44	4	0	0	-1	8.36e-09	LOC102546778 Mcrs1 Prph Spats2
Reaction time mean minus median AUC	17.14	1	0	0	0	1.00e+00	Ly75
Reaction time mean	9.87	1	0	0	0	1.00e+00	Ly75
Reaction time mean AUC	10.73	1	0	0	0	1.00e+00	Ly75
Reaction time omissions	10.01	22	0	0	-1	6.19e-136	Aqp5 Asic1 Bcdin3d C1ql4 Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Reaction time premature initiation rate	14.82	2	1	12.5	0	1.00e+00	Ilf2 Ly75
Reaction time premature initiations	12.93	1	0	0	0	1.00e+00	Ilf2
Std. dev. reaction times	14.29	1	0	0	0	1.00e+00	Ly75
Social response proportion	11.26	1	0	0	0	1.00e+00	Ilf2
Condit. Reinf. active minus inactive responses	28.62	1	1	12.5	0	1.00e+00	Ly75
Condit. Reinf. active-inactive response ratio	11.56	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active responses	24.88	1	1	12.5	0	1.00e+00	Ly75
Condit. Reinf. lever reinforcers received	19.5	1	1	12.5	0	1.00e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Locomotion distance, session 3	14.48	1	0	0	0	1.00e+00	Ly75
Stereotopy head waving bouts, day 7	23.7	1	0	0	0	1.00e+00	Ly75
Stereotopy head waving duration, day 7	21.6	1	0	0	0	1.00e+00	Ly75
Locomotion velocity, session 8	12.76	2	0	0	0	1.00e+00	Ilf2 Wnt5a
Degree of sensitization stereotypy	38.66	1	1	12.5	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	16.76	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active responses	13.63	1	0	0	0	1.00e+00	Ly75
Incentive salience index mean	15.42	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. lever presses	10.84	1	0	0	0	1.00e+00	Ilf2
Total zone transitions, hab. session 2	19.52	1	0	0	0	1.00e+00	Ly75
Total locomotion distance, hab. session 2	24.97	1	1	12.5	0	1.00e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	12.5	0	1.00e+00	Ly75
Pavlov. Cond. lever latency	21.9	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. magazine entry latency	28.91	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. change in total contacts	18.74	1	0	0	0	1.00e+00	Ilf2
Pavlov. Cond. index score	34.08	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. latency score	30.82	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. lever contacts	37.24	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. magazine entry number	42.75	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. intertrial magazine entries	13.5	1	0	0	0	1.00e+00	Ilf2
Pavlov. Cond. lever-magazine prob. diff.	35.53	1	1	12.5	0	1.00e+00	Ilf2
Pavlov. Cond. response bias	41.38	1	1	12.5	0	1.00e+00	Ilf2
Bone: apparent density	10.64	24	1	12.5	1	3.61e-103	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone surface	12.85	24	1	12.5	1	7.00e-91	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone volume	10.19	24	1	12.5	0.99	8.52e-86	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone: connectivity density	8.46	11	1	12.5	1	1.38e-25	Dnajc22 Kcnh3 LOC102546778 Ly75 Prkag1 Prpf40b Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone: cortical apparent density	18.66	1	0	0	0	1.00e+00	Ly75
Bone: cortical area	9.38	25	1	12.5	1	1.36e-91	Asic1 B3gntl1 Bcdin3d C1ql4 Dnajc22 Erc2 Faim2 Fmnl3 Gtpbp3 Ilf2 Kcnh3 LOC100362820 LOC102546778 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: cortical thickness	20.09	2	1	12.5	0	1.00e+00	B3gntl1 Gtpbp3
Bone: cortical thickness	12.83	1	0	0	0	1.00e+00	B3gntl1
Bone: cortical tissue density	17.88	1	0	0	0	1.00e+00	Ly75
Bone: elastic work	13.74	2	0	0	0	1.00e+00	B3gntl1 Ly75
Bone: endosteal estimation	8.33	27	0	0	1	6.53e-118	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Erc2 Faim2 Fmnl3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: endosteal perimeter	7.03	23	0	0	1	1.73e-136	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone: final force	11.89	30	3	37.5	1	7.29e-106	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Efhd1 Erc2 Faim2 Fmnl3 Gtpbp3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: final moment	13	30	4	50	1	1.42e-97	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Efhd1 Erc2 Faim2 Fmnl3 Gtpbp3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: marrow area	8.07	27	0	0	1	5.31e-118	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Erc2 Faim2 Fmnl3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: maximum moment	17.55	30	28	350	1	2.07e-147	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Efhd1 Erc2 Faim2 Fmnl3 Gtpbp3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: minimum diameter	9.54	27	1	12.5	1	8.81e-115	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Erc2 Faim2 Fmnl3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: periosteal estimation	11.84	27	3	37.5	1	2.34e-115	Aqp5 Asic1 Bcdin3d C1ql4 Dip2b Dnajc22 Erc2 Faim2 Fmnl3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: periosteal perimeter	10.29	27	0	0	1	1.08e-123	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Faim2 Fmnl3 Gtpbp3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: post-yield work	9.78	22	0	0	1	6.32e-163	Aqp5 Asic1 Bcdin3d C1ql4 Dnajc22 Faim2 Fmnl3 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b
Bone: stiffness	18.33	30	22	275	1	6.03e-98	Aqp5 Asic1 B3gntl1 Bcdin3d C1ql4 Dip2b Dnajc22 Efhd1 Erc2 Faim2 Fmnl3 Gtpbp3 Ilf2 Kcnh3 LOC100362820 LOC102546778 LOC108351553 Ly75 Mcrs1 Nckap5l Prkag1 Prpf40b Prph Smarcd1 Spats2 Tmbim6 Tuba1b Tuba1c Wnt10b Wnt5a
Bone: tissue strength	19.03	1	0	0	0	1.00e+00	Efhd1
Bone: trabecular number	12.8	4	1	12.5	0.96	2.42e-03	LOC100362820 Ly75 Prkag1 Tuba1b
Bone: trabecular spacing	60.24	1	1	12.5	0	1.00e+00	Ly75
Bone: trabecular thickness	47.42	1	1	12.5	0	1.00e+00	Ly75
Rest time, locomotor task time 1	12.3	1	0	0	0	1.00e+00	Ly75
Distance moved, locomotor task time 1	13.8	1	0	0	0	1.00e+00	Ly75
Weight adjusted by age	20.87	1	0	0	0	1.00e+00	Ly75
Locomotion in novel chamber	34.01	1	1	12.5	0	1.00e+00	Ly75
Progressive ratio	12.89	1	0	0	0	1.00e+00	Ilf2
Food seeking constrained by brief footshock	13.79	1	0	0	0	1.00e+00	Ly75
Run reversals in cocaine runway, females	21.72	1	0	0	0	1.00e+00	Ly75
Latency to leave start box in cocaine runway, M	14.76	1	0	0	0	1.00e+00	Ilf2
Cd content in liver	13.38	1	0	0	0	1.00e+00	Ilf2
K content in liver	12.92	1	0	0	0	1.00e+00	Ly75
Mg content in liver	13.79	1	0	0	0	1.00e+00	Ly75
Mn content in liver	32.26	1	1	12.5	0	1.00e+00	Ly75
Na content in liver	12.24	1	0	0	0	1.00e+00	Ly75
Sr content in liver	14.16	1	0	0	0	1.00e+00	Ly75
Zn content in liver	12.81	1	0	0	0	1.00e+00	Ly75

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	2	0.1	1.8
Adipose	alternative TSS	1	0	1.74
Adipose	gene expression	4	0	1.68
Adipose	isoform ratio	1	0	1.65
Adipose	intron excision ratio	0	0	1.65
Adipose	mRNA stability	2	0	1.73
BLA	alternative polyA	0	0	1.95
BLA	alternative TSS	0	0	1.67
BLA	gene expression	4	0.1	1.81
BLA	isoform ratio	1	0	1.69
BLA	intron excision ratio	0	0	1.66
BLA	mRNA stability	1	0	1.76
Brain	alternative polyA	0	0	1.8
Brain	alternative TSS	0	0	1.68
Brain	gene expression	6	0.1	1.69
Brain	isoform ratio	3	0.1	1.71
Brain	intron excision ratio	1	0	1.65
Brain	mRNA stability	2	0	1.7
Eye	alternative polyA	0	0	2.12
Eye	alternative TSS	0	0	1.44
Eye	gene expression	0	0	1.71
Eye	isoform ratio	0	0	1.98
Eye	intron excision ratio	0	0	1.52
Eye	mRNA stability	0	0	1.59
IL	alternative polyA	0	0	1.86
IL	alternative TSS	0	0	1.7
IL	gene expression	2	0	1.81
IL	isoform ratio	0	0	1.72
IL	intron excision ratio	0	0	1.81
IL	mRNA stability	0	0	1.85
LHb	alternative polyA	0	0	1.9
LHb	alternative TSS	1	0.2	1.67
LHb	gene expression	6	0.2	1.77
LHb	isoform ratio	0	0	1.63
LHb	intron excision ratio	0	0	1.7
LHb	mRNA stability	1	0.1	1.69
Liver	alternative polyA	0	0	1.72
Liver	alternative TSS	0	0	1.7
Liver	gene expression	2	0	1.65
Liver	isoform ratio	2	0.1	1.65
Liver	intron excision ratio	0	0	1.5
Liver	mRNA stability	2	0.1	1.63
NAcc	alternative polyA	0	0	1.75
NAcc	alternative TSS	0	0	1.82
NAcc	gene expression	7	0.1	1.74
NAcc	isoform ratio	0	0	1.73
NAcc	intron excision ratio	2	0	1.71
NAcc	mRNA stability	4	0.1	1.74
OFC	alternative polyA	0	0	1.94
OFC	alternative TSS	0	0	1.85
OFC	gene expression	2	0	1.77
OFC	isoform ratio	0	0	1.65
OFC	intron excision ratio	0	0	1.69
OFC	mRNA stability	1	0.1	1.8
PL	alternative polyA	1	0	1.76
PL	alternative TSS	4	0.1	1.79
PL	gene expression	6	0.1	1.78
PL	isoform ratio	3	0.1	1.82
PL	intron excision ratio	1	0	1.74
PL	mRNA stability	5	0.1	1.75
pVTA	alternative polyA	2	0.1	1.97
pVTA	alternative TSS	0	0	1.66
pVTA	gene expression	5	0.1	1.8
pVTA	isoform ratio	1	0	1.76
pVTA	intron excision ratio	0	0	1.74
pVTA	mRNA stability	1	0.1	1.77
RMTg	alternative polyA	0	0	1.82
RMTg	alternative TSS	0	0	1.82
RMTg	gene expression	2	0.1	1.72
RMTg	isoform ratio	0	0	1.85
RMTg	intron excision ratio	0	0	1.55
RMTg	mRNA stability	3	0.5	1.84