Hub : Traits

Bone volume

Tags: Physiology · Bone

Project: r01_doug_adams

2 loci · 3 genes with independent associations · 4 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	44152620	45549784	1	1	1.08e-17	7.05e-04	5.72e-12	Ly75
2	chr5	137680740	138752373	3	2	9.31e-08	4.53e-02	2.41e-01	Stk40

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	2.75	1	0	0	0	1.00e+00	Stk40
BMI without tail	3.94	1	0	0	0	1.00e+00	Ly75
Body weight	2.82	1	0	0	0	1.00e+00	Stk40
Epididymis fat weight	3.44	1	0	0	0	1.00e+00	Ly75
Glucose	17.38	1	1	33.3	0	1.00e+00	Stk40
Length with tail	2.82	1	0	0	0	1.00e+00	Ly75
Length without tail	8.83	1	0	0	0	1.00e+00	Ly75
Retroperitoneal fat weight	8.85	1	1	33.3	0	1.00e+00	Ly75
Intraocular pressure	4.57	1	0	0	0	1.00e+00	Stk40
Extensor digitorum longus weight	5.16	2	1	33.3	0.88	1.20e-01	Ly75 Stk40
Soleus weight	7.93	1	1	33.3	0	1.00e+00	Stk40
Tibialis anterior weight	3.82	2	0	0	0	1.00e+00	Ly75 Stk40
Number of licking bursts	7.94	1	0	0	0	1.00e+00	Ly75
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 indifference point 0 sec	3.93	1	0	0	0	1.00e+00	Stk40
Patch foraging indifference point AUC	10.55	1	0	0	0	1.00e+00	Stk40
Patch foraging total patch changes 0 sec	4.01	1	0	0	0	1.00e+00	Stk40
Patch foraging total patch changes 18 sec	15.07	2	0	0	0.95	5.14e-02	Ly75 Stk40
Patch foraging total patch changes 24 sec	10.91	1	0	0	0	1.00e+00	Stk40
Patch foraging total patch changes 6 sec	5.12	1	0	0	0	1.00e+00	Stk40
Locomotor activity	7.17	2	0	0	0	1.00e+00	Ly75 Stk40
Locomotor testing distance	8.03	2	0	0	0	1.00e+00	Ly75 Stk40
Locomotor testing rearing	9.87	2	0	0	-0.5	4.97e-01	Ly75 Stk40
Light reinforcement 1	4.81	1	0	0	0	1.00e+00	Stk40
Reaction time mean minus median	5.26	1	0	0	0	1.00e+00	Ly75
Reaction time mean minus median AUC	17.14	1	0	0	0	1.00e+00	Ly75
Reaction time num false alarms	5.82	1	0	0	0	1.00e+00	Stk40
Reaction time num false alarms AUC	6.6	1	0	0	0	1.00e+00	Stk40
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
Median of all reaction times	5.14	1	0	0	0	1.00e+00	Ly75
Reaction time premature initiation rate	9.14	1	0	0	0	1.00e+00	Ly75
Reaction time premature initiations	4.53	1	0	0	0	1.00e+00	Ly75
Std. dev. reaction times	14.29	1	0	0	0	1.00e+00	Ly75
Cocaine response before conditioning	5.81	2	0	0	0	1.00e+00	Ly75 Stk40
Condit. Reinf. active minus inactive responses	28.62	1	1	33.3	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	33.3	0	1.00e+00	Ly75
Condit. Reinf. lever presses	6.71	2	0	0	0.97	2.67e-02	Ly75 Stk40
Condit. Reinf. lever reinforcers received	19.5	1	1	33.3	0	1.00e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Intermitt. access escalation Index	7.73	1	0	0	0	1.00e+00	Stk40
Short access day 10 total inactive lever presses	7.04	1	0	0	0	1.00e+00	Stk40
Locomotion velocity, session 1	6.3	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
Degree of sensitization distance	10.32	1	0	0	0	1.00e+00	Ly75
Degree of sensitization stereotypy	38.66	1	1	33.3	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	10.85	2	0	0	0.99	6.35e-03	Ly75 Stk40
Condit. Reinf. active-inactive response ratio	8.1	2	0	0	0	1.00e+00	Ly75 Stk40
Condit. Reinf. active responses	10.46	2	0	0	0	1.00e+00	Ly75 Stk40
Incentive salience index mean	15.36	2	0	0	0.97	3.42e-02	Ly75 Stk40
Condit. Reinf. lever presses	11.32	1	0	0	0	1.00e+00	Stk40
Total zone transitions, hab. session 1	7.48	1	0	0	0	1.00e+00	Ly75
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	33.3	0	1.00e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	33.3	0	1.00e+00	Ly75
Total zone transitions, NPP test	5.39	1	0	0	0	1.00e+00	Ly75
Total locomotion distance, NPP test	4.87	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. lever latency	9.31	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. magazine entry latency	5.8	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. change in total contacts	9.81	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. index score	6.15	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. latency score	5.91	2	0	0	0	1.00e+00	Ly75 Stk40
Pavlov. Cond. lever contacts	8.48	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. intertrial magazine entries	11.69	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. lever-magazine prob. diff.	7.51	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. response bias	5.5	1	0	0	0	1.00e+00	Stk40
Bone: apparent density	12.19	2	1	33.3	0.99	6.78e-03	Ly75 Stk40
Bone surface	18.65	2	1	33.3	0.98	2.08e-02	Ly75 Stk40
Bone: connectivity density	21.24	1	1	33.3	0	1.00e+00	Ly75
Bone: cortical apparent density	18.66	1	0	0	0	1.00e+00	Ly75
Bone: cortical area	12.58	1	0	0	0	1.00e+00	Ly75
Bone: cortical thickness	5.93	1	0	0	0	1.00e+00	Ly75
Bone: cortical thickness	7.09	1	0	0	0	1.00e+00	Ly75
Bone: cortical tissue density	17.88	1	0	0	0	1.00e+00	Ly75
Bone: elastic work	15.82	1	0	0	0	1.00e+00	Ly75
Bone: endosteal estimation	9.05	1	0	0	0	1.00e+00	Ly75
Bone: final force	35.73	1	1	33.3	0	1.00e+00	Ly75
Bone: final moment	48.32	1	1	33.3	0	1.00e+00	Ly75
Bone: marrow area	9.02	1	0	0	0	1.00e+00	Ly75
Bone: maximum diameter	5.12	1	0	0	0	1.00e+00	Ly75
Bone: maximum force	20.87	1	1	33.3	0	1.00e+00	Ly75
Bone: maximum moment	29.34	1	1	33.3	0	1.00e+00	Ly75
Bone: minimum diameter	8.69	1	0	0	0	1.00e+00	Ly75
Bone: periosteal estimation	14.82	1	1	33.3	0	1.00e+00	Ly75
Bone: periosteal perimeter	7.52	1	0	0	0	1.00e+00	Ly75
Bone: stiffness	8.72	1	0	0	0	1.00e+00	Ly75
Bone: trabecular number	35.45	1	1	33.3	0	1.00e+00	Ly75
Bone: trabecular spacing	60.24	1	1	33.3	0	1.00e+00	Ly75
Bone: trabecular thickness	47.42	1	1	33.3	0	1.00e+00	Ly75
Bone: trabecular tissue density	4.55	1	0	0	0	1.00e+00	Stk40
Time to tail flick, vehicle, after self-admin	7.33	1	0	0	0	1.00e+00	Stk40
Total resting periods, locomotor time 1	5.85	1	0	0	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	33.3	0	1.00e+00	Ly75
Food seeking constrained by brief footshock	13.79	1	0	0	0	1.00e+00	Ly75
Seeking ratio, punishment vs. effort	5.43	1	0	0	0	1.00e+00	Ly75
Run reversals in cocaine runway, females	15.87	2	0	0	0	1.00e+00	Ly75 Stk40
Cu content in liver	8.78	1	0	0	0	1.00e+00	Ly75
Fe content in liver	7.43	1	0	0	0	1.00e+00	Ly75
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	33.3	0	1.00e+00	Ly75
Na content in liver	12.24	1	0	0	0	1.00e+00	Ly75
Sr content in liver	56.81	2	1	33.3	0.55	4.51e-01	Ly75 Stk40
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	1.7
Adipose	alternative TSS	0	0	1.75
Adipose	gene expression	0	0	1.69
Adipose	isoform ratio	0	0	1.71
Adipose	intron excision ratio	0	0	1.62
Adipose	mRNA stability	0	0	1.74
BLA	alternative polyA	0	0	1.84
BLA	alternative TSS	0	0	1.85
BLA	gene expression	0	0	1.77
BLA	isoform ratio	0	0	1.69
BLA	intron excision ratio	0	0	1.6
BLA	mRNA stability	0	0	1.82
Brain	alternative polyA	0	0	1.73
Brain	alternative TSS	0	0	1.76
Brain	gene expression	0	0	1.68
Brain	isoform ratio	0	0	1.72
Brain	intron excision ratio	0	0	1.59
Brain	mRNA stability	0	0	1.73
Eye	alternative polyA	0	0	1.97
Eye	alternative TSS	0	0	1.55
Eye	gene expression	0	0	1.69
Eye	isoform ratio	0	0	1.83
Eye	intron excision ratio	0	0	1.51
Eye	mRNA stability	0	0	1.7
IL	alternative polyA	0	0	1.79
IL	alternative TSS	0	0	1.87
IL	gene expression	0	0	1.72
IL	isoform ratio	0	0	1.62
IL	intron excision ratio	0	0	1.48
IL	mRNA stability	0	0	1.85
LHb	alternative polyA	0	0	1.7
LHb	alternative TSS	0	0	1.61
LHb	gene expression	1	0	1.7
LHb	isoform ratio	0	0	1.6
LHb	intron excision ratio	0	0	1.38
LHb	mRNA stability	0	0	1.74
Liver	alternative polyA	0	0	1.75
Liver	alternative TSS	0	0	1.74
Liver	gene expression	0	0	1.7
Liver	isoform ratio	1	0	1.73
Liver	intron excision ratio	0	0	1.63
Liver	mRNA stability	0	0	1.7
NAcc	alternative polyA	0	0	1.76
NAcc	alternative TSS	0	0	1.79
NAcc	gene expression	0	0	1.73
NAcc	isoform ratio	0	0	1.69
NAcc	intron excision ratio	0	0	1.6
NAcc	mRNA stability	0	0	1.75
OFC	alternative polyA	0	0	1.66
OFC	alternative TSS	0	0	1.84
OFC	gene expression	0	0	1.66
OFC	isoform ratio	0	0	1.54
OFC	intron excision ratio	0	0	1.53
OFC	mRNA stability	0	0	1.8
PL	alternative polyA	0	0	1.82
PL	alternative TSS	0	0	1.8
PL	gene expression	0	0	1.73
PL	isoform ratio	0	0	1.75
PL	intron excision ratio	0	0	1.61
PL	mRNA stability	0	0	1.76
pVTA	alternative polyA	0	0	1.8
pVTA	alternative TSS	0	0	1.78
pVTA	gene expression	0	0	1.67
pVTA	isoform ratio	0	0	1.68
pVTA	intron excision ratio	0	0	1.58
pVTA	mRNA stability	0	0	1.77
RMTg	alternative polyA	0	0	1.87
RMTg	alternative TSS	0	0	1.7
RMTg	gene expression	0	0	1.72
RMTg	isoform ratio	0	0	1.59
RMTg	intron excision ratio	0	0	1.32
RMTg	mRNA stability	0	0	1.87