Hub : Traits

Bone: trabecular thickness

Tags: Physiology · Bone

Project: r01_doug_adams

1 locus · 1 gene with independent associations · 1 total associated gene

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	5.16e-14	5.99e-03	4e-15	Ly75

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	1.55	1	0	0	0	1e+00	Ly75
BMI without tail	3.94	1	0	0	0	1e+00	Ly75
Epididymis fat weight	3.44	1	0	0	0	1e+00	Ly75
Glucose	3.95	1	0	0	0	1e+00	Ly75
Length with tail	2.82	1	0	0	0	1e+00	Ly75
Length without tail	8.83	1	0	0	0	1e+00	Ly75
Liver weight, left	3.24	1	0	0	0	1e+00	Ly75
Parametrial fat weight	2.38	1	0	0	0	1e+00	Ly75
Retroperitoneal fat weight	8.85	1	1	100	0	1e+00	Ly75
Intraocular pressure	3.09	1	0	0	0	1e+00	Ly75
Extensor digitorum longus weight	1.63	1	0	0	0	1e+00	Ly75
Tibialis anterior weight	3.75	1	0	0	0	1e+00	Ly75
Number of licking bursts	7.94	1	0	0	0	1e+00	Ly75
Food consumed during 24 hour testing period	11.76	1	0	0	0	1e+00	Ly75
Times rat made contact with spout	3.58	1	0	0	0	1e+00	Ly75
Mean time between licks in bursts	2.99	1	0	0	0	1e+00	Ly75
Mean num. licks in bursts	4.84	1	0	0	0	1e+00	Ly75
Std. dev. time between licks in bursts	3.96	1	0	0	0	1e+00	Ly75
Water consumed over 24 hours	19.18	1	0	0	0	1e+00	Ly75
Patch foraging indifference point 0 sec	3.47	1	0	0	0	1e+00	Ly75
Patch foraging total patch changes 0 sec	2.94	1	0	0	0	1e+00	Ly75
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1e+00	Ly75
Locomotor activity	6.86	1	0	0	0	1e+00	Ly75
Locomotor testing distance	6.84	1	0	0	0	1e+00	Ly75
Locomotor testing rearing	4.53	1	0	0	0	1e+00	Ly75
Reaction time mean minus median	5.26	1	0	0	0	1e+00	Ly75
Reaction time mean minus median AUC	17.14	1	0	0	0	1e+00	Ly75
Reaction time num false alarms	2.93	1	0	0	0	1e+00	Ly75
Reaction time mean	9.87	1	0	0	0	1e+00	Ly75
Reaction time mean AUC	10.73	1	0	0	0	1e+00	Ly75
Median of all reaction times	5.14	1	0	0	0	1e+00	Ly75
Reaction time false alarm rate	4.06	1	0	0	0	1e+00	Ly75
Reaction time premature initiation rate	9.14	1	0	0	0	1e+00	Ly75
Reaction time premature initiations	4.53	1	0	0	0	1e+00	Ly75
Std. dev. reaction times	14.29	1	0	0	0	1e+00	Ly75
Cocaine response after cond. corrected	4.76	1	0	0	0	1e+00	Ly75
Cocaine response before conditioning	5.9	1	0	0	0	1e+00	Ly75
Saline control response	3.55	1	0	0	0	1e+00	Ly75
Condit. Reinf. active minus inactive responses	28.62	1	1	100	0	1e+00	Ly75
Condit. Reinf. active-inactive response ratio	11.56	1	0	0	0	1e+00	Ly75
Condit. Reinf. active responses	24.88	1	1	100	0	1e+00	Ly75
Condit. Reinf. inactive responses	3.32	1	0	0	0	1e+00	Ly75
Condit. Reinf. lever presses	8.53	1	0	0	0	1e+00	Ly75
Condit. Reinf. lever reinforcers received	19.5	1	1	100	0	1e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1e+00	Ly75
Locomotion velocity, session 1	6.3	1	0	0	0	1e+00	Ly75
Locomotion distance, session 3	14.48	1	0	0	0	1e+00	Ly75
Stereotopy head waving bouts, day 7	23.7	1	0	0	0	1e+00	Ly75
Stereotopy head waving duration, day 7	21.6	1	0	0	0	1e+00	Ly75
Degree of sensitization distance	10.32	1	0	0	0	1e+00	Ly75
Degree of sensitization stereotypy	38.66	1	1	100	0	1e+00	Ly75
Condit. Reinf. active minus inactive responses	16.76	1	0	0	0	1e+00	Ly75
Condit. Reinf. active-inactive response ratio	9.84	1	0	0	0	1e+00	Ly75
Condit. Reinf. active responses	13.63	1	0	0	0	1e+00	Ly75
Incentive salience index mean	15.42	1	0	0	0	1e+00	Ly75
Condit. Reinf. lever presses	3.87	1	0	0	0	1e+00	Ly75
Time in novel zone, hab. session 1	4.94	1	0	0	0	1e+00	Ly75
Total zone transitions, hab. session 1	7.48	1	0	0	0	1e+00	Ly75
Total zone transitions, hab. session 2	19.52	1	0	0	0	1e+00	Ly75
Total locomotion distance, hab. session 2	24.97	1	1	100	0	1e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	100	0	1e+00	Ly75
Total zone transitions, NPP test	5.39	1	0	0	0	1e+00	Ly75
Total locomotion distance, NPP test	4.87	1	0	0	0	1e+00	Ly75
Locomotion velocity, NPP test	4.37	1	0	0	0	1e+00	Ly75
Pavlov. Cond. index score	3.57	1	0	0	0	1e+00	Ly75
Pavlov. Cond. latency score	6.68	1	0	0	0	1e+00	Ly75
Pavlov. Cond. lever contacts	4.09	1	0	0	0	1e+00	Ly75
Bone: apparent density	27.67	1	1	100	0	1e+00	Ly75
Bone surface	47.59	1	1	100	0	1e+00	Ly75
Bone volume	43.15	1	1	100	0	1e+00	Ly75
Bone: connectivity density	21.24	1	1	100	0	1e+00	Ly75
Bone: cortical apparent density	18.66	1	0	0	0	1e+00	Ly75
Bone: cortical area	12.58	1	0	0	0	1e+00	Ly75
Bone: cortical thickness	5.93	1	0	0	0	1e+00	Ly75
Bone: cortical thickness	7.09	1	0	0	0	1e+00	Ly75
Bone: cortical tissue density	17.88	1	0	0	0	1e+00	Ly75
Bone: elastic work	15.82	1	0	0	0	1e+00	Ly75
Bone: endosteal estimation	9.05	1	0	0	0	1e+00	Ly75
Bone: final force	35.73	1	1	100	0	1e+00	Ly75
Bone: final moment	48.32	1	1	100	0	1e+00	Ly75
Bone: marrow area	9.02	1	0	0	0	1e+00	Ly75
Bone: maximum diameter	5.12	1	0	0	0	1e+00	Ly75
Bone: maximum force	20.87	1	1	100	0	1e+00	Ly75
Bone: maximum moment	29.34	1	1	100	0	1e+00	Ly75
Bone: minimum diameter	8.69	1	0	0	0	1e+00	Ly75
Bone: periosteal estimation	14.82	1	1	100	0	1e+00	Ly75
Bone: periosteal perimeter	7.52	1	0	0	0	1e+00	Ly75
Bone: stiffness	8.72	1	0	0	0	1e+00	Ly75
Bone: trabecular number	35.45	1	1	100	0	1e+00	Ly75
Bone: trabecular spacing	60.24	1	1	100	0	1e+00	Ly75
Diff in mean of infusions in LGA sessions	4.9	1	0	0	0	1e+00	Ly75
Delta time to tail flick, test, before/after SA	4.75	1	0	0	0	1e+00	Ly75
Total resting periods, locomotor time 1	5.85	1	0	0	0	1e+00	Ly75
Rest time, locomotor task time 1	12.3	1	0	0	0	1e+00	Ly75
Distance moved, locomotor task time 1	13.8	1	0	0	0	1e+00	Ly75
Rest time, locomotor task time 2	4.68	1	0	0	0	1e+00	Ly75
Distance moved, locomotor task time 2	4.29	1	0	0	0	1e+00	Ly75
Weight adjusted by age	20.87	1	0	0	0	1e+00	Ly75
Locomotion in novel chamber	34.01	1	1	100	0	1e+00	Ly75
Locomotion in novel chamber post-restriction	4.28	1	0	0	0	1e+00	Ly75
Food seeking constrained by brief footshock	13.79	1	0	0	0	1e+00	Ly75
Seeking ratio, punishment vs. effort	5.43	1	0	0	0	1e+00	Ly75
Run reversals in cocaine runway, females	21.72	1	0	0	0	1e+00	Ly75
Cd content in liver	5.1	1	0	0	0	1e+00	Ly75
Cu content in liver	8.78	1	0	0	0	1e+00	Ly75
Fe content in liver	7.43	1	0	0	0	1e+00	Ly75
K content in liver	12.92	1	0	0	0	1e+00	Ly75
Mg content in liver	13.79	1	0	0	0	1e+00	Ly75
Mn content in liver	32.26	1	1	100	0	1e+00	Ly75
Na content in liver	12.24	1	0	0	0	1e+00	Ly75
Rb content in liver	4.86	1	0	0	0	1e+00	Ly75
Sr content in liver	14.16	1	0	0	0	1e+00	Ly75
Zn content in liver	12.81	1	0	0	0	1e+00	Ly75

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	1.22
Adipose	alternative TSS	0	0	1.22
Adipose	gene expression	0	0	1.26
Adipose	isoform ratio	0	0	1.25
Adipose	intron excision ratio	0	0	1.2
Adipose	mRNA stability	0	0	1.27
BLA	alternative polyA	0	0	1.17
BLA	alternative TSS	0	0	1.19
BLA	gene expression	0	0	1.21
BLA	isoform ratio	0	0	1.11
BLA	intron excision ratio	0	0	1.17
BLA	mRNA stability	0	0	1.3
Brain	alternative polyA	0	0	1.19
Brain	alternative TSS	0	0	1.16
Brain	gene expression	0	0	1.2
Brain	isoform ratio	0	0	1.18
Brain	intron excision ratio	0	0	1.15
Brain	mRNA stability	0	0	1.24
Eye	alternative polyA	0	0	1.3
Eye	alternative TSS	0	0	1.18
Eye	gene expression	0	0	1.2
Eye	isoform ratio	0	0	1.18
Eye	intron excision ratio	0	0	1.23
Eye	mRNA stability	0	0	1.18
IL	alternative polyA	0	0	1.18
IL	alternative TSS	0	0	1.22
IL	gene expression	0	0	1.19
IL	isoform ratio	0	0	1.12
IL	intron excision ratio	0	0	1.08
IL	mRNA stability	0	0	1.26
LHb	alternative polyA	0	0	1.06
LHb	alternative TSS	0	0	1.06
LHb	gene expression	1	0	1.2
LHb	isoform ratio	0	0	1.12
LHb	intron excision ratio	0	0	1.04
LHb	mRNA stability	0	0	1.24
Liver	alternative polyA	0	0	1.26
Liver	alternative TSS	0	0	1.24
Liver	gene expression	0	0	1.26
Liver	isoform ratio	0	0	1.23
Liver	intron excision ratio	0	0	1.18
Liver	mRNA stability	0	0	1.26
NAcc	alternative polyA	0	0	1.18
NAcc	alternative TSS	0	0	1.17
NAcc	gene expression	0	0	1.22
NAcc	isoform ratio	0	0	1.21
NAcc	intron excision ratio	0	0	1.12
NAcc	mRNA stability	0	0	1.24
OFC	alternative polyA	0	0	1.1
OFC	alternative TSS	0	0	1.12
OFC	gene expression	0	0	1.19
OFC	isoform ratio	0	0	1.1
OFC	intron excision ratio	0	0	1.18
OFC	mRNA stability	0	0	1.24
PL	alternative polyA	0	0	1.17
PL	alternative TSS	0	0	1.15
PL	gene expression	0	0	1.23
PL	isoform ratio	0	0	1.18
PL	intron excision ratio	0	0	1.15
PL	mRNA stability	0	0	1.23
pVTA	alternative polyA	0	0	1.16
pVTA	alternative TSS	0	0	1.15
pVTA	gene expression	0	0	1.18
pVTA	isoform ratio	0	0	1.14
pVTA	intron excision ratio	0	0	1.13
pVTA	mRNA stability	0	0	1.24
RMTg	alternative polyA	0	0	1.31
RMTg	alternative TSS	0	0	1.24
RMTg	gene expression	0	0	1.13
RMTg	isoform ratio	0	0	1.08
RMTg	intron excision ratio	0	0	1.03
RMTg	mRNA stability	0	0	1.24