Hub : Traits

Bone volume

Tags: Physiology · Bone

Project: r01_doug_adams

2 loci · 2 genes with independent associations · 2 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	5	137682119	138752373	1	1	4.81e-12	4.53e-02	7.25e-25	Stk40
2	7	16845355	16970279	1	1	2.76e-19	NaN	NA	ENSRNOG00000064438

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	4.29	1	0	0	0	1e+00	Stk40
BMI without tail	72.67	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Body weight	6.44	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Epididymis fat weight	87.61	1	1	50	0	1e+00	ENSRNOG00000064438
Glucose	15.37	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Heart weight	11.41	1	0	0	0	1e+00	ENSRNOG00000064438
Left kidney weight	37.46	1	1	50	0	1e+00	ENSRNOG00000064438
Right kidney weight	41.88	1	1	50	0	1e+00	ENSRNOG00000064438
Tail length	39.87	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Length with tail	3.24	1	0	0	0	1e+00	ENSRNOG00000064438
Length without tail	71.11	1	1	50	0	1e+00	ENSRNOG00000064438
Liver weight, left	23.57	1	1	50	0	1e+00	ENSRNOG00000064438
Liver weight, right	9.6	1	0	0	0	1e+00	ENSRNOG00000064438
Parametrial fat weight	14.9	1	1	50	0	1e+00	ENSRNOG00000064438
Retroperitoneal fat weight	3.02	1	0	0	0	1e+00	ENSRNOG00000064438
Intraocular pressure	18.97	1	1	50	0	1e+00	ENSRNOG00000064438
Extensor digitorum longus weight	19.09	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Soleus weight	13.82	2	2	100	0	1e+00	Stk40 ENSRNOG00000064438
Tibialis anterior weight	40.54	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Tibia length	5.35	1	0	0	0	1e+00	ENSRNOG00000064438
Number of licking bursts	155.04	1	1	50	0	1e+00	ENSRNOG00000064438
Food consumed during 24 hour testing period	17.5	1	0	0	0	1e+00	ENSRNOG00000064438
Times rat made contact with spout	75.14	1	1	50	0	1e+00	ENSRNOG00000064438
Mean time between licks in bursts	54.91	1	1	50	0	1e+00	ENSRNOG00000064438
Mean num. licks in bursts	164.17	1	1	50	0	1e+00	ENSRNOG00000064438
Std. dev. time between licks in bursts	177.72	1	1	50	0	1e+00	ENSRNOG00000064438
Water consumed over 24 hours	5.74	1	0	0	0	1e+00	ENSRNOG00000064438
Indifference point 0 sec	18.72	1	1	50	0	1e+00	ENSRNOG00000064438
Indifference point AUC	30.17	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Indifference point function ln k	4.41	1	0	0	0	1e+00	ENSRNOG00000064438
Indifference point function log k	4.41	1	0	0	0	1e+00	ENSRNOG00000064438
Delay discounting total patch changes 0 sec	17.74	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting total patch changes 12 sec	102.69	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting total patch changes 18 sec	119.18	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Delay discounting total patch changes 24 sec	28.3	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting total patch changes 6 sec	98.45	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting water rate 0 sec	8.14	1	0	0	0	1e+00	ENSRNOG00000064438
Delay discounting water rate 12 sec	26.07	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting water rate 18 sec	10.52	1	0	0	0	1e+00	ENSRNOG00000064438
Delay discounting water rate 24 sec	62.69	1	1	50	0	1e+00	ENSRNOG00000064438
Delay discounting water rate 6 sec	44.17	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotor testing distance	11.51	1	0	0	0	1e+00	ENSRNOG00000064438
Locomotor testing rearing	16.22	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Light reinforcement 1	54.81	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time number correct	6.91	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time num false alarms	39.48	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time num false alarms AUC	56.81	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time trials correct on left	6.91	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time trials on left	7.52	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time mean	41.28	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time mean AUC	57.96	1	1	50	0	1e+00	ENSRNOG00000064438
Median of all reaction times	51.19	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time false alarm rate	63.39	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time premature initiation rate	32.14	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time premature initiations	24.29	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Std. dev. reaction times	17.36	1	1	50	0	1e+00	ENSRNOG00000064438
Reaction time trials completed	7.52	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Reaction time trials AUC	10.58	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Social responses	74.35	1	1	50	0	1e+00	ENSRNOG00000064438
Social time	7.75	1	0	0	0	1e+00	ENSRNOG00000064438
Conditioned locomotion	5.32	1	0	0	0	1e+00	Stk40
Cocaine response after cond. corrected	77.95	1	1	50	0	1e+00	ENSRNOG00000064438
Cocaine response after cond. not corrected	102.33	1	1	50	0	1e+00	ENSRNOG00000064438
Cocaine response before conditioning	13.79	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Saline control response	30.34	1	1	50	0	1e+00	ENSRNOG00000064438
Condit. Reinf. active minus inactive responses	29.4	1	1	50	0	1e+00	ENSRNOG00000064438
Condit. Reinf. active-inactive response ratio	40.66	1	1	50	0	1e+00	ENSRNOG00000064438
Condit. Reinf. active responses	11.07	1	0	0	0	1e+00	ENSRNOG00000064438
Condit. Reinf. inactive responses	20.59	1	0	0	0	1e+00	ENSRNOG00000064438
Condit. Reinf. lever presses	7.23	1	0	0	0	1e+00	Stk40
Pavlov. Cond. lever latency	36.27	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. magazine entry latency	104.88	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. change in total contacts	130.08	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. index score	62.19	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. latency score	67.08	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. lever contacts	17.16	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. magazine entry number	150.01	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. intertrial magazine entries	63.93	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. lever-magazine prob. diff.	55.11	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. response bias	30.81	1	1	50	0	1e+00	ENSRNOG00000064438
Conditioned reinforcement - actives	13.02	1	0	0	0	1e+00	ENSRNOG00000064438
Conditioned locomotion	9.86	1	0	0	0	1e+00	ENSRNOG00000064438
Intermittent access intake day 1-15 change	61.45	1	1	50	0	1e+00	ENSRNOG00000064438
Intermittent access intake escalation	82.51	1	1	50	0	1e+00	ENSRNOG00000064438
Intermittent access intake escalation 2	24.72	1	1	50	0	1e+00	ENSRNOG00000064438
Intermitt. access day 1 inactive lever presses	19.44	1	1	50	0	1e+00	ENSRNOG00000064438
Intermitt. access escalation Index	9.22	1	0	0	0	1e+00	ENSRNOG00000064438
Intermittent access day 1 total infusions	32.74	1	1	50	0	1e+00	ENSRNOG00000064438
Intermittent access day 1 locomotion	18.42	1	1	50	0	1e+00	ENSRNOG00000064438
Post-drug Anxiety	13.65	1	0	0	0	1e+00	ENSRNOG00000064438
Progressive ratio test 1 active lever presses	11.8	1	0	0	0	1e+00	ENSRNOG00000064438
Progressive ratio test 1 breakpoint	10.37	1	0	0	0	1e+00	ENSRNOG00000064438
Progressive ratio test 1 inactive lever presses	10.82	1	0	0	0	1e+00	ENSRNOG00000064438
Progressive ratio test 2 active lever presses	12.24	1	0	0	0	1e+00	ENSRNOG00000064438
Progressive ratio test 2 breakpoint	38.7	1	1	50	0	1e+00	ENSRNOG00000064438
Short access day 10 total inactive lever presses	8.14	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Short access day 10 total infusions	24.04	1	1	50	0	1e+00	ENSRNOG00000064438
Short access day 1 locomotion	11.36	1	0	0	0	1e+00	ENSRNOG00000064438
Compulsive drug intake	28.2	1	1	50	0	1e+00	ENSRNOG00000064438
One hour access (0.3 mA shock)	10.45	1	0	0	0	1e+00	ENSRNOG00000064438
Context. condit. distance diff. score	149.78	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, session 1	117.78	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion distance, session 1	374.74	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, session 2	82.2	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion distance, session 2	775.97	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, session 3	116.11	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion distance, session 3	82.39	1	1	50	0	1e+00	ENSRNOG00000064438
Stereotopy head waving bouts, day 3	8.83	1	0	0	0	1e+00	ENSRNOG00000064438
Stereotopy head waving duration, day 3	25.57	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, session 7	66.34	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion distance, session 7	21.3	1	1	50	0	1e+00	ENSRNOG00000064438
Stereotopy head waving bouts, day 7	42.65	1	1	50	0	1e+00	ENSRNOG00000064438
Stereotopy head waving duration, day 7	63.39	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion distance, session 8	102.75	1	1	50	0	1e+00	ENSRNOG00000064438
Degree of sensitization distance	140.58	1	1	50	0	1e+00	ENSRNOG00000064438
Degree of sensitization stereotypy	22.91	1	1	50	0	1e+00	ENSRNOG00000064438
Condit. Reinf. active minus inactive responses	10.13	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Condit. Reinf. active-inactive response ratio	46.37	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Condit. Reinf. active responses	14.11	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Condit. Reinf. inactive responses	17.25	1	0	0	0	1e+00	ENSRNOG00000064438
Incentive salience index mean	21.93	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Condit. Reinf. lever presses	21.81	2	2	100	0	1e+00	Stk40 ENSRNOG00000064438
Time in familiar zone, hab. session 1	16.37	1	0	0	0	1e+00	ENSRNOG00000064438
Time in novel zone, hab. session 1	12.91	1	0	0	0	1e+00	ENSRNOG00000064438
Total zone transitions, hab. session 1	415.63	1	1	50	0	1e+00	ENSRNOG00000064438
Total locomotion distance, hab. session 1	171.39	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, hab. session 1	218.59	1	1	50	0	1e+00	ENSRNOG00000064438
Time in familiar zone, hab. session 2	27.96	1	1	50	0	1e+00	ENSRNOG00000064438
Time in novel zone, hab. session 2	34.06	1	1	50	0	1e+00	ENSRNOG00000064438
Total zone transitions, hab. session 2	256.06	1	1	50	0	1e+00	ENSRNOG00000064438
Total locomotion distance, hab. session 2	133.05	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, hab. session 2	139.44	1	1	50	0	1e+00	ENSRNOG00000064438
Novelty place preference	5.87	1	0	0	0	1e+00	Stk40
Time in novel zone, NPP test	5.48	1	0	0	0	1e+00	Stk40
Total zone transitions, NPP test	228.75	1	1	50	0	1e+00	ENSRNOG00000064438
Total locomotion distance, NPP test	163.42	1	1	50	0	1e+00	ENSRNOG00000064438
Locomotion velocity, NPP test	195.87	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. lever latency	10.38	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. magazine entry latency	40.45	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. change in total contacts	18.38	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. index score	22.43	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. latency score	12.1	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. lever contacts	12.4	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. magazine entry number	34.9	1	1	50	0	1e+00	ENSRNOG00000064438
Pavlov. Cond. intertrial magazine entries	12.34	1	0	0	0	1e+00	Stk40
Pavlov. Cond. lever-magazine prob. diff.	37.35	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Pavlov. Cond. response bias	22.18	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone: apparent density	16.75	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone surface	25.55	2	2	100	0	1e+00	Stk40 ENSRNOG00000064438
Bone: connectivity density	7.98	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Bone: cortical porosity	109.3	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: cortical porosity	91.2	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: cortical thickness	8.79	1	0	0	0	1e+00	ENSRNOG00000064438
Bone: cortical thickness	17.92	1	0	0	0	1e+00	ENSRNOG00000064438
Bone: elastic displacement	17.29	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: endosteal estimation	10.65	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone: endosteal perimeter	3.03	1	0	0	0	1e+00	Stk40
Bone: final force	39.54	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: final moment	31.87	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: marrow area	9.15	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone: maximum force	41.95	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: maximum moment	29.46	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: minimum diameter	39.37	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone: periosteal estimation	6.39	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Bone: periosteal perimeter	6.62	2	0	0	0	1e+00	Stk40 ENSRNOG00000064438
Bone: post-yield work	82.77	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: stiffness	90.38	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: tissue strength	80.98	1	1	50	0	1e+00	ENSRNOG00000064438
Bone: trabecular number	28.59	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Bone: trabecular spacing	5.66	1	0	0	0	1e+00	ENSRNOG00000064438
Bone: trabecular thickness	10.38	1	0	0	0	1e+00	ENSRNOG00000064438
Bone: trabecular tissue density	30.07	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Distance traveled before self-admin	9.75	1	0	0	0	1e+00	ENSRNOG00000064438
Delta time in open arm before/after self-admin	23.55	1	1	50	0	1e+00	ENSRNOG00000064438
Extinction: sum of active levers before priming	12.19	1	0	0	0	1e+00	ENSRNOG00000064438
Active lever presses in extinction session 6	9.21	1	0	0	0	1e+00	ENSRNOG00000064438
Delta distance traveled before/after self-admin	8.72	1	0	0	0	1e+00	ENSRNOG00000064438
Time in closed arm before self-admin	50.04	1	1	50	0	1e+00	ENSRNOG00000064438
Time in closed arm after self-admin	25.79	1	1	50	0	1e+00	ENSRNOG00000064438
Time in open arm after self-admin	18.45	1	1	50	0	1e+00	ENSRNOG00000064438
Delta time to tail flick, vehicle, before/after SA	7.54	1	0	0	0	1e+00	ENSRNOG00000064438
Delta time to tail flick, test, before/after SA	20.03	1	0	0	0	1e+00	ENSRNOG00000064438
Ambulatory time before self-admin	5.66	1	0	0	0	1e+00	ENSRNOG00000064438
Fecal boli incidents, locomotor time 1	11.77	1	0	0	0	1e+00	ENSRNOG00000064438
Change in fecal boli incidents, locomotor task	8.82	1	0	0	0	1e+00	ENSRNOG00000064438
Time >=10cm from walls, locomotor time 1	19.54	1	0	0	0	1e+00	ENSRNOG00000064438
Rest time, locomotor task time 1	5.42	1	0	0	0	1e+00	Stk40
Time >=10cm from walls, locomotor time 2	19.42	1	1	50	0	1e+00	ENSRNOG00000064438
Total resting periods, locomotor time 2	6.01	1	0	0	0	1e+00	ENSRNOG00000064438
Rest time, locomotor task time 2	7	1	0	0	0	1e+00	ENSRNOG00000064438
Distance moved, locomotor task time 2	9.35	1	0	0	0	1e+00	ENSRNOG00000064438
Weight adjusted by age	16.68	1	1	50	0	1e+00	ENSRNOG00000064438
Seeking ratio, delayed vs. immediate footshock	5.34	1	0	0	0	1e+00	ENSRNOG00000064438
Locomotion in novel chamber	10.2	1	0	0	0	1e+00	ENSRNOG00000064438
Run reversals in cocaine runway, males	25.4	1	1	50	0	1e+00	ENSRNOG00000064438
Latency to leave start box in cocaine runway	18.78	1	0	0	0	1e+00	ENSRNOG00000064438
Cd content in liver	96.4	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Co content in liver	83.15	1	1	50	0	1e+00	ENSRNOG00000064438
Cu content in liver	4.78	1	0	0	0	1e+00	Stk40
Fe content in liver	10.34	1	0	0	0	1e+00	ENSRNOG00000064438
K content in liver	62.65	1	1	50	0	1e+00	ENSRNOG00000064438
Mg content in liver	13.66	1	0	0	0	1e+00	Stk40
Mn content in liver	130.23	1	1	50	0	1e+00	ENSRNOG00000064438
Rb content in liver	18.62	1	1	50	0	1e+00	ENSRNOG00000064438
Se content in liver	29.81	2	1	50	0	1e+00	Stk40 ENSRNOG00000064438
Sr content in liver	132.45	1	1	50	0	1e+00	Stk40
Zn content in liver	25.95	1	1	50	0	1e+00	ENSRNOG00000064438

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	1.69
Adipose	alternative TSS	0	0	1.73
Adipose	gene expression	0	0	1.7
Adipose	isoform ratio	0	0	1.63
Adipose	intron excision ratio	0	0	1.65
Adipose	mRNA stability	0	0	1.75
BLA	alternative polyA	0	0	1.65
BLA	alternative TSS	0	0	1.89
BLA	gene expression	0	0	1.74
BLA	isoform ratio	0	0	1.7
BLA	intron excision ratio	0	0	1.62
BLA	mRNA stability	0	0	1.74
Brain	alternative polyA	0	0	1.73
Brain	alternative TSS	0	0	1.86
Brain	gene expression	0	0	1.7
Brain	isoform ratio	0	0	1.61
Brain	intron excision ratio	0	0	1.61
Brain	mRNA stability	0	0	1.68
Eye	alternative polyA	0	0	1.83
Eye	alternative TSS	0	0	1.86
Eye	gene expression	0	0	1.74
Eye	isoform ratio	0	0	1.47
Eye	intron excision ratio	0	0	1.6
Eye	mRNA stability	0	0	1.87
IL	alternative polyA	0	0	1.84
IL	alternative TSS	0	0	1.98
IL	gene expression	0	0	1.7
IL	isoform ratio	0	0	1.62
IL	intron excision ratio	0	0	1.65
IL	mRNA stability	0	0	1.78
LHb	alternative polyA	0	0	1.73
LHb	alternative TSS	0	0	2.28
LHb	gene expression	0	0	1.72
LHb	isoform ratio	0	0	1.59
LHb	intron excision ratio	0	0	1.49
LHb	mRNA stability	0	0	1.75
Liver	alternative polyA	0	0	1.5
Liver	alternative TSS	0	0	1.79
Liver	gene expression	0	0	1.7
Liver	isoform ratio	0	0	1.66
Liver	intron excision ratio	0	0	1.65
Liver	mRNA stability	1	0	1.71
NAcc	alternative polyA	0	0	1.64
NAcc	alternative TSS	0	0	1.81
NAcc	gene expression	0	0	1.74
NAcc	isoform ratio	0	0	1.75
NAcc	intron excision ratio	0	0	1.57
NAcc	mRNA stability	0	0	1.75
OFC	alternative polyA	0	0	1.67
OFC	alternative TSS	0	0	1.7
OFC	gene expression	0	0	1.71
OFC	isoform ratio	0	0	1.59
OFC	intron excision ratio	0	0	1.58
OFC	mRNA stability	0	0	1.74
PL	alternative polyA	0	0	1.66
PL	alternative TSS	0	0	1.86
PL	gene expression	0	0	1.73
PL	isoform ratio	2	0.1	1.68
PL	intron excision ratio	0	0	1.59
PL	mRNA stability	0	0	1.75