Hub : Traits

Bone: final force

Tags: Physiology · Bone

Project: r01_doug_adams

3 loci · 3 genes with independent associations · 3 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	2.48e-09	4.29e-01	2.80e-28	Ilf2
2	chr3	44152620	45549784	1	1	3.01e-14	1.77e-03	5.66e-09	Ly75
3	chr10	106235924	107195627	1	1	1.19e-07	7.62e-08	1.70e-05	B3gntl1

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	2.87	1	0	0	0	1e+00	B3gntl1
BMI without tail	3.94	1	0	0	0	1e+00	Ly75
Body weight	3.48	1	0	0	0	1e+00	B3gntl1
Epididymis fat weight	3.44	1	0	0	0	1e+00	Ly75
Glucose	3.95	1	0	0	0	1e+00	Ly75
Heart weight	4.14	1	0	0	0	1e+00	B3gntl1
Left kidney weight	4.02	2	0	0	0	1e+00	B3gntl1 Ilf2
Right kidney weight	3.59	2	0	0	0	1e+00	B3gntl1 Ilf2
Tail length	1.99	1	0	0	0	1e+00	B3gntl1
Length with tail	2.82	1	0	0	0	1e+00	Ly75
Length without tail	9.91	2	0	0	0	1e+00	B3gntl1 Ly75
Retroperitoneal fat weight	8.85	1	1	33.3	0	1e+00	Ly75
Intraocular pressure	5.72	1	0	0	0	1e+00	Ilf2
Extensor digitorum longus weight	1.74	2	0	0	0	1e+00	Ilf2 Ly75
Tibialis anterior weight	3.75	1	0	0	0	1e+00	Ly75
Tibia length	16.89	1	1	33.3	0	1e+00	B3gntl1
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
Mean num. licks in bursts	4.84	1	0	0	0	1e+00	Ly75
Water consumed over 24 hours	19.18	1	0	0	0	1e+00	Ly75
Patch foraging total patch changes 12 sec	5.98	1	0	0	0	1e+00	Ilf2
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 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 premature initiation rate	14.82	2	1	33.3	0	1e+00	Ilf2 Ly75
Reaction time premature initiations	8.73	2	0	0	0	1e+00	Ilf2 Ly75
Std. dev. reaction times	14.29	1	0	0	0	1e+00	Ly75
Social response proportion	11.26	1	0	0	0	1e+00	Ilf2
Social time	4.65	1	0	0	0	1e+00	Ilf2
Cocaine response before conditioning	5.9	1	0	0	0	1e+00	Ly75
Condit. Reinf. active minus inactive responses	28.62	1	1	33.3	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	33.3	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	33.3	0	1e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1e+00	Ly75
Conditioned locomotion	6.8	1	0	0	0	1e+00	Ilf2
Intermittent access intake escalation 2	6.44	1	0	0	0	1e+00	Ilf2
Intermittent access day 15 total locomotion	5.95	1	0	0	0	1e+00	Ilf2
Intermittent access total locomotion	6.46	1	0	0	0	1e+00	Ilf2
Locomotion velocity, session 1	6.3	1	0	0	0	1e+00	Ly75
Locomotion velocity, session 2	6.62	1	0	0	0	1e+00	Ilf2
Locomotion distance, session 3	14.48	1	0	0	0	1e+00	Ly75
Stereotopy head waving bouts, day 3	7.08	1	0	0	0	1e+00	Ilf2
Stereotopy head waving duration, day 3	5.56	1	0	0	0	1e+00	Ilf2
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
Locomotion velocity, session 8	12.45	1	0	0	0	1e+00	Ilf2
Degree of sensitization distance	10.32	1	0	0	0	1e+00	Ly75
Degree of sensitization stereotypy	38.66	1	1	33.3	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	10.84	1	0	0	0	1e+00	Ilf2
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	33.3	0	1e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	33.3	0	1e+00	Ly75
Novel to familiar place preference ratio	7.16	1	0	0	0	1e+00	Ilf2
Novelty place preference	6.43	1	0	0	0	1e+00	Ilf2
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. lever latency	21.9	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. magazine entry latency	28.91	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. change in total contacts	18.74	1	0	0	0	1e+00	Ilf2
Pavlov. Cond. index score	34.08	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. latency score	18.75	2	1	33.3	0	1e+00	Ilf2 Ly75
Pavlov. Cond. lever contacts	37.24	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. magazine entry number	42.75	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. intertrial magazine entries	13.5	1	0	0	0	1e+00	Ilf2
Pavlov. Cond. lever-magazine prob. diff.	35.53	1	1	33.3	0	1e+00	Ilf2
Pavlov. Cond. response bias	41.38	1	1	33.3	0	1e+00	Ilf2
Bone: apparent density	27.67	1	1	33.3	0	1e+00	Ly75
Bone surface	47.59	1	1	33.3	0	1e+00	Ly75
Bone volume	43.15	1	1	33.3	0	1e+00	Ly75
Bone: connectivity density	21.24	1	1	33.3	0	1e+00	Ly75
Bone: cortical apparent density	18.66	1	0	0	0	1e+00	Ly75
Bone: cortical area	14.48	3	1	33.3	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: cortical thickness	17.09	2	1	33.3	0	1e+00	B3gntl1 Ly75
Bone: cortical thickness	9.96	2	0	0	0	1e+00	B3gntl1 Ly75
Bone: cortical tissue density	17.88	1	0	0	0	1e+00	Ly75
Bone: elastic work	10.72	3	0	0	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: endosteal estimation	7.31	2	0	0	0	1e+00	Ilf2 Ly75
Bone: endosteal perimeter	2.98	1	0	0	0	1e+00	Ilf2
Bone: final moment	28.98	3	3	100	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: marrow area	7.3	2	0	0	0	1e+00	Ilf2 Ly75
Bone: maximum diameter	4.91	2	0	0	0	1e+00	B3gntl1 Ly75
Bone: maximum force	20.58	3	3	100	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: maximum moment	22.61	3	3	100	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: minimum diameter	6.5	3	0	0	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: periosteal estimation	9.03	3	1	33.3	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: periosteal perimeter	6.77	3	0	0	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: post-yield work	5.96	1	0	0	0	1e+00	Ilf2
Bone: stiffness	10.2	3	0	0	0	1e+00	B3gntl1 Ilf2 Ly75
Bone: trabecular number	35.45	1	1	33.3	0	1e+00	Ly75
Bone: trabecular spacing	60.24	1	1	33.3	0	1e+00	Ly75
Bone: trabecular thickness	47.42	1	1	33.3	0	1e+00	Ly75
Distance traveled after self-admin	7.31	1	0	0	0	1e+00	B3gntl1
Delta time in open arm before/after self-admin	7.55	1	0	0	0	1e+00	Ilf2
Delta distance traveled before/after self-admin	6.31	1	0	0	0	1e+00	B3gntl1
Delta ambulatory time before/after self-admin	7.6	1	0	0	0	1e+00	B3gntl1
Time in open arm before self-admin	9.47	1	0	0	0	1e+00	Ilf2
Total heroin consumption	8.23	1	0	0	0	1e+00	B3gntl1
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
Distance moved, locomotor task time 2	9.43	1	0	0	0	1e+00	Ilf2
Weight adjusted by age	20.87	1	0	0	0	1e+00	Ly75
Locomotion in novel chamber	34.01	1	1	33.3	0	1e+00	Ly75
Progressive ratio	12.89	1	0	0	0	1e+00	Ilf2
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
Run reversals in cocaine runway, males	6.86	1	0	0	0	1e+00	Ilf2
Latency to leave start box in cocaine runway	7.72	1	0	0	0	1e+00	Ilf2
Latency to leave start box in cocaine runway, M	14.76	1	0	0	0	1e+00	Ilf2
Cd content in liver	13.38	1	0	0	0	1e+00	Ilf2
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	10.86	2	0	0	0	1e+00	B3gntl1 Ly75
Mn content in liver	32.26	1	1	33.3	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	10.69	2	0	0	0	1e+00	Ilf2 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	1.68
Adipose	alternative TSS	0	0	1.64
Adipose	gene expression	0	0	1.59
Adipose	isoform ratio	0	0	1.56
Adipose	intron excision ratio	0	0	1.6
Adipose	mRNA stability	0	0	1.61
BLA	alternative polyA	0	0	1.75
BLA	alternative TSS	0	0	1.56
BLA	gene expression	0	0	1.68
BLA	isoform ratio	0	0	1.56
BLA	intron excision ratio	0	0	1.58
BLA	mRNA stability	0	0	1.62
Brain	alternative polyA	0	0	1.69
Brain	alternative TSS	0	0	1.59
Brain	gene expression	0	0	1.58
Brain	isoform ratio	0	0	1.6
Brain	intron excision ratio	0	0	1.56
Brain	mRNA stability	0	0	1.59
Eye	alternative polyA	0	0	2.03
Eye	alternative TSS	0	0	1.31
Eye	gene expression	0	0	1.55
Eye	isoform ratio	0	0	1.74
Eye	intron excision ratio	0	0	1.5
Eye	mRNA stability	0	0	1.49
IL	alternative polyA	0	0	1.73
IL	alternative TSS	0	0	1.63
IL	gene expression	0	0	1.71
IL	isoform ratio	0	0	1.62
IL	intron excision ratio	0	0	1.68
IL	mRNA stability	0	0	1.72
LHb	alternative polyA	0	0	1.72
LHb	alternative TSS	1	0.2	1.58
LHb	gene expression	1	0	1.66
LHb	isoform ratio	0	0	1.49
LHb	intron excision ratio	0	0	1.59
LHb	mRNA stability	0	0	1.56
Liver	alternative polyA	0	0	1.61
Liver	alternative TSS	0	0	1.57
Liver	gene expression	0	0	1.55
Liver	isoform ratio	0	0	1.57
Liver	intron excision ratio	0	0	1.42
Liver	mRNA stability	0	0	1.52
NAcc	alternative polyA	0	0	1.64
NAcc	alternative TSS	0	0	1.69
NAcc	gene expression	1	0	1.62
NAcc	isoform ratio	0	0	1.64
NAcc	intron excision ratio	0	0	1.63
NAcc	mRNA stability	0	0	1.63
OFC	alternative polyA	0	0	1.77
OFC	alternative TSS	0	0	1.76
OFC	gene expression	0	0	1.67
OFC	isoform ratio	0	0	1.58
OFC	intron excision ratio	0	0	1.68
OFC	mRNA stability	0	0	1.71
PL	alternative polyA	0	0	1.59
PL	alternative TSS	0	0	1.67
PL	gene expression	0	0	1.65
PL	isoform ratio	0	0	1.65
PL	intron excision ratio	0	0	1.66
PL	mRNA stability	0	0	1.6
pVTA	alternative polyA	0	0	1.78
pVTA	alternative TSS	0	0	1.6
pVTA	gene expression	0	0	1.67
pVTA	isoform ratio	0	0	1.62
pVTA	intron excision ratio	0	0	1.71
pVTA	mRNA stability	0	0	1.67
RMTg	alternative polyA	0	0	1.75
RMTg	alternative TSS	0	0	1.82
RMTg	gene expression	0	0	1.6
RMTg	isoform ratio	0	0	1.73
RMTg	intron excision ratio	0	0	1.47
RMTg	mRNA stability	0	0	1.56