Hub : Traits

Bone: final moment

Tags: Physiology · Bone

Project: r01_doug_adams

4 loci · 5 genes with independent associations · 6 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	1.02e-08	3.02e-01	2.67e-23	Ilf2
2	chr3	44152620	45549784	1	1	8.42e-19	1.50e-03	1.21e-14	Ly75
3	chr9	87238851	88635740	1	1	1.41e-07	3.19e-05	2.72e-01	Efhd1
4	chr10	106235924	107195627	3	2	4.72e-08	1.99e-08	2.45e-01	B3gntl1

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	2.87	1	0	0	0	1.00e+00	B3gntl1
BMI without tail	3.94	1	0	0	0	1.00e+00	Ly75
Body weight	4.55	1	0	0	0	1.00e+00	B3gntl1
Epididymis fat weight	3.44	1	0	0	0	1.00e+00	Ly75
Heart weight	5.08	1	0	0	0	1.00e+00	B3gntl1
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 with tail	2.3	2	0	0	0	1.00e+00	B3gntl1 Ly75
Length without tail	9.91	2	0	0	0	1.00e+00	B3gntl1 Ly75
Retroperitoneal fat weight	8.85	1	1	20	0	1.00e+00	Ly75
Intraocular pressure	5.72	1	0	0	0	1.00e+00	Ilf2
Extensor digitorum longus weight	1.85	1	0	0	0	1.00e+00	Ilf2
Tibialis anterior weight	3.75	1	0	0	0	1.00e+00	Ly75
Tibia length	16.32	2	1	20	1	4.47e-03	B3gntl1 Efhd1
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 total patch changes 12 sec	5.98	1	0	0	0	1.00e+00	Ilf2
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1.00e+00	Ly75
Locomotor activity	6.86	1	0	0	0	1.00e+00	Ly75
Locomotor testing distance	6.84	1	0	0	0	1.00e+00	Ly75
Locomotor testing rearing	4.53	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 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	14.82	2	1	20	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
Cocaine response before conditioning	5.9	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	28.62	1	1	20	0	1.00e+00	Ly75
Condit. Reinf. active-inactive response ratio	9.17	2	0	0	0	1.00e+00	B3gntl1 Ly75
Condit. Reinf. active responses	24.88	1	1	20	0	1.00e+00	Ly75
Condit. Reinf. lever presses	8.53	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. lever reinforcers received	19.5	1	1	20	0	1.00e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Conditioned locomotion	6.8	1	0	0	0	1.00e+00	Ilf2
Intermittent access total locomotion	6.46	1	0	0	0	1.00e+00	Ilf2
Locomotion velocity, session 2	6.62	1	0	0	0	1.00e+00	Ilf2
Locomotion distance, session 3	14.48	1	0	0	0	1.00e+00	Ly75
Stereotopy head waving bouts, day 3	7.08	1	0	0	0	1.00e+00	Ilf2
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	12.45	1	0	0	0	1.00e+00	Ilf2
Degree of sensitization distance	10.32	1	0	0	0	1.00e+00	Ly75
Degree of sensitization stereotypy	38.66	1	1	20	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	16.76	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active-inactive response ratio	9.84	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 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	20	0	1.00e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	20	0	1.00e+00	Ly75
Novel to familiar place preference ratio	7.16	1	0	0	0	1.00e+00	Ilf2
Total zone transitions, NPP test	5.39	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. lever latency	21.9	1	1	20	0	1.00e+00	Ilf2
Pavlov. Cond. magazine entry latency	28.91	1	1	20	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	20	0	1.00e+00	Ilf2
Pavlov. Cond. latency score	18.75	2	1	20	0	1.00e+00	Ilf2 Ly75
Pavlov. Cond. lever contacts	37.24	1	1	20	0	1.00e+00	Ilf2
Pavlov. Cond. magazine entry number	42.75	1	1	20	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	20	0	1.00e+00	Ilf2
Pavlov. Cond. response bias	41.38	1	1	20	0	1.00e+00	Ilf2
Bone: apparent density	27.67	1	1	20	0	1.00e+00	Ly75
Bone surface	47.59	1	1	20	0	1.00e+00	Ly75
Bone volume	43.15	1	1	20	0	1.00e+00	Ly75
Bone: connectivity density	21.24	1	1	20	0	1.00e+00	Ly75
Bone: cortical apparent density	18.66	1	0	0	0	1.00e+00	Ly75
Bone: cortical area	16.39	3	1	20	0.92	2.76e-02	B3gntl1 Ilf2 Ly75
Bone: cortical thickness	18.92	2	1	20	-0.94	6.21e-02	B3gntl1 Ly75
Bone: cortical thickness	9.12	2	0	0	-0.5	5.01e-01	B3gntl1 Ly75
Bone: cortical tissue density	17.88	1	0	0	0	1.00e+00	Ly75
Bone: elastic work	15.2	2	0	0	0.12	8.77e-01	B3gntl1 Ly75
Bone: endosteal estimation	6.37	3	0	0	0	1.00e+00	Efhd1 Ilf2 Ly75
Bone: final force	20.23	4	3	60	1	4.54e-06	B3gntl1 Efhd1 Ilf2 Ly75
Bone: marrow area	6.29	3	0	0	0	1.00e+00	Efhd1 Ilf2 Ly75
Bone: maximum diameter	4.52	2	0	0	0.79	2.07e-01	B3gntl1 Ly75
Bone: maximum force	17.98	4	4	80	0.98	3.42e-04	B3gntl1 Efhd1 Ilf2 Ly75
Bone: maximum moment	19.72	4	4	80	0.99	6.57e-05	B3gntl1 Efhd1 Ilf2 Ly75
Bone: minimum diameter	6.84	3	0	0	0.98	1.54e-02	B3gntl1 Ilf2 Ly75
Bone: periosteal estimation	6.91	4	1	20	1	2.61e-06	B3gntl1 Efhd1 Ilf2 Ly75
Bone: periosteal perimeter	7.49	3	0	0	0.95	1.32e-02	B3gntl1 Ilf2 Ly75
Bone: post-yield work	5.64	2	0	0	0	1.00e+00	Efhd1 Ilf2
Bone: stiffness	8.54	4	0	0	0.98	3.67e-03	B3gntl1 Efhd1 Ilf2 Ly75
Bone: tissue strength	19.03	1	0	0	0	1.00e+00	Efhd1
Bone: trabecular number	35.45	1	1	20	0	1.00e+00	Ly75
Bone: trabecular spacing	60.24	1	1	20	0	1.00e+00	Ly75
Bone: trabecular thickness	47.42	1	1	20	0	1.00e+00	Ly75
Distance traveled after self-admin	7.31	1	0	0	0	1.00e+00	B3gntl1
Delta time in open arm before/after self-admin	7.55	1	0	0	0	1.00e+00	Ilf2
Delta ambulatory time before/after self-admin	7.6	1	0	0	0	1.00e+00	B3gntl1
Time in open arm before self-admin	9.47	1	0	0	0	1.00e+00	Ilf2
Total heroin consumption	8.23	1	0	0	0	1.00e+00	B3gntl1
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
Distance moved, locomotor task time 2	9.43	1	0	0	0	1.00e+00	Ilf2
Weight adjusted by age	20.87	1	0	0	0	1.00e+00	Ly75
Locomotion in novel chamber	34.01	1	1	20	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	7.72	1	0	0	0	1.00e+00	Ilf2
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
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	10.86	2	0	0	0	1.00e+00	B3gntl1 Ly75
Mn content in liver	32.26	1	1	20	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	1.68
Adipose	alternative TSS	0	0	1.65
Adipose	gene expression	0	0	1.61
Adipose	isoform ratio	0	0	1.55
Adipose	intron excision ratio	0	0	1.6
Adipose	mRNA stability	1	0	1.62
BLA	alternative polyA	0	0	1.75
BLA	alternative TSS	0	0	1.55
BLA	gene expression	0	0	1.69
BLA	isoform ratio	0	0	1.56
BLA	intron excision ratio	0	0	1.56
BLA	mRNA stability	0	0	1.65
Brain	alternative polyA	0	0	1.69
Brain	alternative TSS	0	0	1.6
Brain	gene expression	0	0	1.6
Brain	isoform ratio	0	0	1.62
Brain	intron excision ratio	0	0	1.56
Brain	mRNA stability	0	0	1.61
Eye	alternative polyA	0	0	2.05
Eye	alternative TSS	0	0	1.32
Eye	gene expression	0	0	1.59
Eye	isoform ratio	0	0	1.78
Eye	intron excision ratio	0	0	1.48
Eye	mRNA stability	0	0	1.51
IL	alternative polyA	0	0	1.69
IL	alternative TSS	0	0	1.61
IL	gene expression	0	0	1.72
IL	isoform ratio	0	0	1.6
IL	intron excision ratio	0	0	1.65
IL	mRNA stability	0	0	1.76
LHb	alternative polyA	0	0	1.69
LHb	alternative TSS	1	0.2	1.49
LHb	gene expression	1	0	1.68
LHb	isoform ratio	0	0	1.46
LHb	intron excision ratio	0	0	1.54
LHb	mRNA stability	0	0	1.59
Liver	alternative polyA	0	0	1.64
Liver	alternative TSS	0	0	1.59
Liver	gene expression	0	0	1.57
Liver	isoform ratio	0	0	1.6
Liver	intron excision ratio	0	0	1.44
Liver	mRNA stability	0	0	1.57
NAcc	alternative polyA	0	0	1.63
NAcc	alternative TSS	0	0	1.69
NAcc	gene expression	1	0	1.63
NAcc	isoform ratio	0	0	1.64
NAcc	intron excision ratio	0	0	1.62
NAcc	mRNA stability	0	0	1.65
OFC	alternative polyA	0	0	1.75
OFC	alternative TSS	0	0	1.75
OFC	gene expression	0	0	1.67
OFC	isoform ratio	0	0	1.56
OFC	intron excision ratio	0	0	1.61
OFC	mRNA stability	0	0	1.73
PL	alternative polyA	0	0	1.59
PL	alternative TSS	0	0	1.67
PL	gene expression	0	0	1.66
PL	isoform ratio	0	0	1.67
PL	intron excision ratio	0	0	1.65
PL	mRNA stability	0	0	1.62
pVTA	alternative polyA	0	0	1.76
pVTA	alternative TSS	0	0	1.62
pVTA	gene expression	0	0	1.68
pVTA	isoform ratio	0	0	1.62
pVTA	intron excision ratio	0	0	1.68
pVTA	mRNA stability	0	0	1.7
RMTg	alternative polyA	0	0	1.73
RMTg	alternative TSS	0	0	1.8
RMTg	gene expression	0	0	1.6
RMTg	isoform ratio	0	0	1.72
RMTg	intron excision ratio	0	0	1.46
RMTg	mRNA stability	0	0	1.59