Hub : Traits

Bone: apparent density

Tags: Physiology · Bone

Project: r01_doug_adams

3 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	chr2	151149808	152544955	1	1	1.46e-07	3.65e-06	5.24e-01	Mfsd1
2	chr3	44152620	45549784	1	1	1.02e-11	1.43e-03	6.54e-06	Ly75
3	chr11	68406115	70129920	2	1	2.10e-07	1.49e-07	2.69e-02	Dlg1

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI without tail	3.94	1	0	0	0	1.00e+00	Ly75
Epididymis fat weight	3.44	1	0	0	0	1.00e+00	Ly75
Left kidney weight	2.38	2	0	0	0	1.00e+00	Apod Dlg1
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
Extensor digitorum longus weight	1.67	2	0	0	0	1.00e+00	Ly75 Mfsd1
Tibialis anterior weight	3.75	1	0	0	0	1.00e+00	Ly75
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
Mean time between licks in bursts	5.06	1	0	0	0	1.00e+00	Mfsd1
Water consumed over 24 hours	19.18	1	0	0	0	1.00e+00	Ly75
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1.00e+00	Ly75
Patch foraging water rate 6 sec	4.6	2	0	0	0	1.00e+00	Apod Dlg1
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	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	5.51	1	0	0	0	1.00e+00	Mfsd1
Reaction time num false alarms AUC	5.34	1	0	0	0	1.00e+00	Mfsd1
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	5.9	1	0	0	0	1.00e+00	Ly75
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	8.53	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. lever reinforcers received	19.5	1	1	33.3	0	1.00e+00	Ly75
Pavlov. Cond. lever latency	6.31	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. change in total contacts	8.94	3	0	0	0	1.00e+00	Apod Dlg1 Ly75
Pavlov. Cond. index score	6.75	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. latency score	7.79	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. lever contacts	7.98	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. lever-magazine prob. diff.	6.92	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. response bias	4.82	2	0	0	0	1.00e+00	Apod Dlg1
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	9.36	2	0	0	0	1.00e+00	Ly75 Mfsd1
Degree of sensitization stereotypy	38.66	1	1	33.3	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
Total zone transitions, hab. session 1	7.48	1	0	0	0	1.00e+00	Ly75
Locomotion velocity, hab. session 1	4.92	1	0	0	0	1.00e+00	Mfsd1
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
Locomotion velocity, NPP test	5.31	1	0	0	0	1.00e+00	Mfsd1
Pavlov. Cond. change in total contacts	6.54	2	0	0	0	1.00e+00	Apod Dlg1
Pavlov. Cond. latency score	6.68	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. intertrial magazine entries	5.78	1	0	0	0	1.00e+00	Mfsd1
Bone surface	17.91	4	1	33.3	0.94	6.50e-02	Apod Dlg1 Ly75 Mfsd1
Bone volume	18.78	4	1	33.3	0.97	3.24e-02	Apod Dlg1 Ly75 Mfsd1
Bone: connectivity density	14.75	4	1	33.3	1	2.04e-04	Apod Dlg1 Ly75 Mfsd1
Bone: cortical apparent density	18.66	1	0	0	0	1.00e+00	Ly75
Bone: cortical area	8.57	2	0	0	0	1.00e+00	Ly75 Mfsd1
Bone: cortical thickness	5.93	1	0	0	0	1.00e+00	Ly75
Bone: cortical thickness	7.52	2	0	0	0	1.00e+00	Ly75 Mfsd1
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	20.15	2	1	33.3	0	1.00e+00	Ly75 Mfsd1
Bone: final moment	26.53	2	1	33.3	0	1.00e+00	Ly75 Mfsd1
Bone: marrow area	9.02	1	0	0	0	1.00e+00	Ly75
Bone: maximum diameter	4.47	2	0	0	0	1.00e+00	Ly75 Mfsd1
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	20.69	4	2	66.7	0.99	5.34e-03	Apod Dlg1 Ly75 Mfsd1
Bone: trabecular spacing	22.03	4	1	33.3	-0.92	7.97e-02	Apod Dlg1 Ly75 Mfsd1
Bone: trabecular thickness	19.69	4	1	33.3	0.95	5.13e-02	Apod Dlg1 Ly75 Mfsd1
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	21.72	1	0	0	0	1.00e+00	Ly75
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	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	0	0	1.69
Adipose	alternative TSS	0	0	1.68
Adipose	gene expression	1	0	1.64
Adipose	isoform ratio	0	0	1.67
Adipose	intron excision ratio	0	0	1.62
Adipose	mRNA stability	0	0	1.68
BLA	alternative polyA	0	0	1.83
BLA	alternative TSS	0	0	1.67
BLA	gene expression	0	0	1.7
BLA	isoform ratio	0	0	1.65
BLA	intron excision ratio	1	0	1.67
BLA	mRNA stability	0	0	1.73
Brain	alternative polyA	0	0	1.74
Brain	alternative TSS	0	0	1.68
Brain	gene expression	0	0	1.62
Brain	isoform ratio	0	0	1.67
Brain	intron excision ratio	0	0	1.64
Brain	mRNA stability	0	0	1.66
Eye	alternative polyA	0	0	2.01
Eye	alternative TSS	0	0	1.42
Eye	gene expression	0	0	1.65
Eye	isoform ratio	0	0	1.76
Eye	intron excision ratio	0	0	1.72
Eye	mRNA stability	0	0	1.67
IL	alternative polyA	0	0	1.86
IL	alternative TSS	0	0	1.75
IL	gene expression	1	0	1.68
IL	isoform ratio	0	0	1.66
IL	intron excision ratio	0	0	1.72
IL	mRNA stability	0	0	1.75
LHb	alternative polyA	0	0	1.77
LHb	alternative TSS	0	0	1.61
LHb	gene expression	1	0	1.69
LHb	isoform ratio	0	0	1.72
LHb	intron excision ratio	0	0	1.58
LHb	mRNA stability	0	0	1.68
Liver	alternative polyA	0	0	1.75
Liver	alternative TSS	0	0	1.65
Liver	gene expression	0	0	1.62
Liver	isoform ratio	0	0	1.65
Liver	intron excision ratio	0	0	1.55
Liver	mRNA stability	0	0	1.66
NAcc	alternative polyA	0	0	1.76
NAcc	alternative TSS	0	0	1.67
NAcc	gene expression	0	0	1.68
NAcc	isoform ratio	0	0	1.65
NAcc	intron excision ratio	0	0	1.64
NAcc	mRNA stability	0	0	1.69
OFC	alternative polyA	0	0	1.71
OFC	alternative TSS	0	0	1.81
OFC	gene expression	0	0	1.66
OFC	isoform ratio	0	0	1.64
OFC	intron excision ratio	0	0	1.73
OFC	mRNA stability	0	0	1.78
PL	alternative polyA	0	0	1.79
PL	alternative TSS	0	0	1.69
PL	gene expression	0	0	1.68
PL	isoform ratio	0	0	1.71
PL	intron excision ratio	0	0	1.64
PL	mRNA stability	0	0	1.68
pVTA	alternative polyA	0	0	1.8
pVTA	alternative TSS	0	0	1.73
pVTA	gene expression	0	0	1.67
pVTA	isoform ratio	0	0	1.68
pVTA	intron excision ratio	0	0	1.69
pVTA	mRNA stability	0	0	1.71
RMTg	alternative polyA	0	0	2.08
RMTg	alternative TSS	0	0	1.63
RMTg	gene expression	0	0	1.71
RMTg	isoform ratio	0	0	1.71
RMTg	intron excision ratio	0	0	1.44
RMTg	mRNA stability	0	0	1.89