Hub : Traits

Bone: connectivity density

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	chr3	44152620	45549784	1	1	7.57e-09	2.75e-03	9.36e-04	Ly75
2	chr12	4284804	5681909	1	1	4.81e-08	1.95e-06	3.75e-28	LOC102549494

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	2.41	2	0	0	0	1e+00	LOC102549494 Ly75
BMI without tail	3.94	1	0	0	0	1e+00	Ly75
Body weight	16.94	1	1	50	0	1e+00	LOC102549494
Epididymis fat weight	3.44	1	0	0	0	1e+00	Ly75
Glucose	3.95	1	0	0	0	1e+00	Ly75
Left kidney weight	12.19	1	1	50	0	1e+00	LOC102549494
Right kidney weight	11.9	1	1	50	0	1e+00	LOC102549494
Tail length	1.99	1	0	0	0	1e+00	LOC102549494
Length with tail	8.15	2	1	50	0	1e+00	LOC102549494 Ly75
Length without tail	14.66	2	1	50	0	1e+00	LOC102549494 Ly75
Liver weight, left	4.97	2	0	0	0	1e+00	LOC102549494 Ly75
Liver weight, right	8.1	1	0	0	0	1e+00	LOC102549494
Retroperitoneal fat weight	8.85	1	1	50	0	1e+00	Ly75
Extensor digitorum longus weight	1.63	2	0	0	0	1e+00	LOC102549494 Ly75
Tibialis anterior weight	3.42	2	0	0	0	1e+00	LOC102549494 Ly75
Tibia length	4.75	1	0	0	0	1e+00	LOC102549494
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 indifference point 0 sec	3.47	1	0	0	0	1e+00	Ly75
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1e+00	Ly75
Patch foraging water rate 0 sec	5.33	1	0	0	0	1e+00	LOC102549494
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	7.46	2	0	0	0	1e+00	LOC102549494 Ly75
Reaction time mean AUC	7.91	2	0	0	0	1e+00	LOC102549494 Ly75
Median of all reaction times	5.26	2	0	0	0	1e+00	LOC102549494 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
Condit. Reinf. active minus inactive responses	28.62	1	1	50	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	50	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	50	0	1e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1e+00	Ly75
Post-drug Anxiety	5.89	1	0	0	0	1e+00	LOC102549494
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	50	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
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	50	0	1e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	50	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. latency score	6.68	1	0	0	0	1e+00	Ly75
Bone: apparent density	20.85	2	1	50	0	1e+00	LOC102549494 Ly75
Bone surface	31.03	2	1	50	0	1e+00	LOC102549494 Ly75
Bone volume	27.16	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: cortical apparent density	18.66	1	0	0	0	1e+00	Ly75
Bone: cortical area	8.75	2	0	0	0	1e+00	LOC102549494 Ly75
Bone: cortical thickness	4.71	2	0	0	0	1e+00	LOC102549494 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	10.45	2	0	0	0	1e+00	LOC102549494 Ly75
Bone: endosteal estimation	9.05	1	0	0	0	1e+00	Ly75
Bone: final force	20.18	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: final moment	26.06	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: marrow area	9.02	1	0	0	0	1e+00	Ly75
Bone: maximum diameter	4.34	2	0	0	0	1e+00	LOC102549494 Ly75
Bone: maximum force	13.15	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: maximum moment	16.89	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: minimum diameter	8.69	1	0	0	0	1e+00	Ly75
Bone: periosteal estimation	8.95	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: periosteal perimeter	5.86	2	0	0	0	1e+00	LOC102549494 Ly75
Bone: stiffness	8.72	1	0	0	0	1e+00	Ly75
Bone: trabecular number	25.07	2	1	50	0	1e+00	LOC102549494 Ly75
Bone: trabecular spacing	60.24	1	1	50	0	1e+00	Ly75
Bone: trabecular thickness	27.1	2	1	50	0	1e+00	LOC102549494 Ly75
Delta time in open arm before/after self-admin	6.02	1	0	0	0	1e+00	LOC102549494
Diff in mean of infusions in LGA sessions	4.9	1	0	0	0	1e+00	Ly75
Total heroin consumption	4.77	1	0	0	0	1e+00	LOC102549494
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
Bouts of movement, locomotor time 2	4.79	1	0	0	0	1e+00	LOC102549494
Rest time, locomotor task time 2	4.68	1	0	0	0	1e+00	Ly75
Vertical activity count, locomotor time 2	5.15	1	0	0	0	1e+00	LOC102549494
Weight adjusted by age	20.87	1	0	0	0	1e+00	Ly75
Locomotion in novel chamber	34.01	1	1	50	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	5.27	2	0	0	0	1e+00	LOC102549494 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	8.81	2	0	0	0	1e+00	LOC102549494 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	50	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	1.56
Adipose	alternative TSS	0	0	1.63
Adipose	gene expression	0	0	1.57
Adipose	isoform ratio	0	0	1.57
Adipose	intron excision ratio	0	0	1.51
Adipose	mRNA stability	1	0	1.55
BLA	alternative polyA	0	0	1.65
BLA	alternative TSS	0	0	1.56
BLA	gene expression	0	0	1.61
BLA	isoform ratio	0	0	1.53
BLA	intron excision ratio	0	0	1.57
BLA	mRNA stability	0	0	1.56
Brain	alternative polyA	0	0	1.59
Brain	alternative TSS	0	0	1.63
Brain	gene expression	0	0	1.56
Brain	isoform ratio	0	0	1.56
Brain	intron excision ratio	0	0	1.57
Brain	mRNA stability	0	0	1.53
Eye	alternative polyA	0	0	1.7
Eye	alternative TSS	0	0	1.47
Eye	gene expression	0	0	1.59
Eye	isoform ratio	0	0	1.52
Eye	intron excision ratio	0	0	1.76
Eye	mRNA stability	0	0	1.7
IL	alternative polyA	0	0	1.58
IL	alternative TSS	0	0	1.53
IL	gene expression	0	0	1.56
IL	isoform ratio	0	0	1.4
IL	intron excision ratio	0	0	1.7
IL	mRNA stability	0	0	1.54
LHb	alternative polyA	0	0	1.61
LHb	alternative TSS	0	0	1.53
LHb	gene expression	1	0	1.57
LHb	isoform ratio	0	0	1.57
LHb	intron excision ratio	0	0	1.67
LHb	mRNA stability	0	0	1.56
Liver	alternative polyA	0	0	1.72
Liver	alternative TSS	0	0	1.53
Liver	gene expression	0	0	1.56
Liver	isoform ratio	0	0	1.59
Liver	intron excision ratio	0	0	1.52
Liver	mRNA stability	0	0	1.55
NAcc	alternative polyA	0	0	1.6
NAcc	alternative TSS	0	0	1.54
NAcc	gene expression	0	0	1.58
NAcc	isoform ratio	0	0	1.53
NAcc	intron excision ratio	0	0	1.55
NAcc	mRNA stability	0	0	1.55
OFC	alternative polyA	0	0	1.55
OFC	alternative TSS	0	0	1.56
OFC	gene expression	0	0	1.55
OFC	isoform ratio	0	0	1.5
OFC	intron excision ratio	0	0	1.66
OFC	mRNA stability	0	0	1.64
PL	alternative polyA	0	0	1.61
PL	alternative TSS	0	0	1.65
PL	gene expression	0	0	1.57
PL	isoform ratio	0	0	1.58
PL	intron excision ratio	0	0	1.6
PL	mRNA stability	0	0	1.59
pVTA	alternative polyA	0	0	1.63
pVTA	alternative TSS	0	0	1.63
pVTA	gene expression	0	0	1.55
pVTA	isoform ratio	0	0	1.52
pVTA	intron excision ratio	0	0	1.63
pVTA	mRNA stability	0	0	1.56
RMTg	alternative polyA	0	0	1.92
RMTg	alternative TSS	0	0	1.42
RMTg	gene expression	0	0	1.6
RMTg	isoform ratio	0	0	1.54
RMTg	intron excision ratio	0	0	1.57
RMTg	mRNA stability	0	0	1.58