Bone surface

Tags: Physiology · Bone

3 loci · 3 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	chr3	44152620	45549784	1	1	5.35e-20	5.67e-04	2.98e-14	Ly75
2	chr10	90321052	91848405	3	1	1.37e-07	5.59e-06	7.34e-01	Map3k3
3	chr10	95292638	96688570	2	1	1.18e-07	1.81e-07	1.00e+00	Kcnj16

Pleiotropic Associations

Trait	Chi² ratio	# genes⁺	# genes⁺⁺	% genes⁺⁺	Corr	Corr P	Genes
BMI with tail	3.05	1	0	0	0	1.00e+00	Kcnj16
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
Length with tail	2.92	3	0	0	0.95	5.01e-02	Ccdc47 Ly75 Map3k3
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	6.76	2	1	33.3	0	1.00e+00	Ccdc47 Map3k3
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
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
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	6.25	2	0	0	0	1.00e+00	Kcnj16 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	6.86	2	0	0	0	1.00e+00	Kcnj16 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	15.41	3	1	33.3	1	1.41e-03	Ccdc47 Ly75 Map3k3
Condit. Reinf. active-inactive response ratio	9.64	3	0	0	0.97	2.99e-02	Ccdc47 Ly75 Map3k3
Condit. Reinf. active responses	11.13	3	1	33.3	1	1.99e-03	Ccdc47 Ly75 Map3k3
Condit. Reinf. lever presses	8.53	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. lever reinforcers received	9.46	3	1	33.3	1	6.94e-05	Ccdc47 Ly75 Map3k3
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. intertrial magazine entries	7.05	1	0	0	0	1.00e+00	Ccdc47
Intermittent access total locomotion	6.36	1	0	0	0	1.00e+00	Ccdc47
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	10.32	1	0	0	0	1.00e+00	Ly75
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
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
Pavlov. Cond. latency score	6.68	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. response bias	7.58	2	0	0	0	1.00e+00	Ccdc47 Map3k3
Bone: apparent density	9.75	4	1	33.3	0.99	4.63e-05	Ccdc47 Kcnj16 Ly75 Map3k3
Bone volume	17.47	4	1	33.3	1	1.02e-06	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: connectivity density	9.38	4	1	33.3	1	4.74e-07	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: cortical apparent density	11.66	2	0	0	0	1.00e+00	Kcnj16 Ly75
Bone: cortical area	6.9	3	0	0	1	1.87e-03	Ccdc47 Ly75 Map3k3
Bone: cortical porosity	16.69	2	0	0	0	1.00e+00	Ccdc47 Map3k3
Bone: cortical porosity	12.13	2	0	0	0	1.00e+00	Ccdc47 Map3k3
Bone: cortical thickness	13.25	2	1	33.3	0	1.00e+00	Kcnj16 Ly75
Bone: cortical thickness	7.09	1	0	0	0	1.00e+00	Ly75
Bone: cortical tissue density	11.08	2	0	0	0	1.00e+00	Kcnj16 Ly75
Bone: elastic work	15.82	1	0	0	0	1.00e+00	Ly75
Bone: endosteal estimation	15.36	4	2	66.7	0.94	6.07e-03	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: endosteal perimeter	17.26	3	3	100	1	1.55e-04	Ccdc47 Kcnj16 Map3k3
Bone: final force	20.24	2	1	33.3	0	1.00e+00	Ly75 Map3k3
Bone: final moment	15.61	3	1	33.3	0.94	5.90e-02	Ccdc47 Ly75 Map3k3
Bone: marrow area	15.09	4	2	66.7	0.94	5.85e-03	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: maximum diameter	8.7	4	0	0	0.94	5.49e-03	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: maximum force	8.47	3	1	33.3	0.99	8.75e-03	Ccdc47 Ly75 Map3k3
Bone: maximum moment	10.98	3	1	33.3	0.98	1.98e-02	Ccdc47 Ly75 Map3k3
Bone: minimum diameter	11.29	4	0	0	0.95	3.56e-03	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: periosteal estimation	12.51	4	2	66.7	0.97	9.42e-04	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: periosteal perimeter	9.31	4	0	0	0.95	3.74e-03	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: stiffness	8.72	1	0	0	0	1.00e+00	Ly75
Bone: trabecular number	11.6	4	1	33.3	0.99	2.40e-04	Ccdc47 Kcnj16 Ly75 Map3k3
Bone: trabecular spacing	24.14	2	1	33.3	0	1.00e+00	Kcnj16 Ly75
Bone: trabecular thickness	19.05	3	1	33.3	0.99	1.01e-02	Ccdc47 Ly75 Map3k3
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
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	1.71
Adipose	alternative TSS	2	0.1	1.74
Adipose	gene expression	0	0	1.75
Adipose	isoform ratio	0	0	1.75
Adipose	intron excision ratio	0	0	1.72
Adipose	mRNA stability	0	0	1.81
BLA	alternative polyA	0	0	1.91
BLA	alternative TSS	0	0	1.88
BLA	gene expression	0	0	1.83
BLA	isoform ratio	0	0	1.74
BLA	intron excision ratio	0	0	1.63
BLA	mRNA stability	0	0	1.86
Brain	alternative polyA	0	0	1.84
Brain	alternative TSS	0	0	1.8
Brain	gene expression	0	0	1.74
Brain	isoform ratio	0	0	1.76
Brain	intron excision ratio	0	0	1.66
Brain	mRNA stability	0	0	1.76
Eye	alternative polyA	0	0	1.89
Eye	alternative TSS	0	0	1.59
Eye	gene expression	0	0	1.79
Eye	isoform ratio	0	0	1.76
Eye	intron excision ratio	0	0	1.51
Eye	mRNA stability	0	0	1.87
IL	alternative polyA	0	0	1.86
IL	alternative TSS	0	0	1.86
IL	gene expression	0	0	1.79
IL	isoform ratio	0	0	1.57
IL	intron excision ratio	0	0	1.61
IL	mRNA stability	0	0	1.9
LHb	alternative polyA	0	0	1.86
LHb	alternative TSS	0	0	1.72
LHb	gene expression	1	0	1.75
LHb	isoform ratio	0	0	1.7
LHb	intron excision ratio	0	0	1.48
LHb	mRNA stability	0	0	1.85
Liver	alternative polyA	0	0	1.86
Liver	alternative TSS	0	0	1.77
Liver	gene expression	1	0	1.77
Liver	isoform ratio	0	0	1.82
Liver	intron excision ratio	0	0	1.75
Liver	mRNA stability	0	0	1.75
NAcc	alternative polyA	0	0	1.84
NAcc	alternative TSS	0	0	1.85
NAcc	gene expression	0	0	1.79
NAcc	isoform ratio	0	0	1.74
NAcc	intron excision ratio	0	0	1.67
NAcc	mRNA stability	0	0	1.81
OFC	alternative polyA	0	0	1.71
OFC	alternative TSS	0	0	1.85
OFC	gene expression	0	0	1.73
OFC	isoform ratio	0	0	1.55
OFC	intron excision ratio	0	0	1.56
OFC	mRNA stability	0	0	1.85
PL	alternative polyA	0	0	1.93
PL	alternative TSS	0	0	1.83
PL	gene expression	0	0	1.79
PL	isoform ratio	0	0	1.81
PL	intron excision ratio	0	0	1.71
PL	mRNA stability	0	0	1.82
pVTA	alternative polyA	1	0.1	1.9
pVTA	alternative TSS	0	0	1.88
pVTA	gene expression	1	0	1.74
pVTA	isoform ratio	0	0	1.74
pVTA	intron excision ratio	0	0	1.63
pVTA	mRNA stability	0	0	1.84
RMTg	alternative polyA	0	0	1.89
RMTg	alternative TSS	0	0	1.74
RMTg	gene expression	0	0	1.78
RMTg	isoform ratio	0	0	1.75
RMTg	intron excision ratio	0	0	1.47
RMTg	mRNA stability	0	0	1.82