Hub : Traits

Bone: trabecular number

Tags: Physiology · Bone

Project: r01_doug_adams

3 loci · 4 genes with independent associations · 7 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	149193290	150588085	1	1	9.13e-08	9.13e-08	1.00e+00	Lekr1
2	chr2	150949160	152825152	5	2	7.52e-09	3.01e-07	5.75e-01	Lxn Mfsd1
3	chr3	44152620	45549784	1	1	9.63e-14	6.12e-04	1.51e-05	Ly75

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
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	25	0	1.00e+00	Ly75
Extensor digitorum longus weight	2.2	2	0	0	0	1.00e+00	Gfm1 Schip1
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	6.05	3	0	0	0	1.00e+00	Gfm1 Lekr1 Mlf1
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
Reaction time number correct	5.4	2	0	0	0	1.00e+00	Gfm1 Lekr1
Reaction time mean minus median AUC	11.4	2	0	0	0	1.00e+00	Gfm1 Ly75
Reaction time num false alarms	5.91	2	0	0	0	1.00e+00	Mfsd1 Schip1
Reaction time num false alarms AUC	5.35	3	0	0	0	1.00e+00	Lxn Mfsd1 Schip1
Reaction time trials correct on left	5.4	2	0	0	0	1.00e+00	Gfm1 Lekr1
Reaction time trials on left	5.53	1	0	0	0	1.00e+00	Lekr1
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
Reaction time premature initiation rate	9.14	1	0	0	0	1.00e+00	Ly75
Reaction time premature initiations	5.6	1	0	0	0	1.00e+00	Lekr1
Std. dev. reaction times	14.29	1	0	0	0	1.00e+00	Ly75
Reaction time trials completed	5.53	1	0	0	0	1.00e+00	Lekr1
Reaction time trials AUC	5.3	1	0	0	0	1.00e+00	Lekr1
Condit. Reinf. active minus inactive responses	28.62	1	1	25	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	25	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	25	0	1.00e+00	Ly75
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Compulsive drug intake	9.1	1	0	0	0	1.00e+00	Lxn
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	8.59	4	0	0	-1	2.70e-03	Lxn Ly75 Mfsd1 Schip1
Degree of sensitization stereotypy	38.66	1	1	25	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
Time in familiar zone, hab. session 2	8.32	2	0	0	0	1.00e+00	Gfm1 Lekr1
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	25	0	1.00e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	25	0	1.00e+00	Ly75
Total zone transitions, NPP test	5.39	1	0	0	0	1.00e+00	Ly75
Locomotion velocity, NPP test	5.6	2	0	0	0	1.00e+00	Mfsd1 Schip1
Pavlov. Cond. latency score	6.68	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. intertrial magazine entries	6.35	3	0	0	0	1.00e+00	Gfm1 Lekr1 Mlf1
Bone: apparent density	16.67	7	2	50	1	2.11e-11	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
Bone surface	13.07	7	1	25	0.94	1.47e-03	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
Bone volume	15.53	7	1	25	0.98	1.01e-04	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
Bone: connectivity density	10.91	7	1	25	1	2.94e-07	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
Bone: cortical apparent density	18.66	1	0	0	0	1.00e+00	Ly75
Bone: cortical area	8.88	2	0	0	0	1.00e+00	Lxn Ly75
Bone: cortical thickness	5.93	1	0	0	0	1.00e+00	Ly75
Bone: cortical thickness	7.46	5	0	0	0.99	8.91e-04	Lxn Ly75 Mfsd1 Mlf1 Schip1
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	11.01	5	1	25	0.94	1.66e-02	Lekr1 Lxn Ly75 Mfsd1 Mlf1
Bone: final moment	13.8	5	1	25	0.92	2.54e-02	Lekr1 Lxn Ly75 Mfsd1 Mlf1
Bone: marrow area	9.02	1	0	0	0	1.00e+00	Ly75
Bone: maximum diameter	4.41	3	0	0	0	1.00e+00	Lekr1 Lxn Ly75
Bone: maximum force	20.87	1	1	25	0	1.00e+00	Ly75
Bone: maximum moment	29.34	1	1	25	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	25	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 spacing	19.28	7	1	25	-0.97	4.02e-04	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
Bone: trabecular thickness	21.47	7	1	25	1	3.25e-06	Gfm1 Lekr1 Lxn Ly75 Mfsd1 Mlf1 Schip1
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	25	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	25	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	1.58
Adipose	alternative TSS	0	0	1.6
Adipose	gene expression	2	0	1.54
Adipose	isoform ratio	1	0	1.56
Adipose	intron excision ratio	0	0	1.59
Adipose	mRNA stability	1	0	1.56
BLA	alternative polyA	0	0	1.69
BLA	alternative TSS	1	0.1	1.58
BLA	gene expression	1	0	1.59
BLA	isoform ratio	0	0	1.57
BLA	intron excision ratio	0	0	1.61
BLA	mRNA stability	0	0	1.56
Brain	alternative polyA	0	0	1.57
Brain	alternative TSS	0	0	1.62
Brain	gene expression	0	0	1.55
Brain	isoform ratio	0	0	1.58
Brain	intron excision ratio	0	0	1.59
Brain	mRNA stability	0	0	1.52
Eye	alternative polyA	0	0	1.93
Eye	alternative TSS	0	0	1.4
Eye	gene expression	0	0	1.52
Eye	isoform ratio	0	0	1.68
Eye	intron excision ratio	0	0	1.66
Eye	mRNA stability	0	0	1.47
IL	alternative polyA	0	0	1.66
IL	alternative TSS	0	0	1.53
IL	gene expression	0	0	1.57
IL	isoform ratio	0	0	1.51
IL	intron excision ratio	0	0	1.7
IL	mRNA stability	0	0	1.53
LHb	alternative polyA	0	0	1.54
LHb	alternative TSS	0	0	1.47
LHb	gene expression	1	0	1.55
LHb	isoform ratio	0	0	1.58
LHb	intron excision ratio	0	0	1.58
LHb	mRNA stability	0	0	1.56
Liver	alternative polyA	0	0	1.6
Liver	alternative TSS	0	0	1.5
Liver	gene expression	0	0	1.51
Liver	isoform ratio	0	0	1.51
Liver	intron excision ratio	0	0	1.44
Liver	mRNA stability	0	0	1.51
NAcc	alternative polyA	0	0	1.6
NAcc	alternative TSS	0	0	1.53
NAcc	gene expression	0	0	1.57
NAcc	isoform ratio	0	0	1.56
NAcc	intron excision ratio	0	0	1.56
NAcc	mRNA stability	0	0	1.56
OFC	alternative polyA	0	0	1.58
OFC	alternative TSS	0	0	1.52
OFC	gene expression	0	0	1.58
OFC	isoform ratio	0	0	1.52
OFC	intron excision ratio	0	0	1.75
OFC	mRNA stability	0	0	1.62
PL	alternative polyA	0	0	1.6
PL	alternative TSS	0	0	1.6
PL	gene expression	0	0	1.57
PL	isoform ratio	0	0	1.58
PL	intron excision ratio	0	0	1.59
PL	mRNA stability	0	0	1.56
pVTA	alternative polyA	0	0	1.63
pVTA	alternative TSS	0	0	1.62
pVTA	gene expression	0	0	1.54
pVTA	isoform ratio	0	0	1.57
pVTA	intron excision ratio	0	0	1.67
pVTA	mRNA stability	0	0	1.56
RMTg	alternative polyA	0	0	1.88
RMTg	alternative TSS	0	0	1.63
RMTg	gene expression	0	0	1.54
RMTg	isoform ratio	0	0	1.64
RMTg	intron excision ratio	0	0	1.42
RMTg	mRNA stability	0	0	1.68