Hub : Traits

Bone: trabecular thickness

Tags: Physiology · Bone

Project: r01_doug_adams

1 loci · 1 genes with independent associations · 1 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	2	144900859	146298381	1	1	2.27e-08	6.73e-05	3.06e-03	Rap2b

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
Left kidney weight	1.61	1	0	0	0	1e+00	Rap2b
Extensor digitorum longus weight	2.51	1	0	0	0	1e+00	Rap2b
Number of licking bursts	7.6	1	0	0	0	1e+00	Rap2b
Times rat made contact with spout	8.11	1	0	0	0	1e+00	Rap2b
Mean time between licks in bursts	11.11	1	0	0	0	1e+00	Rap2b
Std. dev. time between licks in bursts	10.79	1	0	0	0	1e+00	Rap2b
Water consumed over 24 hours	7.55	1	0	0	0	1e+00	Rap2b
Locomotor testing distance	3.73	1	0	0	0	1e+00	Rap2b
Reaction time mean minus median	3.23	1	0	0	0	1e+00	Rap2b
Reaction time mean minus median AUC	4.44	1	0	0	0	1e+00	Rap2b
Reaction time mean	3.53	1	0	0	0	1e+00	Rap2b
Reaction time mean AUC	4.72	1	0	0	0	1e+00	Rap2b
Reaction time omissions	4.8	1	0	0	0	1e+00	Rap2b
Std. dev. reaction times	5.24	1	0	0	0	1e+00	Rap2b
Condit. Reinf. lever presses	5.82	1	0	0	0	1e+00	Rap2b
Baseline Anxiety	4.34	1	0	0	0	1e+00	Rap2b
Context. condit. distance diff. score	11.58	1	0	0	0	1e+00	Rap2b
Locomotion distance, session 1	3.12	1	0	0	0	1e+00	Rap2b
Locomotion distance, session 2	3.9	1	0	0	0	1e+00	Rap2b
Locomotion distance, session 3	5.06	1	0	0	0	1e+00	Rap2b
Condit. Reinf. active minus inactive responses	17.95	1	0	0	0	1e+00	Rap2b
Condit. Reinf. active-inactive response ratio	18.94	1	0	0	0	1e+00	Rap2b
Condit. Reinf. active responses	13.71	1	0	0	0	1e+00	Rap2b
Incentive salience index mean	22.6	1	1	100	0	1e+00	Rap2b
Condit. Reinf. lever presses	8.24	1	0	0	0	1e+00	Rap2b
Total zone transitions, hab. session 1	4.73	1	0	0	0	1e+00	Rap2b
Total locomotion distance, hab. session 1	6.97	1	0	0	0	1e+00	Rap2b
Locomotion velocity, hab. session 1	10.08	1	0	0	0	1e+00	Rap2b
Novelty place preference	3.89	1	0	0	0	1e+00	Rap2b
Total locomotion distance, NPP test	3.06	1	0	0	0	1e+00	Rap2b
Locomotion velocity, NPP test	4.09	1	0	0	0	1e+00	Rap2b
Pavlov. Cond. lever latency	4.7	1	0	0	0	1e+00	Rap2b
Pavlov. Cond. intertrial magazine entries	6.24	1	0	0	0	1e+00	Rap2b
Bone: apparent density	14.38	1	0	0	0	1e+00	Rap2b
Bone surface	4.84	1	0	0	0	1e+00	Rap2b
Bone volume	7.49	1	0	0	0	1e+00	Rap2b
Bone: connectivity density	10.55	1	0	0	0	1e+00	Rap2b
Bone: cortical apparent density	4.26	1	0	0	0	1e+00	Rap2b
Bone: cortical porosity	8.71	1	0	0	0	1e+00	Rap2b
Bone: cortical porosity	6.35	1	0	0	0	1e+00	Rap2b
Bone: cortical tissue density	4.88	1	0	0	0	1e+00	Rap2b
Bone: maximum diameter	3.77	1	0	0	0	1e+00	Rap2b
Bone: post-yield work	3.83	1	0	0	0	1e+00	Rap2b
Bone: trabecular number	19.79	1	1	100	0	1e+00	Rap2b
Bone: trabecular spacing	13.96	1	0	0	0	1e+00	Rap2b
Extinction: sum of active levers before priming	6.6	1	0	0	0	1e+00	Rap2b
Time to tail flick, vehicle, after self-admin	9.36	1	0	0	0	1e+00	Rap2b
Seeking ratio, delayed vs. immediate footshock	4.32	1	0	0	0	1e+00	Rap2b
Seeking ratio, punishment vs. effort	6.54	1	0	0	0	1e+00	Rap2b
Co content in liver	7.05	1	0	0	0	1e+00	Rap2b
Fe content in liver	6.07	1	0	0	0	1e+00	Rap2b
Se content in liver	6.66	1	0	0	0	1e+00	Rap2b

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	1.32
Adipose	alternative TSS	0	0	1.27
Adipose	gene expression	0	0	1.27
Adipose	isoform ratio	0	0	1.24
Adipose	intron excision ratio	0	0	1.22
Adipose	mRNA stability	0	0	1.27
BLA	alternative polyA	0	0	1.19
BLA	alternative TSS	0	0	1.23
BLA	gene expression	0	0	1.21
BLA	isoform ratio	0	0	1.21
BLA	intron excision ratio	0	0	1.18
BLA	mRNA stability	0	0	1.23
Brain	alternative polyA	0	0	1.31
Brain	alternative TSS	0	0	1.2
Brain	gene expression	0	0	1.19
Brain	isoform ratio	0	0	1.19
Brain	intron excision ratio	0	0	1.15
Brain	mRNA stability	0	0	1.22
Eye	alternative polyA	0	0	1.24
Eye	alternative TSS	0	0	0.98
Eye	gene expression	0	0	1.23
Eye	isoform ratio	0	0	1.26
Eye	intron excision ratio	0	0	1.29
Eye	mRNA stability	0	0	1.15
IL	alternative polyA	0	0	1.12
IL	alternative TSS	0	0	1.39
IL	gene expression	0	0	1.16
IL	isoform ratio	0	0	1.13
IL	intron excision ratio	0	0	1.07
IL	mRNA stability	0	0	1.23
LHb	alternative polyA	0	0	1.32
LHb	alternative TSS	0	0	1.45
LHb	gene expression	0	0	1.19
LHb	isoform ratio	0	0	1.18
LHb	intron excision ratio	0	0	1.09
LHb	mRNA stability	0	0	1.28
Liver	alternative polyA	0	0	1.21
Liver	alternative TSS	0	0	1.25
Liver	gene expression	1	0	1.27
Liver	isoform ratio	0	0	1.23
Liver	intron excision ratio	0	0	1.14
Liver	mRNA stability	0	0	1.26
NAcc	alternative polyA	0	0	1.23
NAcc	alternative TSS	0	0	1.2
NAcc	gene expression	0	0	1.21
NAcc	isoform ratio	0	0	1.28
NAcc	intron excision ratio	0	0	1.14
NAcc	mRNA stability	0	0	1.24
OFC	alternative polyA	0	0	1.17
OFC	alternative TSS	0	0	1.26
OFC	gene expression	0	0	1.22
OFC	isoform ratio	0	0	1.23
OFC	intron excision ratio	0	0	1.17
OFC	mRNA stability	0	0	1.21
PL	alternative polyA	0	0	1.2
PL	alternative TSS	0	0	1.22
PL	gene expression	0	0	1.21
PL	isoform ratio	0	0	1.19
PL	intron excision ratio	0	0	1.12
PL	mRNA stability	0	0	1.21