Hub : Traits

Sr content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

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	chr5	142950162	144036879	5	2	2.71e-22	2.66e-01	1.41e-12	Stk40
2	chr5	170075070	170847497	1	1	1.18e-08	1.73e-01	1.00e+00	Arhgef16
3	chr16	72470120	73870022	1	1	1.20e-07	2.56e-04	8.53e-01	Nsd3

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	2.72	2	0	0	1	4.20e-05	Lsm10 Stk40
Body weight	5.11	2	1	25	0.99	1.98e-04	Lsm10 Stk40
Glucose	13.58	2	0	0	-0.99	6.49e-06	Lsm10 Stk40
Left kidney weight	1.41	2	0	0	0	1.00e+00	Lsm10 Stk40
Right kidney weight	1.2	1	0	0	0	1.00e+00	Lsm10
Length with tail	2.69	2	0	0	0	1.00e+00	Lsm10 Stk40
Length without tail	1.57	1	0	0	0	1.00e+00	Stk40
Liver weight, left	12.36	2	0	0	1	5.48e-05	Lsm10 Stk40
Retroperitoneal fat weight	2.87	1	0	0	0	1.00e+00	Arhgef16
Extensor digitorum longus weight	7.32	3	1	25	0.83	1.09e-02	Arhgef16 Lsm10 Stk40
Soleus weight	10.03	3	2	50	0.78	6.60e-02	Arhgef16 Lsm10 Stk40
Tibialis anterior weight	6.84	2	1	25	0.59	3.00e-01	Arhgef16 Stk40
Tibia length	8.54	1	0	0	0	1.00e+00	Arhgef16
Food consumed during 24 hour testing period	35.72	1	1	25	0	1.00e+00	Arhgef16
Times rat made contact with spout	12.61	1	0	0	0	1.00e+00	Arhgef16
Mean time between licks in bursts	4.62	1	1	25	0	1.00e+00	Arhgef16
Mean num. licks in bursts	4.24	1	0	0	0	1.00e+00	Arhgef16
Std. dev. time between licks in bursts	7.5	1	0	0	0	1.00e+00	Arhgef16
Patch foraging indifference point AUC	4.81	1	0	0	0.97	5.66e-03	Stk40
Patch foraging total patch changes 18 sec	6.08	1	0	0	0.99	2.64e-04	Stk40
Patch foraging water rate 18 sec	4.84	1	0	0	0	1.00e+00	Arhgef16
Locomotor activity	6.67	2	0	0	-0.99	2.36e-04	Lsm10 Stk40
Locomotor testing distance	4.39	3	0	0	-0.98	8.05e-05	Arhgef16 Lsm10 Stk40
Locomotor testing rearing	6.56	2	0	0	-1	2.39e-04	Lsm10 Stk40
Reaction time number correct	2.89	1	0	0	0	1.00e+00	Lsm10
Reaction time mean minus median AUC	2.99	1	0	0	0	1.00e+00	Arhgef16
Reaction time num false alarms	6.13	1	0	0	0	1.00e+00	Stk40
Reaction time num false alarms AUC	6.34	1	0	0	1	8.44e-04	Stk40
Reaction time trials correct on left	2.89	1	0	0	0	1.00e+00	Lsm10
Reaction time trials on left	3.12	1	0	0	0	1.00e+00	Lsm10
Reaction time mean	6.37	1	0	0	0	1.00e+00	Arhgef16
Reaction time mean AUC	4.19	1	0	0	0	1.00e+00	Arhgef16
Median of all reaction times	12.63	2	1	25	0	1.00e+00	Arhgef16 Stk40
Reaction time premature initiation rate	13.32	2	1	25	0	1.00e+00	Arhgef16 Nsd3
Reaction time premature initiations	5.29	2	0	0	0	1.00e+00	Arhgef16 Nsd3
Reaction time trials completed	3.12	1	0	0	0	1.00e+00	Lsm10
Reaction time trials AUC	3.67	1	0	0	0	1.00e+00	Lsm10
Social time	7.25	1	0	0	0	1.00e+00	Arhgef16
Conditioned locomotion	29.07	1	1	25	0	1.00e+00	Arhgef16
Cocaine response after cond. corrected	7.53	1	0	0	0	1.00e+00	Arhgef16
Cocaine response after cond. not corrected	13.39	1	0	0	0	1.00e+00	Arhgef16
Condit. Reinf. lever presses	6.06	1	0	0	0	1.00e+00	Stk40
Pavlov. Cond. magazine entry latency	6.25	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. index score	9.37	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. latency score	4.83	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. lever-magazine prob. diff.	11.1	1	0	0	0	1.00e+00	Arhgef16
Cocaine induced anxiety	2.99	1	0	0	0	1.00e+00	Arhgef16
Post-drug Anxiety	8.67	1	0	0	0	1.00e+00	Arhgef16
Short access day 10 total inactive lever presses	1.79	2	0	0	-1	1.88e-04	Lsm10 Stk40
Short access day 1 total infusions	3.96	1	0	0	0	1.00e+00	Arhgef16
Short access day 1 locomotion	8.32	1	0	0	0	1.00e+00	Arhgef16
Short access day 10 total locomotion	2.03	1	0	0	0	1.00e+00	Stk40
Short access total locomotion	7.07	1	0	0	0	1.00e+00	Arhgef16
Condit. Reinf. active minus inactive responses	12.05	2	0	0	1	5.55e-05	Lsm10 Stk40
Condit. Reinf. active-inactive response ratio	12.35	2	0	0	1	2.10e-04	Lsm10 Stk40
Condit. Reinf. active responses	6.29	2	0	0	0	1.00e+00	Arhgef16 Stk40
Incentive salience index mean	17.51	3	1	25	0.87	2.44e-02	Arhgef16 Lsm10 Stk40
Condit. Reinf. lever presses	14.21	3	0	0	0.85	3.37e-02	Arhgef16 Lsm10 Stk40
Total zone transitions, hab. session 1	5.63	1	0	0	0	1.00e+00	Nsd3
Novel to familiar place preference ratio	6.98	1	0	0	0	1.00e+00	Nsd3
Novelty place preference	7.58	1	0	0	0	1.00e+00	Nsd3
Time in novel zone, NPP test	8.61	1	0	0	0	1.00e+00	Nsd3
Total zone transitions, NPP test	9.7	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. lever latency	7.9	3	0	0	-0.8	1.08e-01	Arhgef16 Lsm10 Stk40
Pavlov. Cond. magazine entry latency	9.71	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. change in total contacts	8.76	1	0	0	0	1.00e+00	Lsm10
Pavlov. Cond. index score	8.01	3	0	0	0.76	1.33e-01	Arhgef16 Lsm10 Stk40
Pavlov. Cond. latency score	6.86	3	0	0	0	1.00e+00	Arhgef16 Lsm10 Stk40
Pavlov. Cond. lever contacts	11.17	3	0	0	0.82	4.33e-02	Arhgef16 Lsm10 Stk40
Pavlov. Cond. magazine entry number	7.27	1	0	0	0	1.00e+00	Arhgef16
Pavlov. Cond. intertrial magazine entries	9.8	2	0	0	-0.8	1.01e-01	Arhgef16 Stk40
Pavlov. Cond. lever-magazine prob. diff.	9.66	3	0	0	0.83	4.11e-02	Arhgef16 Lsm10 Stk40
Pavlov. Cond. response bias	9.06	3	0	0	0.75	1.47e-01	Arhgef16 Lsm10 Stk40
Bone: apparent density	8.51	1	0	0	1	5.61e-04	Stk40
Bone surface	8.86	2	0	0	1	1.65e-04	Lsm10 Stk40
Bone volume	13.71	2	1	25	1	2.03e-08	Lsm10 Stk40
Bone: connectivity density	5.59	1	0	0	0	1.00e+00	Stk40
Bone: cortical porosity	9.55	1	0	0	0	1.00e+00	Arhgef16
Bone: cortical thickness	6.63	1	0	0	0	1.00e+00	Arhgef16
Bone: cortical thickness	6.35	1	0	0	0	1.00e+00	Arhgef16
Bone: endosteal perimeter	4.85	1	0	0	0	1.00e+00	Arhgef16
Bone: stiffness	5.18	1	0	0	0	1.00e+00	Nsd3
Bone: tissue strength	9.81	1	0	0	0	1.00e+00	Arhgef16
Bone: trabecular number	4.65	1	0	0	0	1.00e+00	Arhgef16
Bone: trabecular thickness	6.99	1	0	0	0	1.00e+00	Stk40
Bone: trabecular tissue density	5.73	1	0	0	0	1.00e+00	Arhgef16
Delta time in closed arm before/after self-admin	10.2	1	0	0	0	1.00e+00	Arhgef16
Extinction: sum of active levers before priming	42.26	1	1	25	0	1.00e+00	Arhgef16
Time to tail flick, test, before self-admin	47.2	1	1	25	0	1.00e+00	Arhgef16
Time to tail flick, test, after self-admin	21.82	1	0	0	0	1.00e+00	Arhgef16
Total heroin consumption	28.93	1	1	25	0	1.00e+00	Arhgef16
Area under the delay curve	33.96	1	1	25	0	1.00e+00	Arhgef16
Delay disc. indifference point, 0s delay	8.11	1	0	0	0	1.00e+00	Arhgef16
Delay disc. indifference point, 16s delay	16.75	1	0	0	0	1.00e+00	Arhgef16
Delay disc. indifference point, 2s delay	25.25	1	1	25	0	1.00e+00	Arhgef16
Delay disc. indifference point, 8s delay	63.48	1	1	25	0	1.00e+00	Arhgef16
Delay discount exponential model param	48.46	1	1	25	0	1.00e+00	Arhgef16
Delay discount hyperbolic model param	41.42	1	1	25	0	1.00e+00	Arhgef16
Latency to leave start box in cocaine runway	6.26	1	0	0	0	1.00e+00	Arhgef16
Latency to leave start box in cocaine runway, F	20.84	1	0	0	0	1.00e+00	Arhgef16
Cd content in liver	9.57	2	0	0	1	1.95e-03	Lsm10 Stk40
Cu content in liver	22.75	1	0	0	0	1.00e+00	Arhgef16
Fe content in liver	7.76	2	0	0	0	1.00e+00	Arhgef16 Nsd3
K content in liver	93.31	1	1	25	0	1.00e+00	Arhgef16
Mg content in liver	11.23	3	0	0	-0.93	6.64e-02	Arhgef16 Lsm10 Stk40
Mn content in liver	9.62	3	0	0	0	1.00e+00	Arhgef16 Lsm10 Stk40
Na content in liver	30.82	1	1	25	0	1.00e+00	Arhgef16
Rb content in liver	14.76	3	0	0	-0.83	4.19e-02	Arhgef16 Lsm10 Stk40
Se content in liver	7.81	2	0	0	0	1.00e+00	Arhgef16 Lsm10
Zn content in liver	8.22	1	0	0	0	1.00e+00	Arhgef16

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	0.92
Adipose	alternative TSS	0	0	0.9
Adipose	gene expression	0	0	0.89
Adipose	isoform ratio	2	0	0.9
Adipose	intron excision ratio	0	0	0.87
Adipose	mRNA stability	0	0	0.88
BLA	alternative polyA	0	0	0.9
BLA	alternative TSS	0	0	0.86
BLA	gene expression	0	0	0.88
BLA	isoform ratio	0	0	0.86
BLA	intron excision ratio	0	0	0.86
BLA	mRNA stability	0	0	0.89
Brain	alternative polyA	0	0	0.89
Brain	alternative TSS	0	0	0.94
Brain	gene expression	0	0	0.87
Brain	isoform ratio	0	0	0.87
Brain	intron excision ratio	0	0	0.86
Brain	mRNA stability	0	0	0.9
Eye	alternative polyA	0	0	1.03
Eye	alternative TSS	0	0	0.88
Eye	gene expression	0	0	0.93
Eye	isoform ratio	0	0	0.95
Eye	intron excision ratio	0	0	0.79
Eye	mRNA stability	0	0	0.81
IC	alternative polyA	0	0	0.9
IC	alternative TSS	0	0	0.87
IC	gene expression	0	0	0.86
IC	isoform ratio	0	0	0.87
IC	intron excision ratio	0	0	0.85
IC	mRNA stability	0	0	0.84
IL	alternative polyA	0	0	0.82
IL	alternative TSS	0	0	0.9
IL	gene expression	0	0	0.92
IL	isoform ratio	0	0	0.89
IL	intron excision ratio	0	0	0.79
IL	mRNA stability	0	0	0.89
LHb	alternative polyA	0	0	0.86
LHb	alternative TSS	0	0	0.96
LHb	gene expression	0	0	0.88
LHb	isoform ratio	0	0	0.88
LHb	intron excision ratio	0	0	0.83
LHb	mRNA stability	0	0	0.88
Liver	alternative polyA	2	0.1	0.94
Liver	alternative TSS	0	0	0.87
Liver	gene expression	2	0	0.91
Liver	isoform ratio	2	0.1	0.92
Liver	intron excision ratio	0	0	0.86
Liver	mRNA stability	0	0	0.89
NAcc	alternative polyA	0	0	0.92
NAcc	alternative TSS	0	0	0.85
NAcc	gene expression	0	0	0.89
NAcc	isoform ratio	0	0	0.84
NAcc	intron excision ratio	0	0	0.84
NAcc	mRNA stability	0	0	0.88
OFC	alternative polyA	0	0	0.86
OFC	alternative TSS	0	0	0.82
OFC	gene expression	0	0	0.89
OFC	isoform ratio	0	0	0.92
OFC	intron excision ratio	0	0	0.76
OFC	mRNA stability	0	0	0.85
PL	alternative polyA	0	0	0.95
PL	alternative TSS	0	0	0.87
PL	gene expression	0	0	0.9
PL	isoform ratio	0	0	0.86
PL	intron excision ratio	0	0	0.82
PL	mRNA stability	1	0	0.87
pVTA	alternative polyA	0	0	0.89
pVTA	alternative TSS	0	0	0.83
pVTA	gene expression	0	0	0.89
pVTA	isoform ratio	0	0	0.82
pVTA	intron excision ratio	0	0	0.85
pVTA	mRNA stability	0	0	0.84
RMTg	alternative polyA	0	0	0.78
RMTg	alternative TSS	0	0	0.83
RMTg	gene expression	0	0	0.88
RMTg	isoform ratio	0	0	0.97
RMTg	intron excision ratio	0	0	0.8
RMTg	mRNA stability	0	0	0.91