Hub : Traits

Sr content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

3 loci · 3 genes with independent associations · 3 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	1	68581504	69974370	1	1	5.49e-15	5.83e-03	8.04e-20	Syt5
2	5	137682119	138752373	1	1	3.45e-28	2.59e-01	8.18e-15	Stk40
3	8	33238527	34621030	1	1	2.67e-07	4.68e-03	6.72e-02	Hyls1

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	4.29	1	0	0	0	1e+00	Stk40
BMI without tail	4.6	1	0	0	0	1e+00	Stk40
Body weight	3.3	2	0	0	0	1e+00	Syt5 Stk40
Glucose	18.12	2	1	33.3	0	1e+00	Syt5 Stk40
Right kidney weight	2.57	1	0	0	0	1e+00	Syt5
Tail length	3.34	1	0	0	0	1e+00	Stk40
Length without tail	3.25	1	0	0	0	1e+00	Syt5
Liver weight, left	10.21	1	0	0	0	1e+00	Syt5
Liver weight, right	11.2	1	0	0	0	1e+00	Syt5
Extensor digitorum longus weight	5.66	1	0	0	0	1e+00	Stk40
Soleus weight	14.02	1	1	33.3	0	1e+00	Stk40
Tibialis anterior weight	2.08	2	0	0	0	1e+00	Syt5 Stk40
Tibia length	7.53	1	0	0	0	1e+00	Syt5
Std. dev. time between licks in bursts	22.72	1	1	33.3	0	1e+00	Syt5
Indifference point 0 sec	6.32	1	0	0	0	1e+00	Syt5
Indifference point AUC	6.34	1	0	0	0	1e+00	Stk40
Indifference point function ln k	8.79	1	0	0	0	1e+00	Syt5
Indifference point function log k	8.79	1	0	0	0	1e+00	Syt5
Delay discounting total patch changes 0 sec	5.75	1	0	0	0	1e+00	Syt5
Delay discounting total patch changes 18 sec	6.87	1	0	0	0	1e+00	Stk40
Delay discounting total patch changes 24 sec	10.35	1	0	0	0	1e+00	Syt5
Delay discounting time to switch 0 sec	55.89	1	1	33.3	0	1e+00	Syt5
Delay discounting water rate 0 sec	10.34	1	0	0	0	1e+00	Syt5
Delay discounting water rate 12 sec	22.12	1	1	33.3	0	1e+00	Syt5
Delay discounting water rate 18 sec	19.1	1	0	0	0	1e+00	Syt5
Delay discounting water rate 24 sec	7.99	1	0	0	0	1e+00	Syt5
Locomotor testing rearing	15	1	0	0	0	1e+00	Stk40
Light reinforcement 1	21.59	1	1	33.3	0	1e+00	Syt5
Light reinforcement 2	21.57	1	1	33.3	0	1e+00	Syt5
Reaction time number correct	4.38	1	0	0	0	1e+00	Stk40
Reaction time num false alarms	4.92	2	0	0	0	1e+00	Hyls1 Stk40
Reaction time num false alarms AUC	9.71	3	0	0	0	1e+00	Hyls1 Syt5 Stk40
Reaction time trials correct on left	4.38	1	0	0	0	1e+00	Stk40
Reaction time trials on left	4.71	1	0	0	0	1e+00	Stk40
Reaction time mean	5.11	1	0	0	0	1e+00	Syt5
Reaction time mean AUC	6.17	1	0	0	0	1e+00	Syt5
Median of all reaction times	6.98	1	0	0	0	1e+00	Syt5
Reaction time omissions	5.26	1	0	0	0	1e+00	Syt5
Reaction time false alarm rate	5.47	2	0	0	0	1e+00	Hyls1 Syt5
Reaction time premature initiations	4.23	1	0	0	0	1e+00	Stk40
Reaction time trials completed	4.71	1	0	0	0	1e+00	Stk40
Reaction time trials AUC	5.59	1	0	0	0	1e+00	Stk40
Social response proportion	7.98	1	0	0	0	1e+00	Syt5
Social time	18.13	1	0	0	0	1e+00	Syt5
Conditioned locomotion	5.6	2	0	0	0	1e+00	Syt5 Stk40
Cocaine response after cond. corrected	18.2	1	0	0	0	1e+00	Syt5
Cocaine response after cond. not corrected	16.42	1	0	0	0	1e+00	Syt5
Cocaine response before conditioning	6.62	1	0	0	0	1e+00	Stk40
Saline control response	9.68	2	0	0	0	1e+00	Hyls1 Syt5
Condit. Reinf. lever presses	8.57	2	0	0	0	1e+00	Syt5 Stk40
Pavlov. Cond. change in total contacts	5.83	1	0	0	0	1e+00	Syt5
Conditioned reinforcement - actives	22.28	1	0	0	0	1e+00	Syt5
Conditioned locomotion	15.14	1	0	0	0	1e+00	Syt5
Intermittent access intake day 1-15 change	7.2	1	0	0	0	1e+00	Syt5
Intermitt. access day 1 inactive lever presses	19.07	1	0	0	0	1e+00	Syt5
Intermitt. access day 15 inactive lever presses	38.52	1	1	33.3	0	1e+00	Syt5
Intermitt. access escalation Index	17.22	1	0	0	0	1e+00	Syt5
Intermittent access standard deviation	9.35	1	0	0	0	1e+00	Syt5
Post-drug Anxiety	10.17	1	0	0	0	1e+00	Syt5
Baseline Anxiety	26.3	1	1	33.3	0	1e+00	Syt5
Incentive Sensitization - Responses	6.78	1	0	0	0	1e+00	Syt5
Incentive Sensitization - Breakpoint	8.61	1	0	0	0	1e+00	Syt5
Short access day 1 total inactive lever presses	24.45	1	1	33.3	0	1e+00	Syt5
Short access day 10 total inactive lever presses	6.32	1	0	0	0	1e+00	Stk40
Short access day 10 total locomotion	11.18	1	0	0	0	1e+00	Syt5
Short access total locomotion	13.05	1	0	0	0	1e+00	Syt5
One hour access (shock baseline)	24.39	1	1	33.3	0	1e+00	Syt5
Number of responses in last shaping day	9.84	1	0	0	0	1e+00	Syt5
Locomotion velocity, session 1	61.51	1	1	33.3	0	1e+00	Syt5
Locomotion distance, session 1	22.42	1	1	33.3	0	1e+00	Syt5
Locomotion velocity, session 2	20.55	1	0	0	0	1e+00	Syt5
Locomotion distance, session 2	5.4	1	0	0	0	1e+00	Syt5
Locomotion distance, session 3	8.71	1	0	0	0	1e+00	Syt5
Locomotion velocity, session 7	5.99	1	0	0	0	1e+00	Syt5
Locomotion distance, session 7	10.24	1	0	0	0	1e+00	Syt5
Locomotion velocity, session 8	15.73	1	0	0	0	1e+00	Syt5
Locomotion distance, session 8	9.21	1	0	0	0	1e+00	Syt5
Condit. Reinf. active minus inactive responses	14.65	1	0	0	0	1e+00	Stk40
Condit. Reinf. active-inactive response ratio	8.92	1	0	0	0	1e+00	Stk40
Condit. Reinf. active responses	8.2	1	0	0	0	1e+00	Stk40
Incentive salience index mean	28.28	1	1	33.3	0	1e+00	Stk40
Condit. Reinf. lever presses	24.79	1	1	33.3	0	1e+00	Stk40
Time in familiar zone, hab. session 1	12.82	1	0	0	0	1e+00	Syt5
Total zone transitions, hab. session 1	25.53	1	1	33.3	0	1e+00	Syt5
Total locomotion distance, hab. session 1	19.26	1	1	33.3	0	1e+00	Syt5
Locomotion velocity, hab. session 1	12.27	1	0	0	0	1e+00	Syt5
Time in familiar zone, hab. session 2	14.1	1	0	0	0	1e+00	Syt5
Total zone transitions, hab. session 2	7.86	1	0	0	0	1e+00	Syt5
Total locomotion distance, hab. session 2	10.72	1	0	0	0	1e+00	Syt5
Locomotion velocity, hab. session 2	13.63	1	0	0	0	1e+00	Syt5
Novelty place preference	5.87	1	0	0	0	1e+00	Stk40
Time in novel zone, NPP test	5.48	1	0	0	0	1e+00	Stk40
Total zone transitions, NPP test	4.12	1	0	0	0	1e+00	Syt5
Pavlov. Cond. lever latency	13.9	1	0	0	0	1e+00	Stk40
Pavlov. Cond. magazine entry latency	9.49	2	0	0	0	1e+00	Syt5 Stk40
Pavlov. Cond. change in total contacts	8.91	1	0	0	0	1e+00	Stk40
Pavlov. Cond. index score	9.42	1	0	0	0	1e+00	Stk40
Pavlov. Cond. latency score	7.62	1	0	0	0	1e+00	Stk40
Pavlov. Cond. lever contacts	10.64	1	0	0	0	1e+00	Stk40
Pavlov. Cond. intertrial magazine entries	15.94	2	0	0	0	1e+00	Syt5 Stk40
Pavlov. Cond. lever-magazine prob. diff.	11.11	1	0	0	0	1e+00	Stk40
Pavlov. Cond. response bias	10.58	2	0	0	0	1e+00	Syt5 Stk40
Bone: apparent density	13.14	1	0	0	0	1e+00	Stk40
Bone surface	18.86	1	1	33.3	0	1e+00	Stk40
Bone volume	28.24	1	1	33.3	0	1e+00	Stk40
Bone: connectivity density	7.46	1	0	0	0	1e+00	Stk40
Bone: cortical area	13.82	1	0	0	0	1e+00	Hyls1
Bone: cortical porosity	8.08	1	0	0	0	1e+00	Hyls1
Bone: cortical porosity	7.76	2	0	0	0	1e+00	Hyls1 Syt5
Bone: cortical thickness	8.18	1	0	0	0	1e+00	Hyls1
Bone: cortical thickness	8.82	1	0	0	0	1e+00	Hyls1
Bone: elastic displacement	7.66	1	0	0	0	1e+00	Syt5
Bone: elastic work	7.91	2	0	0	0	1e+00	Hyls1 Syt5
Bone: endosteal estimation	6.58	1	0	0	0	1e+00	Stk40
Bone: endosteal perimeter	3.03	1	0	0	0	1e+00	Stk40
Bone: final force	8.15	1	0	0	0	1e+00	Hyls1
Bone: final moment	6.98	1	0	0	0	1e+00	Hyls1
Bone: marrow area	6.24	1	0	0	0	1e+00	Stk40
Bone: maximum diameter	3.32	1	0	0	0	1e+00	Hyls1
Bone: maximum force	14.02	1	0	0	0	1e+00	Hyls1
Bone: maximum moment	12.16	1	0	0	0	1e+00	Hyls1
Bone: minimum diameter	4.61	2	0	0	0	1e+00	Hyls1 Stk40
Bone: periosteal estimation	5.53	2	0	0	0	1e+00	Hyls1 Stk40
Bone: periosteal perimeter	5.66	2	0	0	0	1e+00	Hyls1 Stk40
Bone: post-yield work	11.59	1	0	0	0	1e+00	Syt5
Bone: stiffness	7.14	2	0	0	0	1e+00	Hyls1 Syt5
Bone: tissue strength	13.13	1	0	0	0	1e+00	Syt5
Bone: trabecular number	7.06	1	0	0	0	1e+00	Stk40
Bone: trabecular thickness	5.74	1	0	0	0	1e+00	Hyls1
Bone: trabecular tissue density	6.16	2	0	0	0	1e+00	Syt5 Stk40
Distance traveled before self-admin	57.56	1	1	33.3	0	1e+00	Syt5
Distance traveled after self-admin	56.65	1	1	33.3	0	1e+00	Syt5
Delta time in open arm before/after self-admin	18.04	1	0	0	0	1e+00	Syt5
Diff in mean of infusions in LGA sessions	20.43	1	0	0	0	1e+00	Syt5
Extinction: sum of active levers before priming	36.46	1	1	33.3	0	1e+00	Syt5
Active lever presses in extinction session 6	17.94	1	0	0	0	1e+00	Syt5
Time in closed arm after self-admin	22.26	1	0	0	0	1e+00	Syt5
Time in open arm after self-admin	17.09	1	0	0	0	1e+00	Syt5
Sum of active levers in priming session hrs 5-6	17.22	1	0	0	0	1e+00	Syt5
Time to tail flick, test, before self-admin	57.17	1	1	33.3	0	1e+00	Syt5
Time to tail flick, test, after self-admin	5.74	1	0	0	0	1e+00	Syt5
Delta time to tail flick, vehicle, before/after SA	8.61	1	0	0	0	1e+00	Syt5
Delta time to tail flick, test, before/after SA	42.42	1	1	33.3	0	1e+00	Syt5
Ambulatory time before self-admin	36.65	1	1	33.3	0	1e+00	Syt5
Ambulatory time after self-admin	61.31	1	1	33.3	0	1e+00	Syt5
Total heroin consumption	5.77	1	0	0	0	1e+00	Syt5
Delay disc. indifference point, 0s delay	27.96	1	1	33.3	0	1e+00	Syt5
Delay disc. indifference point, 16s delay	24.13	1	0	0	0	1e+00	Syt5
Delay disc. indifference point, 24s delay	9.61	1	0	0	0	1e+00	Syt5
Change in fecal boli incidents, locomotor task	6.15	1	0	0	0	1e+00	Syt5
Bouts of movement, locomotor time 1	56.89	1	1	33.3	0	1e+00	Syt5
Total resting periods, locomotor time 1	37.3	1	1	33.3	0	1e+00	Syt5
Rest time, locomotor task time 1	5.42	1	0	0	0	1e+00	Stk40
Vertical activity count, locomotor time 1	24.22	1	0	0	0	1e+00	Syt5
Rest time, locomotor task time 2	9.12	1	0	0	0	1e+00	Syt5
Vertical activity count, locomotor time 2	5.62	1	0	0	0	1e+00	Syt5
Weight adjusted by age	8.26	1	0	0	0	1e+00	Syt5
Seeking ratio, delayed vs. immediate footshock	29.67	1	1	33.3	0	1e+00	Syt5
Locomotion in novel chamber	12.66	1	0	0	0	1e+00	Syt5
Progressive ratio	7.56	1	0	0	0	1e+00	Syt5
Food seeking constrained by brief footshock	133.39	1	1	33.3	0	1e+00	Syt5
Seeking ratio, punishment vs. effort	16.51	1	0	0	0	1e+00	Syt5
Run reversals in cocaine runway, females	8.33	1	0	0	0	1e+00	Syt5
Cd content in liver	7.99	2	0	0	0	1e+00	Syt5 Stk40
Co content in liver	19.62	2	0	0	0	1e+00	Hyls1 Syt5
Cu content in liver	4.78	1	0	0	0	1e+00	Stk40
Mg content in liver	13.66	1	0	0	0	1e+00	Stk40
Rb content in liver	6.49	1	0	0	0	1e+00	Syt5
Se content in liver	12.67	1	0	0	0	1e+00	Stk40
Zn content in liver	12.43	1	0	0	0	1e+00	Syt5

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	0.88
Adipose	alternative TSS	0	0	0.86
Adipose	gene expression	1	0	0.93
Adipose	isoform ratio	0	0	0.93
Adipose	intron excision ratio	0	0	0.88
Adipose	mRNA stability	0	0	0.9
BLA	alternative polyA	0	0	0.89
BLA	alternative TSS	0	0	0.9
BLA	gene expression	0	0	0.92
BLA	isoform ratio	0	0	0.96
BLA	intron excision ratio	0	0	0.9
BLA	mRNA stability	1	0	0.94
Brain	alternative polyA	0	0	0.9
Brain	alternative TSS	0	0	0.94
Brain	gene expression	0	0	0.91
Brain	isoform ratio	0	0	0.96
Brain	intron excision ratio	0	0	0.92
Brain	mRNA stability	0	0	0.96
Eye	alternative polyA	0	0	0.9
Eye	alternative TSS	0	0	0.82
Eye	gene expression	0	0	0.94
Eye	isoform ratio	0	0	0.81
Eye	intron excision ratio	0	0	0.83
Eye	mRNA stability	0	0	0.87
IL	alternative polyA	0	0	0.92
IL	alternative TSS	0	0	0.83
IL	gene expression	0	0	0.95
IL	isoform ratio	0	0	0.97
IL	intron excision ratio	0	0	0.96
IL	mRNA stability	0	0	0.91
LHb	alternative polyA	0	0	0.8
LHb	alternative TSS	0	0	1.02
LHb	gene expression	0	0	0.91
LHb	isoform ratio	0	0	0.82
LHb	intron excision ratio	0	0	0.92
LHb	mRNA stability	0	0	0.87
Liver	alternative polyA	0	0	0.79
Liver	alternative TSS	0	0	0.87
Liver	gene expression	0	0	0.91
Liver	isoform ratio	0	0	0.89
Liver	intron excision ratio	0	0	0.9
Liver	mRNA stability	1	0	1
NAcc	alternative polyA	0	0	0.92
NAcc	alternative TSS	0	0	0.91
NAcc	gene expression	0	0	0.93
NAcc	isoform ratio	0	0	0.95
NAcc	intron excision ratio	0	0	0.9
NAcc	mRNA stability	0	0	0.94
OFC	alternative polyA	0	0	0.87
OFC	alternative TSS	0	0	0.79
OFC	gene expression	0	0	0.93
OFC	isoform ratio	0	0	0.94
OFC	intron excision ratio	0	0	0.97
OFC	mRNA stability	0	0	0.94
PL	alternative polyA	0	0	0.89
PL	alternative TSS	0	0	0.88
PL	gene expression	0	0	0.92
PL	isoform ratio	0	0	0.95
PL	intron excision ratio	0	0	0.91
PL	mRNA stability	0	0	0.92