Hub : Traits

Sr content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

3 significantly associated models · 3 unique genes

Significant Loci

# chr p0 p1 # assoc genes # joint models best TWAS P best SNP P cond SNP P % var exp joint genes
1 1 68581504 69974370 1 1 5.5e-15 0.0058 8.0e-20 -992 Syt5
2 5 137682119 138752373 1 1 3.5e-28 0.2586 8.2e-15 -4625 Stk40
3 8 33238527 34621030 1 1 2.7e-07 0.0047 6.7e-02 58 Hyls1

p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.

Pleiotropic Associations

Trait chisq ratio # genes+ # genes++ % genes++ corr corr P genes
BMI with tail 4.3 1 0 0 0 1 Stk40
BMI without tail 4.6 1 0 0 0 1 Stk40
Body weight 3.3 2 0 0 0 1 Syt5 Stk40
Glucose 18.1 2 1 33 0 1 Syt5 Stk40
Right kidney weight 2.6 1 0 0 0 1 Syt5
Tail length 3.3 1 0 0 0 1 Stk40
Length without tail 3.2 1 0 0 0 1 Syt5
Liver weight, left 10.2 1 0 0 0 1 Syt5
Liver weight, right 11.2 1 0 0 0 1 Syt5
Extensor digitorum longus weight 5.7 1 0 0 0 1 Stk40
Soleus weight 14.0 1 1 33 0 1 Stk40
Tibialis anterior weight 2.1 2 0 0 0 1 Syt5 Stk40
Tibia length 7.5 1 0 0 0 1 Syt5
Std. dev. time between licks in bursts 22.7 1 1 33 0 1 Syt5
Indifference point 0 sec 6.3 1 0 0 0 1 Syt5
Indifference point AUC 6.3 1 0 0 0 1 Stk40
Indifference point function ln k 8.8 1 0 0 0 1 Syt5
Indifference point function log k 8.8 1 0 0 0 1 Syt5
Delay discounting total patch changes 0 sec 5.8 1 0 0 0 1 Syt5
Delay discounting total patch changes 18 sec 6.9 1 0 0 0 1 Stk40
Delay discounting total patch changes 24 sec 10.3 1 0 0 0 1 Syt5
Delay discounting time to switch 0 sec 55.9 1 1 33 0 1 Syt5
Delay discounting water rate 0 sec 10.3 1 0 0 0 1 Syt5
Delay discounting water rate 12 sec 22.1 1 1 33 0 1 Syt5
Delay discounting water rate 18 sec 19.1 1 0 0 0 1 Syt5
Delay discounting water rate 24 sec 8.0 1 0 0 0 1 Syt5
Locomotor testing rearing 15.0 1 0 0 0 1 Stk40
Light reinforcement 1 21.6 1 1 33 0 1 Syt5
Light reinforcement 2 21.6 1 1 33 0 1 Syt5
Reaction time number correct 4.4 1 0 0 0 1 Stk40
Reaction time num false alarms 4.9 2 0 0 0 1 Hyls1 Stk40
Reaction time num false alarms AUC 9.7 3 0 0 0 1 Hyls1 Syt5 Stk40
Reaction time trials correct on left 4.4 1 0 0 0 1 Stk40
Reaction time trials on left 4.7 1 0 0 0 1 Stk40
Reaction time mean 5.1 1 0 0 0 1 Syt5
Reaction time mean AUC 6.2 1 0 0 0 1 Syt5
Median of all reaction times 7.0 1 0 0 0 1 Syt5
Reaction time omissions 5.3 1 0 0 0 1 Syt5
Reaction time false alarm rate 5.5 2 0 0 0 1 Hyls1 Syt5
Reaction time premature initiations 4.2 1 0 0 0 1 Stk40
Reaction time trials completed 4.7 1 0 0 0 1 Stk40
Reaction time trials AUC 5.6 1 0 0 0 1 Stk40
Social response proportion 8.0 1 0 0 0 1 Syt5
Social time 18.1 1 0 0 0 1 Syt5
Conditioned locomotion 5.6 2 0 0 0 1 Syt5 Stk40
Cocaine response after cond. corrected 18.2 1 0 0 0 1 Syt5
Cocaine response after cond. not corrected 16.4 1 0 0 0 1 Syt5
Cocaine response before conditioning 6.6 1 0 0 0 1 Stk40
Saline control response 9.7 2 0 0 0 1 Hyls1 Syt5
Condit. Reinf. lever presses 8.6 2 0 0 0 1 Syt5 Stk40
Pavlov. Cond. change in total contacts 5.8 1 0 0 0 1 Syt5
Conditioned reinforcement - actives 22.3 1 0 0 0 1 Syt5
Conditioned locomotion 15.1 1 0 0 0 1 Syt5
Intermittent access intake day 1-15 change 7.2 1 0 0 0 1 Syt5
Intermitt. access day 1 inactive lever presses 19.1 1 0 0 0 1 Syt5
Intermitt. access day 15 inactive lever presses 38.5 1 1 33 0 1 Syt5
Intermitt. access escalation Index 17.2 1 0 0 0 1 Syt5
Intermittent access standard deviation 9.3 1 0 0 0 1 Syt5
Post-drug Anxiety 10.2 1 0 0 0 1 Syt5
Baseline Anxiety 26.3 1 1 33 0 1 Syt5
Incentive Sensitization - Responses 6.8 1 0 0 0 1 Syt5
Incentive Sensitization - Breakpoint 8.6 1 0 0 0 1 Syt5
Short access day 1 total inactive lever presses 24.4 1 1 33 0 1 Syt5
Short access day 10 total inactive lever presses 6.3 1 0 0 0 1 Stk40
Short access day 10 total locomotion 11.2 1 0 0 0 1 Syt5
Short access total locomotion 13.1 1 0 0 0 1 Syt5
One hour access (shock baseline) 24.4 1 1 33 0 1 Syt5
Number of responses in last shaping day 9.8 1 0 0 0 1 Syt5
Locomotion velocity, session 1 61.5 1 1 33 0 1 Syt5
Locomotion distance, session 1 22.4 1 1 33 0 1 Syt5
Locomotion velocity, session 2 20.6 1 0 0 0 1 Syt5
Locomotion distance, session 2 5.4 1 0 0 0 1 Syt5
Locomotion distance, session 3 8.7 1 0 0 0 1 Syt5
Locomotion velocity, session 7 6.0 1 0 0 0 1 Syt5
Locomotion distance, session 7 10.2 1 0 0 0 1 Syt5
Locomotion velocity, session 8 15.7 1 0 0 0 1 Syt5
Locomotion distance, session 8 9.2 1 0 0 0 1 Syt5
Condit. Reinf. active minus inactive responses 14.7 1 0 0 0 1 Stk40
Condit. Reinf. active-inactive response ratio 8.9 1 0 0 0 1 Stk40
Condit. Reinf. active responses 8.2 1 0 0 0 1 Stk40
Incentive salience index mean 28.3 1 1 33 0 1 Stk40
Condit. Reinf. lever presses 24.8 1 1 33 0 1 Stk40
Time in familiar zone, hab. session 1 12.8 1 0 0 0 1 Syt5
Total zone transitions, hab. session 1 25.5 1 1 33 0 1 Syt5
Total locomotion distance, hab. session 1 19.3 1 1 33 0 1 Syt5
Locomotion velocity, hab. session 1 12.3 1 0 0 0 1 Syt5
Time in familiar zone, hab. session 2 14.1 1 0 0 0 1 Syt5
Total zone transitions, hab. session 2 7.9 1 0 0 0 1 Syt5
Total locomotion distance, hab. session 2 10.7 1 0 0 0 1 Syt5
Locomotion velocity, hab. session 2 13.6 1 0 0 0 1 Syt5
Novelty place preference 5.9 1 0 0 0 1 Stk40
Time in novel zone, NPP test 5.5 1 0 0 0 1 Stk40
Total zone transitions, NPP test 4.1 1 0 0 0 1 Syt5
Pavlov. Cond. lever latency 13.9 1 0 0 0 1 Stk40
Pavlov. Cond. magazine entry latency 9.5 2 0 0 0 1 Syt5 Stk40
Pavlov. Cond. change in total contacts 8.9 1 0 0 0 1 Stk40
Pavlov. Cond. index score 9.4 1 0 0 0 1 Stk40
Pavlov. Cond. latency score 7.6 1 0 0 0 1 Stk40
Pavlov. Cond. lever contacts 10.6 1 0 0 0 1 Stk40
Pavlov. Cond. intertrial magazine entries 15.9 2 0 0 0 1 Syt5 Stk40
Pavlov. Cond. lever-magazine prob. diff. 11.1 1 0 0 0 1 Stk40
Pavlov. Cond. response bias 10.6 2 0 0 0 1 Syt5 Stk40
Bone: apparent density 13.1 1 0 0 0 1 Stk40
Bone surface 18.9 1 1 33 0 1 Stk40
Bone volume 28.2 1 1 33 0 1 Stk40
Bone: connectivity density 7.5 1 0 0 0 1 Stk40
Bone: cortical area 13.8 1 0 0 0 1 Hyls1
Bone: cortical porosity 8.1 1 0 0 0 1 Hyls1
Bone: cortical porosity 7.8 2 0 0 0 1 Hyls1 Syt5
Bone: cortical thickness 8.2 1 0 0 0 1 Hyls1
Bone: cortical thickness 8.8 1 0 0 0 1 Hyls1
Bone: elastic displacement 7.7 1 0 0 0 1 Syt5
Bone: elastic work 7.9 2 0 0 0 1 Hyls1 Syt5
Bone: endosteal estimation 6.6 1 0 0 0 1 Stk40
Bone: endosteal perimeter 3.0 1 0 0 0 1 Stk40
Bone: final force 8.2 1 0 0 0 1 Hyls1
Bone: final moment 7.0 1 0 0 0 1 Hyls1
Bone: marrow area 6.2 1 0 0 0 1 Stk40
Bone: maximum diameter 3.3 1 0 0 0 1 Hyls1
Bone: maximum force 14.0 1 0 0 0 1 Hyls1
Bone: maximum moment 12.2 1 0 0 0 1 Hyls1
Bone: minimum diameter 4.6 2 0 0 0 1 Hyls1 Stk40
Bone: periosteal estimation 5.5 2 0 0 0 1 Hyls1 Stk40
Bone: periosteal perimeter 5.7 2 0 0 0 1 Hyls1 Stk40
Bone: post-yield work 11.6 1 0 0 0 1 Syt5
Bone: stiffness 7.1 2 0 0 0 1 Hyls1 Syt5
Bone: tissue strength 13.1 1 0 0 0 1 Syt5
Bone: trabecular number 7.1 1 0 0 0 1 Stk40
Bone: trabecular thickness 5.7 1 0 0 0 1 Hyls1
Bone: trabecular tissue density 6.2 2 0 0 0 1 Syt5 Stk40
Distance traveled before self-admin 57.6 1 1 33 0 1 Syt5
Distance traveled after self-admin 56.6 1 1 33 0 1 Syt5
Delta time in open arm before/after self-admin 18.0 1 0 0 0 1 Syt5
Diff in mean of infusions in LGA sessions 20.4 1 0 0 0 1 Syt5
Extinction: sum of active levers before priming 36.5 1 1 33 0 1 Syt5
Active lever presses in extinction session 6 17.9 1 0 0 0 1 Syt5
Time in closed arm after self-admin 22.3 1 0 0 0 1 Syt5
Time in open arm after self-admin 17.1 1 0 0 0 1 Syt5
Sum of active levers in priming session hrs 5-6 17.2 1 0 0 0 1 Syt5
Time to tail flick, test, before self-admin 57.2 1 1 33 0 1 Syt5
Time to tail flick, test, after self-admin 5.7 1 0 0 0 1 Syt5
Delta time to tail flick, vehicle, before/after SA 8.6 1 0 0 0 1 Syt5
Delta time to tail flick, test, before/after SA 42.4 1 1 33 0 1 Syt5
Ambulatory time before self-admin 36.6 1 1 33 0 1 Syt5
Ambulatory time after self-admin 61.3 1 1 33 0 1 Syt5
Total heroin consumption 5.8 1 0 0 0 1 Syt5
Delay disc. indifference point, 0s delay 28.0 1 1 33 0 1 Syt5
Delay disc. indifference point, 16s delay 24.1 1 0 0 0 1 Syt5
Delay disc. indifference point, 24s delay 9.6 1 0 0 0 1 Syt5
Change in fecal boli incidents, locomotor task 6.2 1 0 0 0 1 Syt5
Bouts of movement, locomotor time 1 56.9 1 1 33 0 1 Syt5
Total resting periods, locomotor time 1 37.3 1 1 33 0 1 Syt5
Rest time, locomotor task time 1 5.4 1 0 0 0 1 Stk40
Vertical activity count, locomotor time 1 24.2 1 0 0 0 1 Syt5
Rest time, locomotor task time 2 9.1 1 0 0 0 1 Syt5
Vertical activity count, locomotor time 2 5.6 1 0 0 0 1 Syt5
Weight adjusted by age 8.3 1 0 0 0 1 Syt5
Seeking ratio, delayed vs. immediate footshock 29.7 1 1 33 0 1 Syt5
Locomotion in novel chamber 12.7 1 0 0 0 1 Syt5
Progressive ratio 7.6 1 0 0 0 1 Syt5
Food seeking constrained by brief footshock 133.4 1 1 33 0 1 Syt5
Seeking ratio, punishment vs. effort 16.5 1 0 0 0 1 Syt5
Run reversals in cocaine runway, females 8.3 1 0 0 0 1 Syt5
Cd content in liver 8.0 2 0 0 0 1 Syt5 Stk40
Co content in liver 19.6 2 0 0 0 1 Hyls1 Syt5
Cu content in liver 4.8 1 0 0 0 1 Stk40
Mg content in liver 13.7 1 0 0 0 1 Stk40
Rb content in liver 6.5 1 0 0 0 1 Syt5
Se content in liver 12.7 1 0 0 0 1 Stk40
Zn content in liver 12.4 1 0 0 0 1 Syt5

chisq ratio: Average Chi2 statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes+: Shared significant genes at Bonferroni correction. # genes++: Shared significant genes at transcriptome-wide significance. % genes++: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.

Associations by panel

tissue modality # hits % hits/tests avg chisq
Adipose alternative polyA 0 0.000 0.88
Adipose alternative TSS 0 0.000 0.86
Adipose gene expression 1 0.012 0.93
Adipose isoform ratio 0 0.000 0.93
Adipose intron excision ratio 0 0.000 0.88
Adipose mRNA stability 0 0.000 0.90
BLA alternative polyA 0 0.000 0.89
BLA alternative TSS 0 0.000 0.90
BLA gene expression 0 0.000 0.92
BLA isoform ratio 0 0.000 0.96
BLA intron excision ratio 0 0.000 0.90
BLA mRNA stability 1 0.049 0.94
Brain alternative polyA 0 0.000 0.90
Brain alternative TSS 0 0.000 0.94
Brain gene expression 0 0.000 0.91
Brain isoform ratio 0 0.000 0.96
Brain intron excision ratio 0 0.000 0.92
Brain mRNA stability 0 0.000 0.96
Eye alternative polyA 0 0.000 0.90
Eye alternative TSS 0 0.000 0.82
Eye gene expression 0 0.000 0.94
Eye isoform ratio 0 0.000 0.81
Eye intron excision ratio 0 0.000 0.83
Eye mRNA stability 0 0.000 0.87
IL alternative polyA 0 0.000 0.92
IL alternative TSS 0 0.000 0.83
IL gene expression 0 0.000 0.95
IL isoform ratio 0 0.000 0.97
IL intron excision ratio 0 0.000 0.96
IL mRNA stability 0 0.000 0.91
LHb alternative polyA 0 0.000 0.80
LHb alternative TSS 0 0.000 1.02
LHb gene expression 0 0.000 0.91
LHb isoform ratio 0 0.000 0.82
LHb intron excision ratio 0 0.000 0.92
LHb mRNA stability 0 0.000 0.87
Liver alternative polyA 0 0.000 0.79
Liver alternative TSS 0 0.000 0.87
Liver gene expression 0 0.000 0.91
Liver isoform ratio 0 0.000 0.89
Liver intron excision ratio 0 0.000 0.90
Liver mRNA stability 1 0.041 1.00
NAcc alternative polyA 0 0.000 0.92
NAcc alternative TSS 0 0.000 0.91
NAcc gene expression 0 0.000 0.93
NAcc isoform ratio 0 0.000 0.95
NAcc intron excision ratio 0 0.000 0.90
NAcc mRNA stability 0 0.000 0.94
OFC alternative polyA 0 0.000 0.87
OFC alternative TSS 0 0.000 0.79
OFC gene expression 0 0.000 0.93
OFC isoform ratio 0 0.000 0.94
OFC intron excision ratio 0 0.000 0.97
OFC mRNA stability 0 0.000 0.94
PL alternative polyA 0 0.000 0.89
PL alternative TSS 0 0.000 0.88
PL gene expression 0 0.000 0.92
PL isoform ratio 0 0.000 0.95
PL intron excision ratio 0 0.000 0.91
PL mRNA stability 0 0.000 0.92

avg chisq: Average Chi2 (squared Z-score) across all models in this panel for this trait.