Hub : Traits

Rb content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

27 significantly associated models · 7 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 7 16845355 16970279 1 1 3.6e-10 NaN NA NA NA
2 8 29620582 31650241 4 1 2.5e-08 1.4e-08 0.13 93 Barx2
3 10 46789397 48185455 1 1 2.6e-08 3.5e-01 0.18 -105 Trim16
4 16 75583273 76982669 1 1 2.6e-07 6.9e-02 0.89 99 Adprhl1

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 without tail 171.8 1 1 25 0.00 1.00 NA
Body weight 11.2 1 1 25 0.00 1.00 NA
Epididymis fat weight 136.2 1 1 25 0.00 1.00 NA
Glucose 6.6 1 0 0 0.00 1.00 NA
Heart weight 9.6 2 0 0 0.00 1.00 Trim16 NA
Left kidney weight 62.7 1 1 25 0.00 1.00 NA
Right kidney weight 67.3 1 1 25 0.00 1.00 NA
Tail length 91.1 1 1 25 0.00 1.00 NA
Length with tail 4.0 1 0 0 0.00 1.00 NA
Length without tail 120.2 1 1 25 0.00 1.00 NA
Liver weight, left 15.7 2 1 25 0.00 1.00 Trim16 NA
Liver weight, right 9.6 1 0 0 0.00 1.00 NA
Parametrial fat weight 26.4 1 1 25 0.00 1.00 NA
Retroperitoneal fat weight 4.2 1 0 0 0.00 1.00 NA
Intraocular pressure 34.1 2 2 50 0.00 1.00 Trim16 NA
Extensor digitorum longus weight 39.2 1 1 25 0.00 1.00 NA
Soleus weight 21.9 1 1 25 0.00 1.00 NA
Tibialis anterior weight 96.0 1 1 25 0.00 1.00 NA
Tibia length 7.4 1 0 0 0.00 1.00 NA
Number of licking bursts 130.8 2 1 25 0.00 1.00 Trim16 NA
Food consumed during 24 hour testing period 18.0 2 0 0 0.00 1.00 Trim16 NA
Times rat made contact with spout 69.1 2 1 25 0.00 1.00 Trim16 NA
Mean time between licks in bursts 90.5 1 1 25 0.00 1.00 NA
Mean num. licks in bursts 152.1 2 2 50 0.00 1.00 Trim16 NA
Std. dev. time between licks in bursts 291.0 1 1 25 0.00 1.00 NA
Water consumed over 24 hours 23.8 1 1 25 0.00 1.00 Trim16
Indifference point 0 sec 14.6 2 1 25 0.00 1.00 Trim16 NA
Indifference point AUC 66.7 1 1 25 0.00 1.00 NA
Delay discounting total patch changes 0 sec 14.3 2 1 25 0.00 1.00 Trim16 NA
Delay discounting total patch changes 12 sec 156.9 1 1 25 0.00 1.00 NA
Delay discounting total patch changes 18 sec 161.7 2 2 50 0.00 1.00 Trim16 NA
Delay discounting total patch changes 24 sec 43.7 1 1 25 0.00 1.00 NA
Delay discounting total patch changes 6 sec 145.0 1 1 25 0.00 1.00 NA
Delay discounting water rate 0 sec 13.4 2 0 0 0.00 1.00 Trim16 NA
Delay discounting water rate 12 sec 44.2 1 1 25 0.00 1.00 NA
Delay discounting water rate 18 sec 10.5 1 0 0 0.00 1.00 NA
Delay discounting water rate 24 sec 100.9 1 1 25 0.00 1.00 NA
Delay discounting water rate 6 sec 38.7 2 1 25 0.00 1.00 Trim16 NA
Locomotor testing distance 14.0 1 0 0 0.00 1.00 NA
Locomotor testing rearing 23.9 1 1 25 0.00 1.00 NA
Light reinforcement 1 84.1 1 1 25 0.00 1.00 NA
Reaction time number correct 8.5 2 0 0 0.00 1.00 Trim16 NA
Reaction time num false alarms 90.1 1 1 25 0.00 1.00 NA
Reaction time num false alarms AUC 128.2 1 1 25 0.00 1.00 NA
Reaction time trials correct on left 8.5 2 0 0 0.00 1.00 Trim16 NA
Reaction time trials on left 8.6 2 0 0 0.00 1.00 Trim16 NA
Reaction time mean 62.5 1 1 25 0.00 1.00 NA
Reaction time mean AUC 89.1 1 1 25 0.00 1.00 NA
Median of all reaction times 80.2 1 1 25 0.00 1.00 NA
Reaction time omissions 7.4 1 0 0 0.00 1.00 Kcnj5
Reaction time false alarm rate 104.2 1 1 25 0.00 1.00 NA
Reaction time premature initiation rate 47.3 1 1 25 0.00 1.00 NA
Reaction time premature initiations 49.8 1 1 25 0.00 1.00 NA
Std. dev. reaction times 27.0 1 1 25 0.00 1.00 NA
Reaction time trials completed 8.6 2 0 0 0.00 1.00 Trim16 NA
Reaction time trials AUC 15.6 1 0 0 0.00 1.00 NA
Social responses 108.6 1 1 25 0.00 1.00 NA
Social time 16.8 2 1 25 0.00 1.00 Trim16 NA
Cocaine response after cond. corrected 75.1 2 1 25 0.00 1.00 Trim16 NA
Cocaine response after cond. not corrected 96.3 2 1 25 0.00 1.00 Trim16 NA
Cocaine response before conditioning 28.6 1 1 25 0.00 1.00 NA
Saline control response 50.6 1 1 25 0.00 1.00 NA
Condit. Reinf. active minus inactive responses 46.4 1 1 25 0.00 1.00 NA
Condit. Reinf. active-inactive response ratio 68.7 1 1 25 0.00 1.00 NA
Condit. Reinf. active responses 11.1 1 0 0 0.00 1.00 NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.00 NA
Condit. Reinf. lever presses 7.4 1 0 0 0.00 1.00 Trim16
Pavlov. Cond. lever latency 20.8 3 1 25 -0.04 0.96 Barx2 Kcnj5 NA
Pavlov. Cond. magazine entry latency 173.4 1 1 25 0.00 1.00 NA
Pavlov. Cond. change in total contacts 216.7 1 1 25 0.00 1.00 NA
Pavlov. Cond. index score 102.2 1 1 25 0.00 1.00 NA
Pavlov. Cond. latency score 110.3 1 1 25 0.00 1.00 NA
Pavlov. Cond. lever contacts 10.9 4 1 25 -0.38 0.45 Barx2 Arhgap32 Kcnj5 NA
Pavlov. Cond. magazine entry number 244.9 1 1 25 0.00 1.00 NA
Pavlov. Cond. intertrial magazine entries 106.2 1 1 25 0.00 1.00 NA
Pavlov. Cond. lever-magazine prob. diff. 90.6 1 1 25 0.00 1.00 NA
Pavlov. Cond. response bias 22.1 3 1 25 0.00 1.00 Arhgap32 Kcnj5 NA
Conditioned reinforcement - actives 18.5 1 0 0 0.00 1.00 NA
Conditioned locomotion 9.9 1 0 0 0.00 1.00 NA
Intermittent access intake day 1-15 change 104.0 1 1 25 0.00 1.00 NA
Intermittent access intake escalation 141.1 1 1 25 0.00 1.00 NA
Intermittent access intake escalation 2 42.5 1 1 25 0.00 1.00 NA
Intermitt. access day 1 inactive lever presses 33.6 2 2 50 0.00 1.00 Trim16 NA
Intermitt. access escalation Index 27.6 1 0 0 0.00 1.00 Trim16
Intermittent access day 1 total infusions 52.9 1 1 25 0.00 1.00 NA
Intermittent access day 1 locomotion 20.0 2 1 25 0.00 1.00 Trim16 NA
Intermittent access total locomotion 9.9 1 0 0 0.00 1.00 Trim16
Cocaine induced anxiety 31.7 1 1 25 0.00 1.00 Trim16
Post-drug Anxiety 15.6 2 0 0 0.00 1.00 Trim16 NA
Baseline Anxiety 29.9 1 1 25 0.00 1.00 Trim16
Progressive ratio test 1 active lever presses 11.8 1 0 0 0.00 1.00 NA
Progressive ratio test 1 breakpoint 10.4 1 0 0 0.00 1.00 NA
Progressive ratio test 1 inactive lever presses 10.7 2 0 0 0.00 1.00 Trim16 NA
Progressive ratio test 2 active lever presses 12.2 1 0 0 0.00 1.00 NA
Progressive ratio test 2 breakpoint 61.6 1 1 25 0.00 1.00 NA
Total sessions with >9 infusions 13.7 1 0 0 0.00 1.00 Trim16
Short access day 1 total inactive lever presses 13.8 1 0 0 0.00 1.00 Trim16
Short access day 10 total inactive lever presses 12.2 1 0 0 0.00 1.00 NA
Short access day 1 total infusions 62.7 1 1 25 0.00 1.00 Trim16
Short access day 10 total infusions 24.0 1 1 25 0.00 1.00 NA
Short access day 1 locomotion 25.2 2 1 25 0.00 1.00 Trim16 NA
Short access day 10 total locomotion 14.3 1 0 0 0.00 1.00 Trim16
Short access total locomotion 10.1 1 0 0 0.00 1.00 Trim16
Compulsive drug intake 28.7 2 1 25 0.00 1.00 Trim16 NA
One hour access (0.3 mA shock) 10.4 1 0 0 0.00 1.00 NA
Number of responses in last shaping day 25.6 1 1 25 0.00 1.00 Trim16
Context. condit. distance diff. score 240.2 1 1 25 0.00 1.00 NA
Locomotion velocity, session 1 190.8 1 1 25 0.00 1.00 NA
Locomotion distance, session 1 320.8 2 2 50 0.00 1.00 Trim16 NA
Locomotion velocity, session 2 139.6 1 1 25 0.00 1.00 NA
Locomotion distance, session 2 642.8 2 1 25 0.00 1.00 Trim16 NA
Locomotion velocity, session 3 178.9 1 1 25 0.00 1.00 NA
Locomotion distance, session 3 117.5 1 1 25 0.00 1.00 NA
Stereotopy head waving bouts, day 3 8.8 1 0 0 0.00 1.00 NA
Stereotopy head waving duration, day 3 33.2 1 1 25 0.00 1.00 NA
Locomotion velocity, session 7 98.9 1 1 25 0.00 1.00 NA
Locomotion distance, session 7 31.8 1 1 25 0.00 1.00 NA
Stereotopy head waving bouts, day 7 46.9 2 2 50 0.00 1.00 Trim16 NA
Stereotopy head waving duration, day 7 102.2 1 1 25 0.00 1.00 NA
Locomotion distance, session 8 89.4 2 1 25 0.00 1.00 Kcnj5 NA
Degree of sensitization distance 198.5 1 1 25 0.00 1.00 NA
Degree of sensitization stereotypy 37.5 1 1 25 0.00 1.00 NA
Condit. Reinf. active-inactive response ratio 107.3 1 1 25 0.00 1.00 NA
Condit. Reinf. active responses 20.0 1 0 0 0.00 1.00 NA
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.00 NA
Incentive salience index mean 15.6 1 0 0 0.00 1.00 NA
Condit. Reinf. lever presses 35.1 1 1 25 0.00 1.00 NA
Time in familiar zone, hab. session 1 16.4 1 0 0 0.00 1.00 NA
Time in novel zone, hab. session 1 17.4 1 0 0 0.00 1.00 NA
Total zone transitions, hab. session 1 355.6 2 2 50 0.00 1.00 Trim16 NA
Total locomotion distance, hab. session 1 158.9 2 2 50 0.00 1.00 Trim16 NA
Locomotion velocity, hab. session 1 189.9 2 2 50 0.00 1.00 Trim16 NA
Time in familiar zone, hab. session 2 48.9 1 1 25 0.00 1.00 NA
Time in novel zone, hab. session 2 58.4 1 1 25 0.00 1.00 NA
Total zone transitions, hab. session 2 421.2 1 1 25 0.00 1.00 NA
Total locomotion distance, hab. session 2 112.9 2 1 25 0.00 1.00 Trim16 NA
Locomotion velocity, hab. session 2 117.5 2 1 25 0.00 1.00 Trim16 NA
Total zone transitions, NPP test 376.1 1 1 25 0.00 1.00 NA
Total locomotion distance, NPP test 269.3 1 1 25 0.00 1.00 NA
Locomotion velocity, NPP test 317.8 1 1 25 0.00 1.00 NA
Pavlov. Cond. lever latency 9.3 1 0 0 0.00 1.00 NA
Pavlov. Cond. magazine entry latency 63.4 2 2 50 0.00 1.00 Trim16 NA
Pavlov. Cond. change in total contacts 40.1 1 1 25 0.00 1.00 NA
Pavlov. Cond. index score 31.3 2 1 25 0.00 1.00 Trim16 NA
Pavlov. Cond. latency score 16.6 1 0 0 0.00 1.00 NA
Pavlov. Cond. lever contacts 16.1 1 0 0 0.00 1.00 NA
Pavlov. Cond. magazine entry number 44.8 2 2 50 0.00 1.00 Trim16 NA
Pavlov. Cond. intertrial magazine entries 14.4 1 0 0 0.00 1.00 Trim16
Pavlov. Cond. lever-magazine prob. diff. 49.2 2 1 25 0.00 1.00 Trim16 NA
Pavlov. Cond. response bias 30.3 2 1 25 0.00 1.00 Trim16 NA
Bone: apparent density 31.2 1 1 25 0.00 1.00 NA
Bone surface 41.3 1 1 25 0.00 1.00 NA
Bone volume 47.7 1 1 25 0.00 1.00 NA
Bone: connectivity density 8.5 1 0 0 0.00 1.00 NA
Bone: cortical apparent density 18.1 1 0 0 0.00 1.00 Trim16
Bone: cortical porosity 105.0 2 1 25 0.00 1.00 Trim16 NA
Bone: cortical porosity 91.6 2 2 50 0.00 1.00 Trim16 NA
Bone: cortical thickness 8.8 1 0 0 0.00 1.00 NA
Bone: cortical thickness 17.9 1 0 0 0.00 1.00 NA
Bone: cortical tissue density 19.6 1 0 0 0.00 1.00 Trim16
Bone: elastic displacement 28.2 1 1 25 0.00 1.00 NA
Bone: endosteal estimation 18.4 1 1 25 0.00 1.00 NA
Bone: final force 57.4 1 1 25 0.00 1.00 NA
Bone: final moment 45.6 1 1 25 0.00 1.00 NA
Bone: marrow area 15.3 1 1 25 0.00 1.00 NA
Bone: maximum force 60.3 1 1 25 0.00 1.00 NA
Bone: maximum moment 41.2 1 1 25 0.00 1.00 NA
Bone: minimum diameter 86.7 1 1 25 0.00 1.00 NA
Bone: periosteal estimation 10.0 1 0 0 0.00 1.00 NA
Bone: periosteal perimeter 8.8 1 0 0 0.00 1.00 NA
Bone: post-yield work 70.3 2 1 25 0.00 1.00 Trim16 NA
Bone: stiffness 136.8 1 1 25 0.00 1.00 NA
Bone: tissue strength 136.0 1 1 25 0.00 1.00 NA
Bone: trabecular number 64.1 1 1 25 0.00 1.00 NA
Bone: trabecular thickness 13.8 1 0 0 0.00 1.00 NA
Bone: trabecular tissue density 66.6 1 1 25 0.00 1.00 NA
Distance traveled before self-admin 12.6 1 0 0 0.00 1.00 NA
Delta time in open arm before/after self-admin 40.2 1 1 25 0.00 1.00 NA
Extinction: sum of active levers before priming 12.2 1 0 0 0.00 1.00 NA
Delta distance traveled before/after self-admin 11.3 1 0 0 0.00 1.00 NA
Time in closed arm before self-admin 78.0 1 1 25 0.00 1.00 NA
Time in closed arm after self-admin 40.2 1 1 25 0.00 1.00 NA
Time in open arm after self-admin 31.3 1 1 25 0.00 1.00 NA
Delta time to tail flick, test, before/after SA 20.0 1 0 0 0.00 1.00 NA
Fecal boli incidents, locomotor time 1 11.8 1 0 0 0.00 1.00 NA
Time >=10cm from walls, locomotor time 1 19.5 1 0 0 0.00 1.00 NA
Time >=10cm from walls, locomotor time 2 27.2 1 1 25 0.00 1.00 NA
Rest time, locomotor task time 2 8.8 1 0 0 0.00 1.00 NA
Distance moved, locomotor task time 2 13.1 1 0 0 0.00 1.00 NA
Weight adjusted by age 25.0 1 1 25 0.00 1.00 NA
Locomotion in novel chamber 10.2 1 0 0 0.00 1.00 NA
Run reversals in cocaine runway, females 11.6 1 0 0 0.00 1.00 Trim16
Run reversals in cocaine runway, males 39.3 1 1 25 0.00 1.00 NA
Latency to leave start box in cocaine runway 14.8 2 0 0 0.00 1.00 Trim16 NA
Cd content in liver 239.3 1 1 25 0.00 1.00 NA
Co content in liver 143.3 1 1 25 0.00 1.00 NA
Fe content in liver 10.3 1 0 0 0.00 1.00 NA
K content in liver 87.3 1 1 25 0.00 1.00 NA
Mg content in liver 28.9 1 1 25 0.00 1.00 Trim16
Mn content in liver 207.1 1 1 25 0.00 1.00 NA
Se content in liver 33.4 2 1 25 0.00 1.00 Trim16 NA
Zn content in liver 46.0 1 1 25 0.00 1.00 NA

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 1.28
Adipose alternative TSS 1 0.062 1.23
Adipose gene expression 2 0.024 1.24
Adipose isoform ratio 1 0.035 1.31
Adipose intron excision ratio 1 0.034 1.14
Adipose mRNA stability 0 0.000 1.30
BLA alternative polyA 0 0.000 1.33
BLA alternative TSS 0 0.000 1.15
BLA gene expression 2 0.033 1.28
BLA isoform ratio 2 0.114 1.31
BLA intron excision ratio 0 0.000 1.23
BLA mRNA stability 0 0.000 1.35
Brain alternative polyA 0 0.000 1.28
Brain alternative TSS 0 0.000 1.12
Brain gene expression 2 0.022 1.25
Brain isoform ratio 0 0.000 1.21
Brain intron excision ratio 1 0.018 1.21
Brain mRNA stability 0 0.000 1.27
Eye alternative polyA 0 0.000 1.10
Eye alternative TSS 0 0.000 0.92
Eye gene expression 0 0.000 1.33
Eye isoform ratio 0 0.000 1.25
Eye intron excision ratio 0 0.000 1.22
Eye mRNA stability 0 0.000 1.26
IL alternative polyA 0 0.000 1.39
IL alternative TSS 0 0.000 1.05
IL gene expression 0 0.000 1.27
IL isoform ratio 0 0.000 1.14
IL intron excision ratio 0 0.000 1.12
IL mRNA stability 0 0.000 1.32
LHb alternative polyA 0 0.000 1.34
LHb alternative TSS 0 0.000 1.12
LHb gene expression 1 0.031 1.24
LHb isoform ratio 0 0.000 1.24
LHb intron excision ratio 1 0.097 1.17
LHb mRNA stability 0 0.000 1.24
Liver alternative polyA 0 0.000 1.25
Liver alternative TSS 0 0.000 1.17
Liver gene expression 3 0.042 1.24
Liver isoform ratio 0 0.000 1.19
Liver intron excision ratio 0 0.000 1.19
Liver mRNA stability 0 0.000 1.25
NAcc alternative polyA 0 0.000 1.34
NAcc alternative TSS 0 0.000 1.30
NAcc gene expression 2 0.032 1.30
NAcc isoform ratio 1 0.053 1.29
NAcc intron excision ratio 2 0.065 1.25
NAcc mRNA stability 1 0.044 1.34
OFC alternative polyA 0 0.000 1.31
OFC alternative TSS 0 0.000 1.55
OFC gene expression 0 0.000 1.28
OFC isoform ratio 0 0.000 1.22
OFC intron excision ratio 0 0.000 1.16
OFC mRNA stability 0 0.000 1.25
PL alternative polyA 0 0.000 1.37
PL alternative TSS 0 0.000 1.18
PL gene expression 3 0.041 1.27
PL isoform ratio 1 0.045 1.33
PL intron excision ratio 0 0.000 1.24
PL mRNA stability 0 0.000 1.30

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