Hub : Traits

Se content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

116 significantly associated models · 33 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 201865024 202832586 1 1 7.1e-11 4.1e-02 0.002 -127 Ccs
2 1 231783442 236943873 25 1 4.0e-10 1.0e-08 0.477 98 Cyp26a1
3 1 238391248 240123287 5 3 7.4e-08 1.0e-07 1.000 100 Entpd1 Sorbs1 Aldh18a1
4 7 16845355 16970279 1 1 4.8e-14 NaN NA NA NA
5 14 34177603 35456143 1 1 3.0e-07 2.2e-03 1.000 100 Ociad2

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 3.8 1 0 0 0.00 1.0e+00 Ociad2
BMI without tail 171.8 1 1 14 0.00 1.0e+00 NA
Body weight 11.2 1 1 14 0.00 1.0e+00 NA
Epididymis fat weight 136.2 1 1 14 0.00 1.0e+00 NA
Heart weight 11.4 1 0 0 0.00 1.0e+00 NA
Left kidney weight 35.7 2 1 14 0.00 1.0e+00 Ociad2 NA
Right kidney weight 67.3 1 1 14 0.00 1.0e+00 NA
Tail length 91.1 1 1 14 0.00 1.0e+00 NA
Length with tail 3.7 3 0 0 -0.99 6.3e-04 Tnks2 Hectd2 NA
Length without tail 120.2 1 1 14 0.00 1.0e+00 NA
Liver weight, left 23.6 1 1 14 0.00 1.0e+00 NA
Liver weight, right 9.6 1 0 0 0.00 1.0e+00 NA
Parametrial fat weight 26.4 1 1 14 0.00 1.0e+00 NA
Retroperitoneal fat weight 4.2 1 0 0 0.00 1.0e+00 NA
Intraocular pressure 29.4 1 1 14 0.00 1.0e+00 NA
Extensor digitorum longus weight 39.2 1 1 14 0.00 1.0e+00 NA
Soleus weight 21.9 1 1 14 0.00 1.0e+00 NA
Tibialis anterior weight 96.0 1 1 14 0.00 1.0e+00 NA
Tibia length 7.4 1 0 0 0.00 1.0e+00 NA
Number of licking bursts 242.4 1 1 14 0.00 1.0e+00 NA
Food consumed during 24 hour testing period 18.0 2 0 0 0.00 1.0e+00 Ccs NA
Times rat made contact with spout 121.6 1 1 14 0.00 1.0e+00 NA
Mean time between licks in bursts 90.5 1 1 14 0.00 1.0e+00 NA
Mean num. licks in bursts 258.2 1 1 14 0.00 1.0e+00 NA
Std. dev. time between licks in bursts 291.0 1 1 14 0.00 1.0e+00 NA
Water consumed over 24 hours 11.5 1 0 0 0.00 1.0e+00 Ccs
Indifference point 0 sec 21.3 1 1 14 0.00 1.0e+00 NA
Indifference point AUC 66.7 1 1 14 0.00 1.0e+00 NA
Delay discounting total patch changes 0 sec 20.1 1 1 14 0.00 1.0e+00 NA
Delay discounting total patch changes 12 sec 156.9 1 1 14 0.00 1.0e+00 NA
Delay discounting total patch changes 18 sec 277.7 1 1 14 0.00 1.0e+00 NA
Delay discounting total patch changes 24 sec 43.7 1 1 14 0.00 1.0e+00 NA
Delay discounting total patch changes 6 sec 145.0 1 1 14 0.00 1.0e+00 NA
Delay discounting water rate 0 sec 11.8 1 0 0 0.00 1.0e+00 NA
Delay discounting water rate 12 sec 44.2 1 1 14 0.00 1.0e+00 NA
Delay discounting water rate 18 sec 10.5 1 0 0 0.00 1.0e+00 NA
Delay discounting water rate 24 sec 100.9 1 1 14 0.00 1.0e+00 NA
Delay discounting water rate 6 sec 70.2 1 1 14 0.00 1.0e+00 NA
Locomotor testing distance 14.0 1 0 0 0.00 1.0e+00 NA
Locomotor testing rearing 23.9 1 1 14 0.00 1.0e+00 NA
Light reinforcement 1 84.1 1 1 14 0.00 1.0e+00 NA
Reaction time number correct 9.4 1 0 0 0.00 1.0e+00 NA
Reaction time num false alarms 90.1 1 1 14 0.00 1.0e+00 NA
Reaction time num false alarms AUC 128.2 1 1 14 0.00 1.0e+00 NA
Reaction time trials correct on left 9.4 1 0 0 0.00 1.0e+00 NA
Reaction time trials on left 10.3 1 0 0 0.00 1.0e+00 NA
Reaction time mean 62.5 1 1 14 0.00 1.0e+00 NA
Reaction time mean AUC 89.1 1 1 14 0.00 1.0e+00 NA
Median of all reaction times 80.2 1 1 14 0.00 1.0e+00 NA
Reaction time false alarm rate 104.2 1 1 14 0.00 1.0e+00 NA
Reaction time premature initiation rate 47.3 1 1 14 0.00 1.0e+00 NA
Reaction time premature initiations 49.8 1 1 14 0.00 1.0e+00 NA
Std. dev. reaction times 27.0 1 1 14 0.00 1.0e+00 NA
Reaction time trials completed 10.3 1 0 0 0.00 1.0e+00 NA
Reaction time trials AUC 15.6 1 0 0 0.00 1.0e+00 NA
Social responses 108.6 1 1 14 0.00 1.0e+00 NA
Cocaine response after cond. corrected 135.7 1 1 14 0.00 1.0e+00 NA
Cocaine response after cond. not corrected 176.6 1 1 14 0.00 1.0e+00 NA
Cocaine response before conditioning 28.6 1 1 14 0.00 1.0e+00 NA
Saline control response 50.6 1 1 14 0.00 1.0e+00 NA
Condit. Reinf. active minus inactive responses 46.4 1 1 14 0.00 1.0e+00 NA
Condit. Reinf. active-inactive response ratio 68.7 1 1 14 0.00 1.0e+00 NA
Condit. Reinf. active responses 11.1 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. inactive responses 20.6 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. lever latency 60.5 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 173.4 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 216.7 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. index score 102.2 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. latency score 110.3 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 29.4 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 244.9 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. intertrial magazine entries 106.2 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 90.6 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. response bias 51.3 1 1 14 0.00 1.0e+00 NA
Conditioned reinforcement - actives 18.5 1 0 0 0.00 1.0e+00 NA
Intermittent access intake day 1-15 change 104.0 1 1 14 0.00 1.0e+00 NA
Intermittent access intake escalation 141.1 1 1 14 0.00 1.0e+00 NA
Intermittent access intake escalation 2 42.5 1 1 14 0.00 1.0e+00 NA
Intermitt. access day 1 inactive lever presses 30.6 1 1 14 0.00 1.0e+00 NA
Intermittent access day 1 total infusions 52.9 1 1 14 0.00 1.0e+00 NA
Intermittent access day 1 locomotion 27.1 1 1 14 0.00 1.0e+00 NA
Post-drug Anxiety 20.6 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 active lever presses 12.2 1 0 0 0.00 1.0e+00 NA
Progressive ratio test 2 breakpoint 61.6 1 1 14 0.00 1.0e+00 NA
Short access day 10 total inactive lever presses 12.2 1 0 0 0.00 1.0e+00 NA
Short access day 10 total infusions 24.0 1 1 14 0.00 1.0e+00 NA
Short access day 1 locomotion 17.2 1 0 0 0.00 1.0e+00 NA
Compulsive drug intake 45.4 1 1 14 0.00 1.0e+00 NA
One hour access (0.3 mA shock) 12.4 6 0 0 -1.00 1.4e-16 Cyp26a1 Ide Marchf5 Cpeb3 Cyp26c1 Exoc6
Context. condit. distance diff. score 240.2 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, session 1 190.8 1 1 14 0.00 1.0e+00 NA
Locomotion distance, session 1 609.6 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, session 2 139.6 1 1 14 0.00 1.0e+00 NA
Locomotion distance, session 2 1269.9 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, session 3 178.9 1 1 14 0.00 1.0e+00 NA
Locomotion distance, session 3 117.5 1 1 14 0.00 1.0e+00 NA
Stereotopy head waving duration, day 3 33.2 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, session 7 98.9 1 1 14 0.00 1.0e+00 NA
Locomotion distance, session 7 31.8 1 1 14 0.00 1.0e+00 NA
Stereotopy head waving bouts, day 7 68.4 1 1 14 0.00 1.0e+00 NA
Stereotopy head waving duration, day 7 102.2 1 1 14 0.00 1.0e+00 NA
Locomotion distance, session 8 171.7 1 1 14 0.00 1.0e+00 NA
Degree of sensitization distance 198.5 1 1 14 0.00 1.0e+00 NA
Degree of sensitization stereotypy 37.5 1 1 14 0.00 1.0e+00 NA
Condit. Reinf. active-inactive response ratio 107.3 1 1 14 0.00 1.0e+00 NA
Condit. Reinf. active responses 20.0 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. inactive responses 17.2 1 0 0 0.00 1.0e+00 NA
Incentive salience index mean 15.6 1 0 0 0.00 1.0e+00 NA
Condit. Reinf. lever presses 35.1 1 1 14 0.00 1.0e+00 NA
Time in familiar zone, hab. session 1 16.4 1 0 0 0.00 1.0e+00 NA
Time in novel zone, hab. session 1 17.4 1 0 0 0.00 1.0e+00 NA
Total zone transitions, hab. session 1 673.8 1 1 14 0.00 1.0e+00 NA
Total locomotion distance, hab. session 1 279.4 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, hab. session 1 349.5 1 1 14 0.00 1.0e+00 NA
Time in familiar zone, hab. session 2 48.9 1 1 14 0.00 1.0e+00 NA
Time in novel zone, hab. session 2 58.4 1 1 14 0.00 1.0e+00 NA
Total zone transitions, hab. session 2 421.2 1 1 14 0.00 1.0e+00 NA
Total locomotion distance, hab. session 2 214.3 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, hab. session 2 225.0 1 1 14 0.00 1.0e+00 NA
Total zone transitions, NPP test 376.1 1 1 14 0.00 1.0e+00 NA
Total locomotion distance, NPP test 269.3 1 1 14 0.00 1.0e+00 NA
Locomotion velocity, NPP test 317.8 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry latency 95.9 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. change in total contacts 40.1 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. index score 51.9 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. latency score 16.6 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. lever contacts 16.1 1 0 0 0.00 1.0e+00 NA
Pavlov. Cond. magazine entry number 61.6 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. lever-magazine prob. diff. 88.1 1 1 14 0.00 1.0e+00 NA
Pavlov. Cond. response bias 52.4 1 1 14 0.00 1.0e+00 NA
Bone: apparent density 9.3 14 1 14 -0.85 2.7e-10 Cyp26a1 Ide Marchf5 Ppp1r3c Pcgf5 Ankrd1 Rpp30 Htr7 Cpeb3 Cyp26c1 Exoc6 Tnks2 NA NA
Bone surface 15.9 3 1 14 -0.95 4.8e-02 Cyp26c1 Exoc6 NA
Bone volume 15.5 3 1 14 -0.93 2.4e-02 Cyp26c1 Exoc6 NA
Bone: connectivity density 8.5 2 0 0 0.00 1.0e+00 Cyp26c1 NA
Bone: cortical porosity 188.5 1 1 14 0.00 1.0e+00 NA
Bone: cortical porosity 155.8 1 1 14 0.00 1.0e+00 NA
Bone: cortical thickness 8.8 1 0 0 0.00 1.0e+00 NA
Bone: cortical thickness 17.9 1 0 0 0.00 1.0e+00 NA
Bone: elastic displacement 28.2 1 1 14 0.00 1.0e+00 NA
Bone: endosteal estimation 8.3 13 1 14 -1.00 5.2e-25 Plce1 Fra10ac1 Myof Pde6c Cyp26a1 Ide Cpeb3 Ffar4 Slc35g1 Cyp26c1 Exoc6 Tnks2 NA
Bone: endosteal perimeter 7.2 12 0 0 -1.00 3.7e-32 Fra10ac1 Myof Pde6c Cyp26a1 Ide Marchf5 Cpeb3 Ffar4 Slc35g1 Cyp26c1 Exoc6 Tnks2
Bone: final force 57.4 1 1 14 0.00 1.0e+00 NA
Bone: final moment 45.6 1 1 14 0.00 1.0e+00 NA
Bone: marrow area 7.7 15 1 14 -1.00 8.1e-34 Plce1 Fra10ac1 Myof Pde6c Cyp26a1 Ide Marchf5 Ankrd1 Cpeb3 Ffar4 Slc35g1 Cyp26c1 Exoc6 Tnks2 NA
Bone: maximum diameter 9.3 22 0 0 -1.00 6.0e-63 Fra10ac1 Myof Pde6c Hhex Cyp26a1 Ide Marchf5 Btaf1 Ppp1r3c Pcgf5 Ankrd1 Rpp30 Htr7 Pank1 Cpeb3 Ffar4 Slc16a12 Cyp26c1 Exoc6 Tnks2 Hectd2 NA
Bone: maximum force 60.3 1 1 14 0.00 1.0e+00 NA
Bone: maximum moment 41.2 1 1 14 0.00 1.0e+00 NA
Bone: minimum diameter 11.1 22 3 43 -0.98 1.5e-58 Plce1 Entpd1 Lgi1 Fra10ac1 Sorbs1 Myof Pdlim1 Pde6c Hhex Cyp26a1 Ide Marchf5 Btaf1 Cpeb3 Ffar4 Slc35g1 Cyp26c1 Exoc6 Tnks2 Tctn3 NA Aldh18a1
Bone: periosteal estimation 7.6 11 0 0 -1.00 1.1e-33 Cyp26a1 Ide Marchf5 Pcgf5 Pank1 Cpeb3 Ffar4 Cyp26c1 Exoc6 Tnks2 NA
Bone: periosteal perimeter 8.2 2 0 0 0.00 1.0e+00 Exoc6 NA
Bone: post-yield work 124.3 1 1 14 0.00 1.0e+00 NA
Bone: stiffness 136.8 1 1 14 0.00 1.0e+00 NA
Bone: tissue strength 136.0 1 1 14 0.00 1.0e+00 NA
Bone: trabecular number 19.6 5 1 14 0.06 9.2e-01 Cpeb3 Cyp26c1 Exoc6 Tnks2 NA
Bone: trabecular thickness 13.8 1 0 0 0.00 1.0e+00 NA
Bone: trabecular tissue density 66.6 1 1 14 0.00 1.0e+00 NA
Distance traveled before self-admin 12.6 1 0 0 0.00 1.0e+00 NA
Delta time in open arm before/after self-admin 40.2 1 1 14 0.00 1.0e+00 NA
Time in closed arm before self-admin 78.0 1 1 14 0.00 1.0e+00 NA
Time in closed arm after self-admin 40.2 1 1 14 0.00 1.0e+00 NA
Time in open arm after self-admin 31.3 1 1 14 0.00 1.0e+00 NA
Delta time to tail flick, vehicle, before/after SA 13.1 1 0 0 0.00 1.0e+00 Cpeb3
Delta time to tail flick, test, before/after SA 20.0 1 0 0 0.00 1.0e+00 NA
Fecal boli incidents, locomotor time 1 11.8 1 0 0 0.00 1.0e+00 NA
Time >=10cm from walls, locomotor time 1 19.5 1 0 0 0.00 1.0e+00 NA
Time >=10cm from walls, locomotor time 2 27.2 1 1 14 0.00 1.0e+00 NA
Distance moved, locomotor task time 2 13.1 1 0 0 0.00 1.0e+00 NA
Weight adjusted by age 25.0 1 1 14 0.00 1.0e+00 NA
Locomotion in novel chamber 10.2 1 0 0 0.00 1.0e+00 NA
Run reversals in cocaine runway, males 39.3 1 1 14 0.00 1.0e+00 NA
Latency to leave start box in cocaine runway 18.8 1 0 0 0.00 1.0e+00 NA
Cd content in liver 239.3 1 1 14 0.00 1.0e+00 NA
Co content in liver 89.3 2 2 29 0.00 1.0e+00 Ccs NA
Cu content in liver 14.0 1 0 0 0.00 1.0e+00 Sorbs1
Fe content in liver 24.0 1 1 14 0.00 1.0e+00 Ccs
K content in liver 87.3 1 1 14 0.00 1.0e+00 NA
Mg content in liver 22.4 1 0 0 0.00 1.0e+00 Ccs
Mn content in liver 207.1 1 1 14 0.00 1.0e+00 NA
Rb content in liver 31.4 1 1 14 0.00 1.0e+00 NA
Zn content in liver 16.4 9 2 29 0.98 3.7e-09 Ide Marchf5 Ankrd1 Rpp30 Cpeb3 Ccs Tnks2 NA 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 1.06
Adipose alternative TSS 0 0.000 1.16
Adipose gene expression 6 0.072 1.18
Adipose isoform ratio 0 0.000 1.14
Adipose intron excision ratio 8 0.274 1.39
Adipose mRNA stability 4 0.116 1.21
BLA alternative polyA 0 0.000 1.16
BLA alternative TSS 0 0.000 1.08
BLA gene expression 4 0.066 1.19
BLA isoform ratio 1 0.057 1.18
BLA intron excision ratio 0 0.000 1.29
BLA mRNA stability 1 0.049 1.18
Brain alternative polyA 0 0.000 1.15
Brain alternative TSS 4 0.233 1.34
Brain gene expression 8 0.088 1.20
Brain isoform ratio 3 0.095 1.17
Brain intron excision ratio 9 0.166 1.32
Brain mRNA stability 3 0.069 1.17
Eye alternative polyA 0 0.000 1.01
Eye alternative TSS 0 0.000 1.21
Eye gene expression 1 0.089 1.30
Eye isoform ratio 0 0.000 1.09
Eye intron excision ratio 1 0.163 1.29
Eye mRNA stability 1 0.429 1.36
IL alternative polyA 0 0.000 1.13
IL alternative TSS 0 0.000 1.24
IL gene expression 4 0.110 1.22
IL isoform ratio 1 0.126 1.33
IL intron excision ratio 1 0.103 1.26
IL mRNA stability 0 0.000 1.10
LHb alternative polyA 0 0.000 1.02
LHb alternative TSS 0 0.000 1.13
LHb gene expression 6 0.187 1.24
LHb isoform ratio 0 0.000 1.11
LHb intron excision ratio 1 0.097 1.38
LHb mRNA stability 1 0.097 1.18
Liver alternative polyA 2 0.133 1.16
Liver alternative TSS 0 0.000 1.31
Liver gene expression 5 0.070 1.20
Liver isoform ratio 2 0.084 1.26
Liver intron excision ratio 1 0.023 1.27
Liver mRNA stability 2 0.081 1.25
NAcc alternative polyA 0 0.000 1.18
NAcc alternative TSS 3 0.324 1.17
NAcc gene expression 5 0.079 1.21
NAcc isoform ratio 2 0.106 1.12
NAcc intron excision ratio 3 0.098 1.31
NAcc mRNA stability 1 0.044 1.19
OFC alternative polyA 0 0.000 1.17
OFC alternative TSS 0 0.000 0.93
OFC gene expression 5 0.135 1.19
OFC isoform ratio 0 0.000 1.20
OFC intron excision ratio 0 0.000 1.33
OFC mRNA stability 0 0.000 1.13
PL alternative polyA 0 0.000 1.10
PL alternative TSS 4 0.340 1.26
PL gene expression 9 0.122 1.18
PL isoform ratio 2 0.090 1.18
PL intron excision ratio 1 0.028 1.30
PL mRNA stability 1 0.034 1.20

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