Hub : Traits

Liver cadmium concentration

Project: vulpe_liver_2014

1 significantly associated model · 1 unique gene

Significant Loci

# chr p0 p1 # assoc genes # joint models best TWAS P best SNP P cond SNP P % var exp joint genes
1 10 24482774 25880494 1 1 1.1e-08 6.2e-06 0.65 99 Ccng1

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
dissection: PC 3 of all traits 1.8 1 0 0 0 1 Ccng1
dissection: PC 2 of all traits 3.0 1 0 0 0 1 Ccng1
heart_g 3.9 1 0 0 0 1 Ccng1
light_reinforcement_lr_relactive 4.2 1 0 0 0 1 Ccng1
Median of all reaction times 8.2 1 0 0 0 1 Ccng1
locomotor_testing_activity 7.7 1 0 0 0 1 Ccng1
reaction_time_corr 3.2 1 0 0 0 1 Ccng1
reaction_time_leftcorr 3.2 1 0 0 0 1 Ccng1
social_reinforcement_socialrfq 6.7 1 0 0 0 1 Ccng1
reaction_time_pinit 3.5 1 0 0 0 1 Ccng1
reaction_time_peropfalsealarm_slope 3.7 1 0 0 0 1 Ccng1
reaction_time_devmedrt_slope 9.0 1 0 0 0 1 Ccng1
pavca_ny_d5_magazine_ncs 3.0 1 0 0 0 1 Ccng1
pavca_mi_d1_avg_mag_lat 6.2 1 0 0 0 1 Ccng1
pavca_mi_d3_magazine_ncs 12.9 1 0 0 0 1 Ccng1
Total cortical area 3.4 1 0 0 0 1 Ccng1
tb_th_sd 4.4 1 0 0 0 1 Ccng1
ctth_sd 5.2 1 0 0 0 1 Ccng1
tautz: manual_mpc3 6.1 1 0 0 0 1 Ccng1
tautz: manual_spc12 2.9 1 0 0 0 1 Ccng1
tautz: manual_mpc16 6.8 1 0 0 0 1 Ccng1
tautz: manual_mpc14 6.0 1 0 0 0 1 Ccng1
tautz: manual_mpc12 4.2 1 0 0 0 1 Ccng1
tautz: manual_mcs 8.7 1 0 0 0 1 Ccng1
tautz: manual_spc24 7.1 1 0 0 0 1 Ccng1
tautz: manual_mpc9 7.4 1 0 0 0 1 Ccng1
tautz: manual_spc13 3.9 1 0 0 0 1 Ccng1
tautz: manual_mpc19 4.2 1 0 0 0 1 Ccng1
tautz: manual_spc6 7.3 1 0 0 0 1 Ccng1
tautz: manual_spc20 4.3 1 0 0 0 1 Ccng1
tautz: manual_mpc2 4.2 1 0 0 0 1 Ccng1
tautz: manual_spc5 6.0 1 0 0 0 1 Ccng1
tautz: manual_mpc6 3.9 1 0 0 0 1 Ccng1
tautz: manual_mpc1 6.1 1 0 0 0 1 Ccng1
Sum of all infusions from LGA sessions 3.5 1 0 0 0 1 Ccng1
The total number of resting periods in time1 9.6 1 0 0 0 1 Ccng1
runstartmale1 6.8 1 0 0 0 1 Ccng1
Liver cobalt concentration 3.8 1 0 0 0 1 Ccng1
Liver sodium concentration 5.5 1 0 0 0 1 Ccng1

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 1.11
Adipose alternative TSS 0 0.000 1.06
Adipose gene expression 0 0.000 1.11
Adipose isoform ratio 0 0.000 1.13
Adipose intron excision ratio 0 0.000 1.10
Adipose mRNA stability 0 0.000 1.11
BLA alternative polyA 0 0.000 0.99
BLA alternative TSS 0 0.000 1.02
BLA gene expression 0 0.000 1.10
BLA isoform ratio 0 0.000 1.06
BLA intron excision ratio 0 0.000 1.04
BLA mRNA stability 0 0.000 1.08
Brain alternative polyA 0 0.000 1.08
Brain alternative TSS 0 0.000 1.10
Brain gene expression 0 0.000 1.10
Brain isoform ratio 0 0.000 1.08
Brain intron excision ratio 0 0.000 1.08
Brain mRNA stability 0 0.000 1.13
Eye alternative polyA 0 0.000 1.27
Eye alternative TSS 0 0.000 1.21
Eye gene expression 0 0.000 1.06
Eye isoform ratio 0 0.000 1.15
Eye intron excision ratio 0 0.000 1.07
Eye mRNA stability 0 0.000 1.16
IL alternative polyA 0 0.000 1.09
IL alternative TSS 0 0.000 0.98
IL gene expression 0 0.000 1.09
IL isoform ratio 0 0.000 1.13
IL intron excision ratio 0 0.000 1.12
IL mRNA stability 0 0.000 1.21
LHb alternative polyA 0 0.000 1.05
LHb alternative TSS 0 0.000 1.19
LHb gene expression 0 0.000 1.11
LHb isoform ratio 0 0.000 1.16
LHb intron excision ratio 0 0.000 1.00
LHb mRNA stability 0 0.000 1.15
Liver alternative polyA 0 0.000 1.04
Liver alternative TSS 0 0.000 1.04
Liver gene expression 0 0.000 1.10
Liver isoform ratio 0 0.000 1.07
Liver intron excision ratio 0 0.000 1.14
Liver mRNA stability 0 0.000 1.08
NAcc alternative polyA 0 0.000 1.03
NAcc alternative TSS 0 0.000 1.06
NAcc gene expression 0 0.000 1.09
NAcc isoform ratio 0 0.000 1.14
NAcc intron excision ratio 0 0.000 1.08
NAcc mRNA stability 0 0.000 1.14
NAcc2 alternative polyA 0 0.000 1.07
NAcc2 alternative TSS 0 0.000 1.00
NAcc2 gene expression 0 0.000 1.08
NAcc2 isoform ratio 0 0.000 1.10
NAcc2 intron excision ratio 0 0.000 1.06
NAcc2 mRNA stability 0 0.000 1.13
OFC alternative polyA 0 0.000 1.12
OFC alternative TSS 0 0.000 1.11
OFC gene expression 0 0.000 1.11
OFC isoform ratio 0 0.000 1.10
OFC intron excision ratio 0 0.000 1.04
OFC mRNA stability 0 0.000 1.22
PL alternative polyA 0 0.000 1.09
PL alternative TSS 0 0.000 1.16
PL gene expression 0 0.000 1.12
PL isoform ratio 0 0.000 1.14
PL intron excision ratio 0 0.000 1.12
PL mRNA stability 0 0.000 1.20
PL2 alternative polyA 0 0.000 1.11
PL2 alternative TSS 0 0.000 1.05
PL2 gene expression 1 0.016 1.10
PL2 isoform ratio 0 0.000 1.17
PL2 intron excision ratio 0 0.000 1.09
PL2 mRNA stability 0 0.000 1.14

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