Hub : Traits

Se content in liver

Tags: Physiology · Liver

Project: vulpe_liver_2014

1 locus · 16 genes with independent associations · 117 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	chr1	241196633	250121656	117	16	5.4e-11	1.95e-09	NaN	Cyp26a1 Cyp26c1 Cyp2c7l1 Exoc6 Fra10ac1 LOC102553702 LOC134483989 Marchf5 Myof Pank1 Plce1 Rbp4 Rpp30 Slc35g1

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
Length with tail	3.79	6	0	0	-1	1.85e-17	Exoc6 LOC120100024 LOC134484921 Pank1 Pcgf5 Rpp30
Length without tail	2.99	2	0	0	-1	4.11e-06	Exoc6 Pcgf5
Progressive ratio test 2 active lever presses	10	1	0	0	0	1.00e+00	LOC102553702
Progressive ratio test 2 breakpoint	11.54	1	0	0	0	1.00e+00	LOC102553702
One hour access (0.3 mA shock)	13	7	0	0	-1	1.26e-27	Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 LOC102553702 Marchf5
Bone: apparent density	8.86	14	0	0	-1	2.77e-109	Btaf1 Cpeb3 Cyp26a1 Exoc6 Htr7 LOC102553702 LOC120100024 LOC120100025 LOC134484921 LOC134485226 Marchf5 Pcgf5 Rpp30 Tnks2
Bone surface	7.76	2	0	0	-1	7.76e-05	Exoc6 Fra10ac1
Bone volume	7.48	8	0	0	-1	3.19e-29	Cpeb3 Exoc6 Htr7 LOC120100025 Marchf5 Pcgf5 Rpp30 Tnks2
Bone: endosteal estimation	6.89	10	0	0	-1	1.00e-47	Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 Marchf5 Myof Pde6c Plce1 Tnks2
Bone: endosteal perimeter	6.65	10	0	0	-1	1.12e-46	Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 LOC102553702 Marchf5 Myof Slc35g1 Tnks2
Bone: marrow area	6.66	14	0	0	-1	1.89e-74	Btaf1 Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 LOC102553702 LOC120100025 Marchf5 Myof Pcgf5 Pde6c Plce1 Tnks2
Bone: maximum diameter	9.86	25	0	0	-1	2.86e-196	Ankrd1 Btaf1 Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 Hectd2 Htr7 Ide LOC102553702 LOC120100024 LOC120100025 LOC134484921 LOC134485226 Marchf5 Myof Pank1 Pcgf5 Pde6c Rbp4 Rpp30 Slc16a12 Slc35g1 Tnks2
Bone: minimum diameter	10.01	31	0	0	-1	1.04e-175	Aldh18a1 Btaf1 Cpeb3 Cyp26a1 Cyp26c1 Cyp2c6v1 Cyp2c7l1 Entpd1 Exoc6 Fra10ac1 Hectd2 Hells Ide Lgi1 LOC100911718 LOC102553702 LOC120097534 LOC120097545 LOC120100025 LOC120100032 LOC134484003 Marchf5 Myof Pde6c Pdlim1 Plce1 Slc35g1 Sorbs1 Tbc1d12 Tctn3 Tnks2
Bone: periosteal estimation	7.21	19	0	0	-1	9.30e-143	Btaf1 Cpeb3 Cyp26a1 Cyp26c1 Exoc6 Fra10ac1 Hectd2 Htr7 Ide LOC102553702 LOC120100024 LOC120100025 Marchf5 Pank1 Pcgf5 Pde6c Rpp30 Slc35g1 Tnks2
Bone: periosteal perimeter	7.51	1	0	0	-1	1.76e-05	Exoc6
Cu content in liver	12.21	1	0	0	0	1.00e+00	Sorbs1

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	4	0.1	1.27
Adipose	alternative TSS	2	0.1	1.19
Adipose	gene expression	7	0.1	1.18
Adipose	isoform ratio	6	0.1	1.19
Adipose	intron excision ratio	6	0.2	1.37
Adipose	mRNA stability	4	0.1	1.2
BLA	alternative polyA	3	0.1	1.27
BLA	alternative TSS	1	0	1.12
BLA	gene expression	7	0.1	1.2
BLA	isoform ratio	2	0.1	1.19
BLA	intron excision ratio	0	0	1.23
BLA	mRNA stability	0	0	1.13
Brain	alternative polyA	2	0.1	1.19
Brain	alternative TSS	8	0.2	1.21
Brain	gene expression	13	0.1	1.21
Brain	isoform ratio	4	0.1	1.17
Brain	intron excision ratio	4	0.1	1.23
Brain	mRNA stability	5	0.1	1.13
Eye	alternative polyA	0	0	1.41
Eye	alternative TSS	0	0	1.15
Eye	gene expression	0	0	1.24
Eye	isoform ratio	0	0	1.07
Eye	intron excision ratio	0	0	1.27
Eye	mRNA stability	0	0	1.31
IC	alternative polyA	4	0.2	1.33
IC	alternative TSS	0	0	1.1
IC	gene expression	8	0.1	1.21
IC	isoform ratio	3	0.1	1.2
IC	intron excision ratio	0	0	1.16
IC	mRNA stability	2	0.1	1.14
IL	alternative polyA	2	0.2	1.38
IL	alternative TSS	0	0	1.15
IL	gene expression	5	0.1	1.18
IL	isoform ratio	3	0.2	1.22
IL	intron excision ratio	1	0.1	1.15
IL	mRNA stability	0	0	1.12
LHb	alternative polyA	2	0.2	1.16
LHb	alternative TSS	2	0.3	1.17
LHb	gene expression	6	0.2	1.21
LHb	isoform ratio	3	0.2	1.23
LHb	intron excision ratio	0	0	1.28
LHb	mRNA stability	0	0	1.16
Liver	alternative polyA	8	0.3	1.32
Liver	alternative TSS	5	0.2	1.27
Liver	gene expression	9	0.1	1.22
Liver	isoform ratio	8	0.2	1.22
Liver	intron excision ratio	4	0.1	1.35
Liver	mRNA stability	6	0.2	1.21
NAcc	alternative polyA	6	0.2	1.24
NAcc	alternative TSS	4	0.1	1.17
NAcc	gene expression	12	0.1	1.17
NAcc	isoform ratio	6	0.1	1.13
NAcc	intron excision ratio	8	0.1	1.2
NAcc	mRNA stability	4	0.1	1.17
OFC	alternative polyA	2	0.2	1.3
OFC	alternative TSS	0	0	1.16
OFC	gene expression	6	0.1	1.17
OFC	isoform ratio	2	0.1	1.18
OFC	intron excision ratio	0	0	1.21
OFC	mRNA stability	1	0.1	1.14
PL	alternative polyA	6	0.2	1.26
PL	alternative TSS	5	0.1	1.18
PL	gene expression	11	0.1	1.18
PL	isoform ratio	4	0.1	1.14
PL	intron excision ratio	4	0.1	1.16
PL	mRNA stability	3	0.1	1.16
pVTA	alternative polyA	2	0.1	1.26
pVTA	alternative TSS	4	0.2	1.17
pVTA	gene expression	7	0.1	1.19
pVTA	isoform ratio	4	0.1	1.14
pVTA	intron excision ratio	1	0	1.17
pVTA	mRNA stability	1	0	1.15
RMTg	alternative polyA	0	0	1.11
RMTg	alternative TSS	0	0	1.14
RMTg	gene expression	2	0.1	1.15
RMTg	isoform ratio	0	0	1.1
RMTg	intron excision ratio	0	0	1.4
RMTg	mRNA stability	1	0.2	1.24