Hub : Traits

Tibia length

Tags: Physiology · Bone

Project: lionikas_2014

533 significantly associated models · 120 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	186942049	188155947	1	1	1.4e-07	1.2e-07	6.2e-07	11	Eef1akmt2
2	1	188769728	190166526	1	1	2.0e-07	1.1e-08	1.5e-02	82	Dock1
3	3	45965821	47365160	1	1	1.2e-07	1.1e-06	3.7e-01	97	Slc4a10
4	7	26575816	30734621	19	1	5.5e-11	9.6e-11	7.8e-03	83	Vezt
5	7	128990726	130910330	4	1	2.7e-07	2.7e-07	1.0e+00	100	Prph
6	8	108584253	109479622	1	1	2.8e-08	9.2e-05	8.6e-02	81	Apeh
7	8	109522056	112100485	3	1	6.0e-08	6.9e-07	3.4e-02	82	Cspg5
8	10	102999385	107195627	79	6	4.4e-15	2.5e-14	NaN	NaN	Lgals3bp Fasn Ccdc57 Gaa Ccdc137 Birc5
9	14	96137477	97690688	4	2	2.0e-08	1.2e-07	1.0e+00	100	B3gnt2 Zrsr1
10	15	47167781	50742046	7	1	1.3e-08	9.2e-09	1.0e+00	100	Nudt15

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	6.5	6	1	6.2	0.99	7.5e-06	Apeh Ccdc57 Prph Kmt2d NA NA
BMI without tail	8.1	15	0	0.0	1.00	4.9e-37	Aatk Lta4h Vezt Cradd Metap2 Pcyt2 NA Gcgr Slc25a10 Oxld1 Ccdc57 Ccdc137 Rfng NA Pde6g
Body weight	7.1	72	28	175.0	0.96	2.4e-138	Endov Nptx1 Rptor Nedd1 Chmp6 Baiap2 Cdk17 Elk3 Aatk Lta4h Slc38a10 Amdhd1 Snrpf Ntn4 Vezt Nr2c1 Ndufa12 Tmcc3 Cep83 Plxnc1 Cradd Socs2 Cspg5 Metap2 AABR07056633.1 Apeh Rnf213 Dclk3 Als2cl Mir331 Tbcd Csnk1d Slc16a3 Notum Pcyt2 NA Alyref Arhgdia P4hb Mcrip1 Gcgr Slc25a10 Hgs Nploc4 Faap100 Fscn2 Actg1 Fasn Eif4a3 Metrnl Gps1 Card14 Oxld1 Ccdc57 Gaa Dus1l Ccdc137 B3gntl1 Rfng Prph Fgd6 Ccdc40 Kmt2d NA Sgsh NA NA NA NA Pde6g NA NA
Epididymis fat weight	10.3	1	0	0.0	0.00	1.0e+00	Slc4a10
Left kidney weight	5.5	2	0	0.0	0.00	1.0e+00	Vezt Metap2
Right kidney weight	6.7	6	0	0.0	1.00	4.2e-09	Esd Fndc3a Rcbtb2 Itm2b Med4 Nudt15
Tail length	8.0	60	16	100.0	0.99	7.7e-162	Endov Rptor Nedd1 Chmp6 Baiap2 Cdk17 Elk3 Aatk Lta4h Slc38a10 Amdhd1 Snrpf Ntn4 Vezt Nr2c1 Ndufa12 Tmcc3 Cep83 Plxnc1 Cradd Socs2 Cspg5 Metap2 AABR07056633.1 Rnf213 Als2cl Mir331 Tbcd Cd7 Csnk1d Slc16a3 Notum Pcyt2 NA Alyref Arhgdia P4hb Mcrip1 Gcgr Slc25a10 Nploc4 Faap100 Fscn2 Fasn Eif4a3 Gps1 Card14 Oxld1 Ccdc57 Gaa Dus1l Ccdc137 Rfng Fgd6 Ccdc40 Sgsh NA NA Pde6g NA
Length with tail	10.8	43	22	137.5	0.95	5.7e-54	Nptx1 Rptor Nedd1 Chmp6 Baiap2 Cdk17 Elk3 Aatk Lta4h Slc38a10 Amdhd1 Snrpf Ntn4 Vezt Nr2c1 Ndufa12 Tmcc3 Cep83 Plxnc1 Cradd Socs2 Cspg5 Metap2 AABR07056633.1 Rnf213 Dclk3 Als2cl Mir331 Pcyt2 Mcrip1 Slc25a10 Hgs Eif4a3 Card14 Oxld1 Gaa Cbx8 Ccdc137 Tbc1d16 Fgd6 Sgsh NA NA
Length without tail	9.3	20	3	18.8	0.99	7.4e-41	Cdk17 Elk3 Lta4h Amdhd1 Snrpf Ntn4 Vezt Ndufa12 Plxnc1 Cradd Socs2 Metap2 AABR07056633.1 Dclk3 Mir331 Prph Fgd6 Kmt2d NA NA
Retroperitoneal fat weight	6.0	42	0	0.0	0.98	1.4e-101	Endov Rptor Chmp6 Baiap2 Aatk Lta4h Slc38a10 Slc4a10 Vezt Nr2c1 Rnf213 Tbcd Csnk1d Pcyt2 NA Alyref Arhgdia P4hb Mcrip1 Gcgr Slc25a10 Nploc4 Faap100 Fscn2 Fasn Eif4a3 Metrnl Gps1 Card14 Oxld1 Ccdc57 Gaa Ccdc137 B3gntl1 Rfng Ccdc40 NA Sgsh NA NA NA Pde6g
Extensor digitorum longus weight	4.7	10	0	0.0	-0.41	1.5e-01	Fndc3a Rcbtb2 Lpar6 Itm2b Med4 Nudt15 Prph Kmt2d NA NA
Soleus weight	5.6	1	0	0.0	0.00	1.0e+00	Cspg5
Reaction time omissions	11.8	1	0	0.0	0.00	1.0e+00	Plxnc1
Cocaine induced anxiety	14.7	2	0	0.0	0.00	1.0e+00	Aspscr1 Pycr1
Progressive ratio test 1 active lever presses	15.1	2	0	0.0	0.00	1.0e+00	Ndufa12 Fgd6
One hour access (shock baseline)	14.4	2	0	0.0	0.00	1.0e+00	Plxnc1 Cradd
Bone: apparent density	9.7	4	0	0.0	1.00	0.0e+00	Prph Kmt2d NA NA
Bone surface	11.6	4	0	0.0	1.00	0.0e+00	Prph Kmt2d NA NA
Bone: cortical area	15.6	12	4	25.0	0.99	3.2e-16	Tbcd Rab40b Csnk1d Znf750 Ccdc57 B3gntl1 Prph Kmt2d NA NA NA NA
Bone: cortical thickness	16.0	12	4	25.0	0.98	9.1e-16	Dnah17 C1qtnf1 Rbfox3 Engase Usp36 Tbcd Csnk1d Znf750 Ccdc57 B3gntl1 NA NA
Bone: cortical thickness	21.6	1	0	0.0	0.00	1.0e+00	Ccdc57
Bone: elastic work	12.5	9	0	0.0	0.99	5.4e-23	Tbcd Ogfod3 Csnk1d Hgs Faap100 Znf750 Ccdc57 Ccdc137 NA
Bone: endosteal estimation	8.1	4	0	0.0	1.00	1.1e-16	Prph Kmt2d NA NA
Bone: endosteal perimeter	8.9	6	0	0.0	1.00	5.4e-07	Pgs1 Dnah17 Prph Kmt2d NA NA
Bone: final force	14.7	7	1	6.2	0.99	5.1e-10	Tbcd Csnk1d Znf750 Ccdc57 B3gntl1 NA NA
Bone: final moment	14.7	8	1	6.2	0.99	7.1e-14	Tbcd Rab40b Csnk1d Znf750 Ccdc57 B3gntl1 NA NA
Bone: marrow area	7.9	4	0	0.0	1.00	0.0e+00	Prph Kmt2d NA NA
Bone: maximum diameter	9.3	8	0	0.0	1.00	9.6e-31	Pgs1 Dnah17 Tnrc6c Usp36 NA Tmem235 Afmid Birc5
Bone: maximum force	14.1	12	3	18.8	0.99	1.4e-16	Tbcd Rab40b Csnk1d Znf750 Ccdc57 B3gntl1 Prph Kmt2d NA NA NA NA
Bone: maximum moment	13.7	13	4	25.0	0.99	1.1e-23	Tbcd Rab40b Csnk1d Metrnl Znf750 Ccdc57 B3gntl1 Prph Kmt2d NA NA NA NA
Bone: minimum diameter	9.8	4	0	0.0	1.00	0.0e+00	Prph Kmt2d NA NA
Bone: periosteal estimation	11.0	7	4	25.0	0.96	1.5e-04	Ccdc57 B3gntl1 Prph Kmt2d NA NA NA
Bone: periosteal perimeter	10.9	5	0	0.0	0.99	1.9e-03	Prph Kmt2d NA NA NA
Bone: stiffness	16.9	5	4	25.0	0.97	1.1e-03	Ccdc57 Prph Kmt2d NA NA
Food seeking constrained by brief footshock	13.1	1	0	0.0	0.00	1.0e+00	Rcbtb2

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	14	0.660	3.1
Adipose	alternative TSS	0	0.000	2.8
Adipose	gene expression	39	0.470	2.7
Adipose	isoform ratio	8	0.284	2.8
Adipose	intron excision ratio	15	0.514	2.9
Adipose	mRNA stability	17	0.492	2.8
BLA	alternative polyA	0	0.000	2.9
BLA	alternative TSS	1	0.119	2.9
BLA	gene expression	23	0.380	2.7
BLA	isoform ratio	1	0.057	2.8
BLA	intron excision ratio	10	0.335	3.0
BLA	mRNA stability	9	0.445	2.8
Brain	alternative polyA	6	0.299	2.9
Brain	alternative TSS	6	0.350	2.9
Brain	gene expression	29	0.320	2.7
Brain	isoform ratio	8	0.253	2.7
Brain	intron excision ratio	26	0.481	3.0
Brain	mRNA stability	19	0.435	2.7
Eye	alternative polyA	0	0.000	2.8
Eye	alternative TSS	2	0.833	3.3
Eye	gene expression	1	0.089	2.9
Eye	isoform ratio	1	0.282	3.0
Eye	intron excision ratio	1	0.163	2.6
Eye	mRNA stability	1	0.429	3.0
IL	alternative polyA	3	0.493	3.2
IL	alternative TSS	0	0.000	2.7
IL	gene expression	9	0.247	2.7
IL	isoform ratio	3	0.381	3.0
IL	intron excision ratio	4	0.415	3.0
IL	mRNA stability	5	0.450	2.7
LHb	alternative polyA	4	0.698	3.1
LHb	alternative TSS	0	0.000	2.7
LHb	gene expression	7	0.218	2.8
LHb	isoform ratio	3	0.398	3.0
LHb	intron excision ratio	6	0.583	3.1
LHb	mRNA stability	5	0.483	2.8
Liver	alternative polyA	7	0.467	3.1
Liver	alternative TSS	11	0.726	2.9
Liver	gene expression	36	0.501	2.7
Liver	isoform ratio	9	0.377	2.8
Liver	intron excision ratio	32	0.731	2.8
Liver	mRNA stability	10	0.407	2.8
NAcc	alternative polyA	7	0.534	3.0
NAcc	alternative TSS	6	0.650	3.1
NAcc	gene expression	24	0.381	2.8
NAcc	isoform ratio	2	0.106	2.8
NAcc	intron excision ratio	10	0.327	3.0
NAcc	mRNA stability	12	0.531	2.9
OFC	alternative polyA	0	0.000	2.9
OFC	alternative TSS	0	0.000	3.1
OFC	gene expression	13	0.351	2.8
OFC	isoform ratio	0	0.000	2.7
OFC	intron excision ratio	5	0.498	3.4
OFC	mRNA stability	4	0.370	2.9
PL	alternative polyA	0	0.000	2.9
PL	alternative TSS	1	0.085	2.9
PL	gene expression	23	0.311	2.7
PL	isoform ratio	7	0.317	2.8
PL	intron excision ratio	15	0.419	3.0
PL	mRNA stability	13	0.446	2.8

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