Hub : Traits

Tibia length in mm

Project: lionikas_2014

530 significantly associated models · 118 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	3.0e-07	1.1e-08	1.0e-02	80	Dock1
3	3	45965821	47365160	1	1	1.1e-07	1.1e-06	3.6e-01	96	Slc4a10
4	7	26575816	30734621	19	1	5.5e-11	9.6e-11	1.0e-02	84	Vezt
5	7	128990726	130910330	3	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	110189566	111564791	1	1	2.3e-07	9.4e-07	1.0e+00	100	Als2cl
8	10	102999385	107195627	79	6	6.7e-15	2.5e-14	NaN	NaN	Aatk Tbcd Gaa Ccdc137 Sgsh NA
9	14	95819498	97690688	5	3	2.0e-08	1.2e-07	1.0e+00	100	B3gnt2 NA 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
dissection: UMAP 1 of all traits	7.8	32	16	94.1	-0.98	1.0e-69	Nedd1 Chmp6 Baiap2 Cdk17 Elk3 Aatk Lta4h Amdhd1 Snrpf Ntn4 Vezt Nr2c1 Ndufa12 Tmcc3 Cep83 Plxnc1 Cradd Socs2 Metap2 AABR07056633.1 Rnf213 Slc26a11 Als2cl Mir331 Eif4a3 Gaa Fgd6 Ccdc40 NA Sgsh NA NA
retroperitoneal_fat_g	6.0	43	0	0.0	0.98	2.1e-98	Rptor Chmp6 Baiap2 Aatk Lta4h Slc38a10 Slc4a10 Vezt Nr2c1 Rnf213 Slc26a11 Fn3krp Csnk1d Aspscr1 Pcyt2 NA Alyref Arhgdia P4hb Mcrip1 Gcgr Slc25a10 Nploc4 Faap100 Fscn2 Eif4a3 Metrnl Gps1 Card14 Oxld1 Ccdc57 Gaa Ccdc137 Arl16 B3gntl1 Rfng Ccdc40 NA Sgsh NA NA NA Pde6g
body_g	7.3	69	24	141.2	0.96	1.8e-131	Nptx1 Rptor Nedd1 Chmp6 Baiap2 Cdk17 Elk3 Aatk Lta4h Slc38a10 Amdhd1 Snrpf Ntn4 Vezt Nr2c1 Ndufa12 Tmcc3 Cep83 Plxnc1 Cradd Socs2 Metap2 AABR07056633.1 Apeh Rnf213 Slc26a11 Als2cl Mir331 Tbcd Csnk1d Aspscr1 Notum Pcyt2 NA Alyref Arhgdia P4hb Mcrip1 Gcgr Slc25a10 Hgs Nploc4 Faap100 Fscn2 Actg1 Eif4a3 Metrnl Gps1 Card14 Oxld1 Ccdc57 Gaa Dus1l Ccdc137 Arl16 B3gntl1 Rfng Prph Fgd6 Ccdc40 NA Sgsh NA NA NA NA Pde6g NA NA
dissection: UMAP 3 of all traits	7.3	18	3	17.6	-0.99	1.2e-42	Lgals3bp Cant1 Endov Nptx1 Elk3 Lta4h Amdhd1 Snrpf Vezt Ndufa12 Cep83 Plxnc1 Socs2 Metap2 Mir331 Gaa Tbc1d16 Fgd6
kidney_right_g	6.7	6	0	0.0	1.00	4.2e-09	Esd Fndc3a Rcbtb2 Itm2b Med4 Nudt15
dissection: PC 3 of all traits	7.6	5	0	0.0	-0.99	7.0e-06	Vezt Cep83 Plxnc1 Socs2 Fgd6
EDL weight in grams	4.7	9	0	0.0	-0.55	4.1e-02	Fndc3a Rcbtb2 Lpar6 Itm2b Med4 Nudt15 Prph NA NA
pavca_mi_d1_avg_lev_lat	11.0	2	0	0.0	0.82	1.8e-01	Nptx1 Gaa
Total cortical area	12.5	6	1	5.9	0.99	7.8e-09	Dnah17 C1qtnf1 Rbfox3 Engase Usp36 Znf750
length	11.1	3	0	0.0	0.00	1.0e+00	Prph NA NA
tautz: manual_spc21	12.3	1	0	0.0	0.00	1.0e+00	Dock1
tautz: manual_mpc16	13.7	3	0	0.0	1.00	1.1e-03	Tbcd B3gntl1 NA
punishment	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	37	0.446	2.7
Adipose	isoform ratio	8	0.284	2.8
Adipose	intron excision ratio	15	0.514	2.9
Adipose	mRNA stability	16	0.463	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	24	0.444	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	35	0.487	2.7
Liver	isoform ratio	8	0.335	2.8
Liver	intron excision ratio	32	0.731	2.8
Liver	mRNA stability	10	0.407	2.8
NAcc	alternative polyA	0	0.000	3.1
NAcc	alternative TSS	0	0.000	3.3
NAcc	gene expression	4	0.122	2.8
NAcc	isoform ratio	2	0.270	2.8
NAcc	intron excision ratio	2	0.210	2.9
NAcc	mRNA stability	2	0.185	2.9
NAcc2	alternative polyA	0	0.000	2.8
NAcc2	alternative TSS	4	0.548	3.1
NAcc2	gene expression	16	0.300	2.8
NAcc2	isoform ratio	2	0.130	2.7
NAcc2	intron excision ratio	10	0.378	2.9
NAcc2	mRNA stability	7	0.392	2.7
OFC	alternative polyA	0	0.000	2.9
OFC	alternative TSS	0	0.000	3.1
OFC	gene expression	12	0.324	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	2	0.334	3.1
PL	alternative TSS	0	0.000	2.8
PL	gene expression	10	0.269	2.7
PL	isoform ratio	1	0.115	2.9
PL	intron excision ratio	5	0.480	2.9
PL	mRNA stability	7	0.609	2.9
PL2	alternative polyA	1	0.080	2.9
PL2	alternative TSS	0	0.000	3.1
PL2	gene expression	19	0.297	2.7
PL2	isoform ratio	5	0.271	2.8
PL2	intron excision ratio	13	0.413	3.0
PL2	mRNA stability	13	0.533	2.9

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