Hub : Traits

EDL weight in grams

Project: lionikas_2014

2836 significantly associated models · 551 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	171727837	174685359	4	1	1.8e-07	9.4e-07	6.7e-77	-1332	Gde1
2	1	176946412	178345186	1	1	3.1e-08	3.7e-07	1.4e-02	77	Tnrc6a
3	1	199398809	208295455	130	10	3.5e-10	1.2e-09	1.0e+00	100	Ttc9c Bbs1 Sf3b2 Cfl1 Kcnk4 Macrod1 Atl3 Ctsw NEWGENE_1310680 Atg2a
4	2	87582105	88973805	1	1	3.2e-10	1.6e-10	1.0e+00	100	Ralyl
5	2	89673058	95023945	16	1	1.8e-13	1.0e-13	1.0e+00	100	Zfp704
6	2	97341393	99049575	2	1	8.4e-08	2.5e-08	1.0e+00	100	Hnf4g
7	2	99787494	102500927	5	1	1.4e-08	1.1e-08	1.0e+00	100	Cyp7b1
8	2	225972996	228461478	7	5	8.3e-10	1.2e-12	NaN	NaN	Metap1 Tspan5 Rap1gds1 Adh7 Eif4e
9	4	146598342	149011707	6	1	1.5e-09	1.2e-09	1.4e-01	94	Slc6a11
10	5	54563228	57839987	6	2	8.2e-08	2.1e-08	8.8e-02	91	Ddx58 Aptx
11	6	129055047	132888501	37	9	3.8e-12	5.1e-11	1.0e+00	100	Crip2 Klc1 Zfyve21 Cdca4 Jag2 Nudt14 Brf1 Pld4 Cep170b
12	7	29535	2057232	28	4	1.5e-07	1.5e-07	1.0e+00	100	Ikzf4 Dnajc14 Sarnp Myl6
13	7	83305298	85971312	3	2	6.8e-08	5.9e-08	0.0e+00	-8766	Med30 NA
14	7	87430397	88835787	2	1	4.2e-08	7.7e-10	1.0e+00	100	Has2
15	7	127692699	129920800	7	2	6.0e-08	1.1e-07	1.0e+00	100	Tmem106c Rapgef3
16	7	130474807	134497678	37	7	6.0e-11	9.7e-09	1.0e+00	100	Dazap2 Scn8a Tns2 Csad Krt1 Krt71 NA
17	8	69336832	75537324	28	3	3.0e-09	1.7e-09	1.0e+00	100	Bnip2 Myzap Myo1e
18	9	44247541	49751781	32	12	6.8e-12	8.1e-12	1.0e+00	100	Col3a1 Wdr75 Tpp2 Inpp1 Nemp2 Mrps9 RGD1310553 Fhl2 Nck2 Ercc5 Tgfbrap1 Ormdl1
19	10	58773413	61500745	16	1	2.7e-08	2.3e-08	1.0e+00	100	Crk
20	10	81422075	86251828	45	8	1.0e-11	1.5e-10	1.0e+00	100	Krt15 Rpl19 Med1 Thra Nr1d1 Msl1 Igfbp4 Srcin1
21	10	87162021	89011911	5	1	8.9e-09	1.7e-07	1.0e+00	100	Acbd4
22	10	90210853	92351292	5	1	4.4e-09	3.4e-07	3.9e-01	97	Map3k3
23	12	27006	4653252	11	6	1.0e-08	7.1e-08	1.0e+00	100	Trappc5 Cers4 N4bp2l2 Insr Pet100 Zfp958
24	14	8196668	10208170	7	1	9.6e-08	1.9e-07	2.9e-01	96	Lin54
25	14	16746616	22686240	33	6	1.6e-16	1.6e-15	NaN	NaN	Alb Ankrd17 Gc Slc4a4 Rufy3 RGD1559459
26	15	35796833	43041493	43	6	3.2e-13	3.2e-13	1.0e+00	100	NA Fam124a Bnip3l Scara3 Ptk2b Stmn4
27	15	43349498	46640839	28	5	1.9e-13	5.5e-13	1.0e+00	100	Polr3d Phyhip Fhip2b R3hcc1 Egr3
28	15	47167781	49440043	6	1	2.1e-11	7.8e-13	4.1e-03	84	Fndc3a

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	9.4	12	10	10	-1.00	1.9e-31	Stxbp2 Trappc5 Snapc2 Timm44 Elavl1 Cers4 N4bp2l2 Med30 Arhgef18 Insr Pet100 Zfp958
retroperitoneal_fat_g	6.1	83	0	0	-1.00	0.0e+00	Znrd2 Tpcn2 Ighmbp2 Ppp6r3 Lrp5 Kmt5b Tcirg1 Ndufs8 Aldh3b1 Gstp1 Actn3 Zdhhc24 Bbs1 Peli3 mrpl11 Slc29a2 Brms1 Yif1a Cnih2 Klc2 Pacs1 Sf3b2 Cst6 Banf1 Eif1ad Sart1 Fibp Efemp2 Mus81 Cfl1 NA Ltbp3 Frmd8 Dpf2 Ccnd1 Fau Tm7sf2 Vps51 Sac3d1 Snx15 Arl2 NA Ppp2r5b Men1 Map4k2 Sf1 Nrxn2 Rps6ka4 Prdx5 Kcnk4 Gpr137 Bad Plcb3 Vegfb Macrod1 Otub1 Naa40 Atl3 Rps6kb2 Tmem134 Aip Fam89b Ccdc88b Ctsw Cdc42bpg Tsga10ip Gal3st3 Slc25a45 Dpp3 Ehd1 Rbm14 Cdca5 Ccs NEWGENE_1310680 Zfpl1 Rin1 NA Majin Sptbn2 Atg2a Rbm4b NA Aldh3b2
body_g	6.0	142	41	41	0.98	0.0e+00	Stxbp2 Trappc5 Snapc2 Timm44 Elavl1 Cers4 N4bp2l2 Cwc25 Lasp1 Cacnb1 Dazap2 Rpl19 Stac2 Med30 Fbxl20 Med1 Cdk12 Erbb2 Ikzf3 Zpbp2 Thra Nr1d1 Tbx21 Msl1 Casc3 Snx16 Rara Ice2 Igfbp4 Srcin1 Krt12 Pcgf2 Znrd2 Metap1 Pip4k2b Tspan5 Rap1gds1 Taf6l Ttc9c Slc11a2 Ganab Bbs1 Rom1 B3gat3 Peli3 mrpl11 Slc29a2 Brms1 Yif1a Rab3il1 Fads3 Sf3b2 Banf1 Eif1ad Sart1 Fibp Efemp2 Mus81 Cfl1 Ovol1 Frmd8 Dpf2 Pola2 Tm7sf2 Vps51 Snx15 Arl2 Ppp2r5b Men1 Nrxn2 Slc22a12 Rps6ka4 Prdx5 Kcnk4 Gpr137 Bad Fermt3 Macrod1 Otub1 Rtn3 Atl3 Flrt1 Slc22a20 Arhgap23 Pced1b Scyl1 Fam89b Ext1 Snx32 Ctsw Cdc42bpg Tsga10ip Rapgefl1 Arhgef18 NA Letmd1 Insr Ormdl3 Slc25a45 Dpp3 Galnt6 Krt26 Fbxo47 Cisd3 Stard3 NA Ehd1 Epop NA Pet100 Gjd3 Eif4e Psmb3 Slc48a1 Tmem106c Mllt6 Rpap3 Ccpg1 Adam10 Majin Aldh1a2 Hdac7 Bnip2 Dip2b Fam81a Ahnak Myzap Pfkm Socs7 Pigb Rapgef3 Rnf111 Atf1 Mindy2 Aqp9 Myo1e Zfp958 Pygo1 Tcap Lrrc3c NA NA
dissection: UMAP 3 of all traits	10.9	41	33	33	-0.99	1.4e-192	Stxbp2 Trappc5 Snapc2 Timm44 Elavl1 Cers4 N4bp2l2 Alb Crip2 Tmem121 Klc1 Xrcc3 Zfyve21 Ppp1r13b NA Tmem179 Kif26a Clba1 Cdca4 Gpr132 Jag2 Nudt14 Brf1 Btbd6 Pacs2 Crip1 Arhgef18 Tex22 Pld4 Siva1 Inf2 Insr Cep170b Rd3l Adssl1 Pet100 Tdrd9 NA Zfp958 NA Tedc1
kidney_right_g	9.3	12	7	7	1.00	2.4e-29	Stxbp2 Trappc5 Snapc2 Timm44 Elavl1 Cers4 N4bp2l2 Tnrc6a Arhgef18 Insr Pet100 Zfp958
dissection: PC 3 of all traits	18.0	1	1	1	0.00	1.0e+00	Snx16
dissection: PC 2 of all traits	9.7	32	14	14	0.96	3.3e-107	Crip2 Tmem121 Klc1 Xrcc3 Zfyve21 Ppp1r13b NA Tmem179 Kif26a Clba1 Cdca4 Gpr132 Jag2 Nudt14 Brf1 Btbd6 Pacs2 Crip1 Tex22 Pld4 Siva1 Inf2 Mrps28 Cep170b Rd3l Adssl1 Tdrd9 Zfp704 Zbtb10 NA NA Tedc1
os_mean	14.4	1	0	0	0.00	1.0e+00	Tmem106c
Tibia length in mm	7.4	3	0	0	0.26	6.2e-01	Fndc3a Itm2b Pet100
sol weight in grams	13.2	58	28	28	0.93	2.0e-99	Ptges3 Atp5f1b Alb Rbms2 Cnpy2 Pa2g4 Erbb3 Ikzf4 Tmem198b Dnajc14 Bloc1s1 Itga7 Ice2 Bbs1 Slc29a2 Brms1 Dgka Rnf41 AC128207.1 Coq10a Ormdl2 Sarnp Stat2 Smarcc2 Gls2 Prim1 Zc3h10 Rab27a Rsl24d1 Ccpg1 Myl6 Adam10 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Bnip2 Unc13c Dnaaf4 Fam81a Myzap Tcf12 Mns1 Pigb Tex9 Rfx7 Rnf111 Esyt1 Mindy2 Rbm4b Aqp9 Myo1e NA NA NA Pygo1 NA
TA weight in grams	10.1	341	300	300	0.98	0.0e+00	Phf24 Stxbp2 Trappc5 Snapc2 Timm44 Elavl1 Cers4 N4bp2l2 Mettl7a Rap1gap2 Gc Rtn4rl1 Rpa1 Slc4a4 Serpinf1 Dck Rufy3 Wdr75 Slc43a2 Myo1c Dazap2 Scn8a Aco1 Ddx58 Aptx Atg101 NA Krt86 Pdlim2 Sorbs3 Hnf4g Dleu7 Rnaseh2b Gucy1b2 Trim35 NA Dpysl2 Cyp7b1 Ppp3cc Fam124a Pnma2 Bnip3l Slc39a14 Piwil2 Ints6 Snx16 Polr3d Wdfy2 Ythdf3 Ice2 Phyhip Fabp4 Bmp1 Igfbp6 Mob1b Trmt10a Ppp2r2a Lgi3 Ralyl Hr Tpd52 Csad Nudt18 Pinx1 Fhip2b Sox7 Znf740 Dmtn Msra Rarg Znrd2 Fgf17 Metap1 Kctd9 Pde7a Kif13b Nudt2 Armc1 Hmbox1 Tpcn2 Ighmbp2 Ints9 Extl3 Nefl Nefm Dok2 Fbxo16 Gfra2 Zfp395 Pnoc Elp3 Scara5 Fndc3a Map3k12 Atp5mc2 Slc25a37 Ppp6r3 Lrp5 Tspan5 Esco2 Ccdc25 Rap1gds1 Scara3 Entpd4 Clu Gulo Loxl2 R3hcc1 Kmt5b Chmp7 Syt17 Tcirg1 Rhobtb2 Chrna2 Ndufs8 Aldh3b1 Unc93b1 Egr3 Bin3 Slc22a8 Slc22a6 Gstp1 Ccar2 Rps15a Slc3a2 Pitpnm1 Stx5 Nxf1 Tmem223 Pc Taf6l Ttc9c Hnrnpul2 Slc11a2 Ubxn1 RGD1597339 Ctsf Ganab Actn3 Zdhhc24 Bbs1 Rom1 B3gat3 Mta2 Peli3 mrpl11 Slc29a2 Tut1 Eef1g Brms1 Yif1a Asrgl1 Cnih2 Klc2 Rab3il1 Pacs1 Fads3 Sf3b2 Cst6 Banf1 Eif1ad Sart1 Fibp Efemp2 Mus81 Ppp1r32 Sdhaf2 Cfl1 Cpsf7 Ovol1 NA Ltbp3 Frmd8 Dpf2 Pola2 Ccnd1 Ccdc86 Fau Tm7sf2 Vps51 Sac3d1 Snx15 Arl2 NA Ppp2r5b Men1 Map4k2 Sf1 Nrxn2 Slc22a12 Rps6ka4 Prdx5 Kcnk4 Gpr137 Bad Plcb3 Vegfb Fermt3 Macrod1 Otub1 Naa40 Rtn3 Atl3 Plaat3 Rps6kb2 Bhlhe22 Tmem134 Aip Zc2hc1a Flrt1 tGap1 Fth1 Slc22a20 Pmp2 Stpg2 Scyl1 Fam89b Dock5 Tnrc6a Ext1 Ccdc88b Crk Krt80 Ints5 Syt7 Snx32 Smyd4 Ctsw Sgsm2 Cdc42bpg Adamts3 Tsga10ip Ptk2b Arhgef18 Gal3st3 Slc4a8 Krt1 Letmd1 Insr Slc25a45 Dpp3 Krt4 Tfcp2 Mrps28 Adh7 Galnt6 Pcbp2 Krt77 Tnfrsf10b Fabp12 Prr13 RGD1559600 NA Ehd1 Uqcc3 Rbm14 Cdca5 Fzd3 Prss55 NA Ccs NA NA Krt71 NEWGENE_1310680 Pet100 Zfpl1 Rin1 Gde1 NA Eif4e Rab27a Rsl24d1 Stmn4 Ccpg1 Soat2 AABR07058899.1 Adam10 Majin Zfp704 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Bnip2 Dip2b Unc13c Dnaaf4 Inpp5k Fam81a Ahnak Myzap Tcf12 Mns1 Sptbn2 Scarf1 Pigb Tex9 Doc2b Rfx7 Atg2a Rnf111 Atf1 Pag1 Mindy2 Rph3al Rbm4b Zbtb10 Aqp9 Myo1e NA NA Hey1 NA NA Zfp958 NA NA Pygo1 NA NA NA NA NA Slc10a5 NA Aldh3b2 NA Krt6a NA NA NA NA Ccdc92b Smim27 NA NA Krt6a NA NA
Delay discounting water rate 0 sec	17.8	37	31	31	1.00	4.1e-221	Crip2 Tmem121 Wdr20 Mok Cinp Traf3 NEWGENE_619861 Mark3 Klc1 Xrcc3 Zfyve21 Ppp1r13b NA Tmem179 Kif26a Clba1 Cdca4 Gpr132 Jag2 Nudt14 Brf1 Btbd6 Pacs2 Crip1 Tex22 Pld4 Siva1 Inf2 Zfp839 Cep170b Rd3l Lbhd2 Adssl1 Tdrd9 NA NA Tedc1
pavca_mi_d3_prob_mag	14.2	1	0	0	0.00	1.0e+00	Thra
Cortical porosity	19.5	3	0	0	0.00	1.0e+00	Ddx42 Dcaf7 Ace
length	10.6	7	0	0	1.00	1.6e-65	Pced1b Slc48a1 Tmem106c Rpap3 Hdac7 Pfkm Rapgef3
Trabecular tissue density	13.7	1	0	0	0.00	1.0e+00	Rsl24d1
tautz: manual_mpc3	13.8	1	0	0	0.00	1.0e+00	Trmt10a
tautz: manual_spc22	14.3	16	0	0	1.00	8.6e-38	Sult1e1 Sult1d1 Ugt2b35 Ugt2b10 Tmprss11b Slc4a4 Rufy3 Uba6 AC114845.1 RGD1559459 Ugt2b Ugt2b10 Ugt2b15 NA Ugt2b Ugt2b7
tautz: manual_mpc14	28.2	1	1	1	0.00	1.0e+00	Snx16
tautz: manual_spc4	13.4	2	0	0	0.00	1.0e+00	Snx16 Zbtb10
tautz: manual_spc20	14.7	1	0	0	0.00	1.0e+00	Snx16
tautz: manual_spc5	13.3	4	0	0	0.70	1.2e-01	Ikzf4 Rnf41 Myl6 Esyt1
tautz: manual_spc3	18.0	1	0	0	0.00	1.0e+00	Snx16
tautz: manual_mpc6	15.8	1	0	0	0.00	1.0e+00	Snx16
punishment	16.8	1	0	0	0.00	1.0e+00	Snx16
Weight adjusted by age	50.2	1	1	1	0.00	1.0e+00	Snx16

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	45	2.1	4.0
Adipose	alternative TSS	36	2.2	4.4
Adipose	gene expression	152	1.8	4.1
Adipose	isoform ratio	53	1.9	3.9
Adipose	intron excision ratio	34	1.2	3.4
Adipose	mRNA stability	61	1.8	3.8
BLA	alternative polyA	23	1.9	4.3
BLA	alternative TSS	16	1.9	4.0
BLA	gene expression	121	2.0	4.1
BLA	isoform ratio	34	1.9	4.4
BLA	intron excision ratio	52	1.7	3.9
BLA	mRNA stability	36	1.8	4.0
Brain	alternative polyA	48	2.4	4.5
Brain	alternative TSS	37	2.2	4.2
Brain	gene expression	169	1.9	4.0
Brain	isoform ratio	46	1.5	4.2
Brain	intron excision ratio	107	2.0	4.0
Brain	mRNA stability	86	2.0	3.9
Eye	alternative polyA	3	1.7	3.8
Eye	alternative TSS	3	1.2	4.1
Eye	gene expression	21	1.9	3.9
Eye	isoform ratio	6	1.7	4.4
Eye	intron excision ratio	12	2.0	4.0
Eye	mRNA stability	5	2.1	4.2
IL	alternative polyA	21	3.4	4.8
IL	alternative TSS	5	1.7	3.8
IL	gene expression	63	1.7	3.8
IL	isoform ratio	11	1.4	3.7
IL	intron excision ratio	17	1.8	3.8
IL	mRNA stability	25	2.3	4.2
LHb	alternative polyA	7	1.2	3.9
LHb	alternative TSS	12	3.4	4.2
LHb	gene expression	57	1.8	3.8
LHb	isoform ratio	11	1.5	3.8
LHb	intron excision ratio	11	1.1	3.3
LHb	mRNA stability	16	1.5	4.0
Liver	alternative polyA	30	2.0	4.1
Liver	alternative TSS	19	1.3	3.8
Liver	gene expression	134	1.9	3.9
Liver	isoform ratio	29	1.2	3.6
Liver	intron excision ratio	93	2.1	3.8
Liver	mRNA stability	61	2.5	4.0
NAcc	alternative polyA	7	1.3	4.2
NAcc	alternative TSS	7	2.1	3.3
NAcc	gene expression	56	1.7	3.8
NAcc	isoform ratio	14	1.9	4.3
NAcc	intron excision ratio	11	1.2	3.7
NAcc	mRNA stability	19	1.8	4.1
NAcc2	alternative polyA	30	2.7	4.6
NAcc2	alternative TSS	12	1.6	4.0
NAcc2	gene expression	108	2.0	4.0
NAcc2	isoform ratio	31	2.0	4.3
NAcc2	intron excision ratio	41	1.5	3.8
NAcc2	mRNA stability	42	2.4	4.3
OFC	alternative polyA	12	2.1	4.1
OFC	alternative TSS	7	2.2	4.0
OFC	gene expression	74	2.0	4.0
OFC	isoform ratio	16	2.0	4.1
OFC	intron excision ratio	31	3.1	4.4
OFC	mRNA stability	26	2.4	4.2
PL	alternative polyA	15	2.5	4.5
PL	alternative TSS	4	1.3	3.7
PL	gene expression	65	1.7	4.0
PL	isoform ratio	14	1.6	3.9
PL	intron excision ratio	17	1.6	3.8
PL	mRNA stability	29	2.5	4.2
PL2	alternative polyA	31	2.5	4.6
PL2	alternative TSS	30	3.2	4.4
PL2	gene expression	123	1.9	4.0
PL2	isoform ratio	41	2.2	4.4
PL2	intron excision ratio	53	1.7	3.8
PL2	mRNA stability	42	1.7	3.9

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