Hub : Traits

TA weight in grams

Project: lionikas_2014

2571 significantly associated models · 495 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	7254793	8653308	1	1	1.2e-07	6.5e-08	1.0000	100	Adat2
2	1	171727837	174685359	10	5	1.1e-08	1.8e-08	1.0000	100	Umod Coq7 Ccp110 Iqck RGD1559600
3	1	176058408	178603594	5	1	1.1e-08	1.0e-08	1.0000	100	Lcmt1
4	1	182621727	184020648	1	1	1.3e-08	1.1e-05	0.0016	49	NA
5	1	199398809	209332281	172	8	9.1e-13	1.1e-11	1.0000	100	Pitpnm1 Ttc9c Klc2 Map4k2 Fth1 Snx32 Sptbn2 Kat5
6	2	89673058	95023945	16	1	1.1e-11	7.1e-12	1.0000	100	Mrps28
7	2	99969887	102351095	2	1	1.4e-07	8.2e-08	0.0604	88	Cyp7b1
8	2	116853286	120258488	11	1	4.2e-09	1.5e-08	0.1183	92	Qrfpr
9	2	120766913	122200263	2	1	1.3e-07	4.0e-08	1.0000	100	Ankrd50
10	2	122912439	125075599	5	1	2.7e-08	2.7e-07	0.5382	99	Larp1b
11	2	134751245	136150616	1	1	3.3e-07	3.6e-07	1.0000	100	Ndufc1
12	2	225664331	228461478	9	4	2.8e-09	1.7e-10	1.0000	100	Trmt10a Metap1 Rap1gds1 Dnajb14
13	5	48482122	49968409	3	2	5.4e-08	2.3e-08	1.0000	100	Rars2 RGD1359108
14	5	54563228	59007126	39	1	5.4e-09	2.7e-10	1.0000	100	Nudt2
15	5	110123645	115818093	22	6	7.4e-09	1.2e-08	NaN	NaN	Dock7 Atg4c Itgb3bp Ube2u Cyp2j4 Cyp2j10
16	6	19725850	21124468	1	1	1.3e-09	3.9e-10	0.0665	91	Ltbp1
17	6	50926403	53588284	4	1	1.9e-09	7.6e-08	0.1742	94	Snx13
18	6	96850756	98694675	4	1	2.8e-08	4.4e-07	0.5649	99	Pigh
19	7	84572641	85971312	1	1	1.1e-07	1.0e-07	0.0301	83	NA
20	7	130684861	134288889	30	8	1.2e-10	1.3e-10	NaN	NaN	Dazap2 Atg101 NA Tns2 Igfbp6 Znf740 Acvrl1 Krt71
21	8	69336832	75537324	34	8	4.6e-14	4.1e-13	1.0000	100	Ice2 Bnip2 Unc13c Fam81a Myzap Pigb Mindy2 NA
22	10	58773413	61792475	24	4	1.5e-10	1.5e-10	1.0000	100	Rtn4rl1 Rpa1 Crk Ccdc92b
23	11	25885318	27372361	3	1	1.7e-07	8.1e-07	0.0964	89	N6amt1
24	11	32148992	35008541	15	5	3.2e-09	2.6e-09	1.0000	100	Kcnj6 Vps26c Setd4 Cbr1 NA
25	12	27006	4653252	21	7	4.0e-10	2.4e-08	NaN	NaN	Pcp2 Trappc5 Stard13 Pex11g Insr Pet100 NA
26	15	35841493	43041493	32	10	7.3e-09	5.4e-09	1.0000	100	Gucy1b2 Trim35 Fam124a Ints6 Wdfy2 Nefm Prss55 Stmn4 NA NA
27	15	43349498	46523169	27	4	3.7e-08	3.7e-08	1.0000	100	Polr3d Phyhip Dmtn Egr3

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	9.3	24	21	24.4	-1.00	2.1e-76	Mcoln1 Pcp2 Stxbp2 Trappc5 Evi5l Snapc2 Timm44 Elavl1 Cers4 Stard13 N4bp2l2 Brca2 Jade1 Lcmt1 Arhgef18 Pex11g Mcemp1 Lrrc8e Insr Larp1b Pet100 N4bp2l1 Zfp958 NA
retroperitoneal_fat_g	6.1	87	0	0.0	-1.00	0.0e+00	Znrd2 Tpcn2 Ighmbp2 Ppp6r3 Lrp5 Kmt5b Tcirg1 Ndufs8 Aldh3b1 Gstp1 Ctsf Actn3 Zdhhc24 Bbs1 Peli3 mrpl11 Slc29a2 Brms1 Yif1a Cnih2 Klc2 Pacs1 Sf3b2 Cst6 Banf1 Eif1ad Sart1 Fen1 Fibp Efemp2 Mus81 Cfl1 NA Ltbp3 Frmd8 Dpf2 Ccnd1 Capn1 Fau Tm7sf2 Vps51 Sac3d1 Snx15 Arl2 NA Ppp2r5b Men1 Map4k2 Sf1 Nrxn2 Rps6ka4 Prdx5 Esrra Kcnk4 Gpr137 Bad Plcb3 Vegfb Macrod1 Otub1 Naa40 Atl3 Tmem134 Aip Tigd3 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	7.0	137	40	46.5	0.95	3.8e-221	Mcoln1 Pcp2 Stxbp2 Trappc5 Evi5l Snapc2 Timm44 Elavl1 Cers4 Stard13 N4bp2l2 Brca2 Rars2 Mpp5 Slc35a1 Atp6v1d RGD1359108 Snx16 Ice2 Ankrd50 NEWGENE_1309446 Mttp Pigh Dcun1d1 Znrd2 Metap1 Mccc1 RGD1565989 Jade1 Acad9 Gne Qrfpr Anxa5 Bbs7 Tspan5 Rap1gds1 Trpc3 Kmt5b Ca9 Ccdc107 Slc22a8 Taf6l Ttc9c Ganab Actn3 Bbs1 Rom1 B3gat3 Peli3 mrpl11 Slc29a2 Brms1 Yif1a Rab3il1 Fads3 Sf3b2 Banf1 Eif1ad Sart1 Fibp Efemp2 Mus81 Cfl1 Ovol1 Frmd8 Dpf2 Pola2 Tm7sf2 Vps51 Naaladl1 Snx15 Arl2 Ppp2r5b Men1 Nrxn2 Slc22a12 Rps6ka4 Prdx5 Kcnk4 Gpr137 Bad Fermt3 Macrod1 Otub1 Rtn3 Atl3 Flrt1 Slc22a20 Scyl1 Fam89b Snx32 Ctsw Cdc42bpg Tsga10ip Arhgef18 Pex11g Mcemp1 Lrrc8e Insr Slc25a45 Dpp3 Incenp Galnt6 RGD1359508 Larp1b NA Ehd1 Vps37c NA Pet100 Atp11b Eif4e Ccpg1 Adam10 Majin Rdh11 Aldh1a2 Bnip2 AABR07010085.2 Dnaaf4 Fam81a Ahnak Myzap N4bp2l1 Pigb Rnf111 Mindy2 Aqp9 Myo1e NA NA Zfp958 NA Pygo1 NA NA NA
dissection: UMAP 3 of all traits	13.6	21	19	22.1	-0.99	3.3e-65	Mcoln1 Pcp2 Stxbp2 Trappc5 Evi5l Snapc2 Timm44 Elavl1 Cers4 Stard13 N4bp2l2 Brca2 Arhgef18 Pex11g Mcemp1 Lrrc8e Insr Pet100 N4bp2l1 Zfp958 NA
kidney_right_g	9.3	23	17	19.8	1.00	5.4e-68	Mcoln1 Pcp2 Stxbp2 Trappc5 Evi5l Snapc2 Timm44 Elavl1 Cers4 Stard13 N4bp2l2 Brca2 Lcmt1 Tnrc6a Arhgef18 Pex11g Mcemp1 Lrrc8e Insr Pet100 N4bp2l1 Zfp958 NA
dissection: PC 3 of all traits	18.0	1	1	1.2	0.00	1.0e+00	Snx16
dissection: PC 2 of all traits	7.5	6	0	0.0	-0.33	4.2e-01	Snx13 Mrps28 Zfp704 Zbtb10 Hey1 NA
EDL weight in grams	7.7	432	300	348.8	0.99	0.0e+00	Phf24 Mcoln1 Pcp2 Stxbp2 Trappc5 Evi5l Snapc2 Timm44 Elavl1 Cers4 Stard13 N4bp2l2 Brca2 Mettl7a Kcnj6 Vps26c Ttc3 Ripply3 Hlcs Cldn14 Setd4 Rap1gap2 Pafah1b1 Mnt Rtn4rl1 Rpa1 Serpinf1 Serpinf2 Slc43a2 Myo1c Snx13 Dazap2 Ywhae Scn8a Ankmy2 Aco1 Ddx58 Aptx Dnaja1 Smu1 Atg101 Glod4 NA Unc13b Krt86 Pdlim2 Rars2 Sorbs3 Slc35a1 Rnaseh2b Fam214b Gucy1b2 Trim35 RGD1359108 NA Stoml2 Dpysl2 Cyp7b1 Ppp3cc Fam124a Bnip3l Slc39a14 Piwil2 Ints6 Pigo Snx16 Polr3d Wdfy2 Ice2 Anxa2 Nol6 Phyhip Tns2 Mttp Fabp4 Bmp1 Igfbp6 Trmt10a Ppp2r2a Lgi3 Hr Tpd52 Csad Nudt18 Ubap1 Pinx1 Fhip2b Sox7 Znf740 Dmtn Msra Dcun1d1 Znrd2 Fgf17 Metap1 Kctd9 Kif13b Nudt2 Armc1 Mccc1 Hmbox1 Tpcn2 Aaas Ighmbp2 Ints9 Extl3 Nefl Nefm Dok2 RGD1565989 Fbxo16 Jade1 Acad9 Cpt1a Gne Qrfpr Anxa5 Lcmt1 Galt Il11ra1 Slc25a37 Ppp6r3 Ccl19 Bbs7 Lrp5 Tspan5 Rap1gds1 Npr2 Vps35l Trpc3 Scara3 Rgp1 Entpd4 Gba2 Gulo Tmc7 Tpm2 Loxl2 R3hcc1 Kmt5b Chka Chmp7 Coq7 Ca9 Tcirg1 Ccdc107 Rhobtb2 Chrna2 Ndufs8 Cd72 Aldh3b1 Unc93b1 Egr3 Acy3 Tbx10 Nudt8 Bin3 Slc22a8 Slc22a6 Gstp1 Ccar2 Rps15a Slc3a2 Pitpnm1 Stx5 Nxf1 Tmem223 Tmem179b Pc Taf6l Ttc9c Rce1 Hnrnpul2 Slc11a2 Gng3 Ubxn1 RGD1597339 Ctsf Ganab Actn3 Zdhhc24 Bbs1 Rom1 B3gat3 Mta2 Peli3 mrpl11 Slc29a2 Tut1 Eef1g Brms1 Yif1a Asrgl1 Cnih2 Klc2 Best1 Rab3il1 Pacs1 Fads3 Sf3b2 Fads2 Cst6 Banf1 Eif1ad Sart1 Fibp Efemp2 Mus81 Ppp1r32 Sdhaf2 Cfl1 Cpsf7 Ovol1 NA Ddb1 Ltbp3 Cd5 Frmd8 Dpf2 Pola2 Ccnd1 Capn1 Fau Tm7sf2 Vps51 Naaladl1 Cblif Sac3d1 Mrpl16 Snx15 Arl2 NA Ppp2r5b Men1 Map4k2 Sf1 Nrxn2 Slc22a12 Rps6ka4 Prdx5 Esrra Kcnk4 Gpr137 Bad Plcb3 Vegfb Fermt3 Macrod1 Otub1 Naa40 Rtn3 Atl3 Plaat3 Tmem132a Slc15a3 Atp8b5p Tmem134 Aip Zc2hc1a Flrt1 tGap1 Fth1 Slc22a20 Pmp2 NA Tigd3 Stpg2 Scyl1 Gpr139 Fam89b Dock5 Tnrc6a Ccdc88b RGD1311946 Crk Krt80 Ints5 Morc3 Syt7 Snx32 Smyd4 Ctsw Sgsm2 Ccp110 Cdc42bpg Tsga10ip Ptk2b Tmem109 Arhgef18 Pex11g Mcemp1 Lrrc8e Acvrl1 Gal3st3 Slc4a8 Krt1 Insr Slc25a45 Dpp3 Krt4 Tfcp2 Mrps28 Incenp Adh7 Galnt6 Ltbp1 Vcp Ccl21 Iqck Krt77 Larp1b Tnfrsf10b Fabp12 Ccl27 Fam219a Prr13 RGD1559600 Tmem215 NA Ehd1 Uqcc3 Rbm14 Rusc2 Vps37c Cdca5 Fzd3 Prss55 NA Ccs NA NA Krt71 Cbr1 NEWGENE_1310680 Pet100 Zfpl1 Rin1 NA Dcaf12 Dop1b Atp11b Eif4e Bscl2 Rab27a Rsl24d1 Ccpg1os Stmn4 Ccpg1 Tesk1 Cgnl1 Sim2 Adam10 Majin Zfp704 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Bnip2 Ehbp1l1 Mir628 AABR07006120.1 Unc13c Dnaaf4 Inpp5k Fam81a Ahnak Myzap Tcf12 Mns1 Krt79 Sptbn2 N4bp2l1 B4galt1 Scarf1 Pigb Tex9 Doc2b Dnajb14 Vwce Lipc Rfx7 Atg2a Rnf111 Atf1 Pag1 Mindy2 Rph3al U4 Rbm4b Zbtb10 Aqp9 Myo1e NA NA NA Hey1 NA NA NA NA Zfp958 NA NA NA Pygo1 NA NA NA NA NA Slc10a5 NA NA Aldh3b2 NA NA NA Krt6a NA NA NA NA Ccdc92b Smim27 NA Knop1 NA Krt6a NA NA
Tibia length in mm	6.9	12	0	0.0	1.00	2.3e-36	Mcoln1 Stxbp2 Trappc5 Evi5l Snapc2 Stard13 N4bp2l2 Brca2 Pex11g Lrrc8e Insr Pet100
sol weight in grams	14.6	44	35	40.7	0.91	9.6e-85	Snx13 Ice2 Anxa2 Bbs1 Slc29a2 Brms1 Cnih2 Gal3st3 Dpp3 Ccs Rab27a Rsl24d1 Ccpg1os Ccpg1 Cgnl1 Adam10 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Zfp280d Bnip2 Mir628 Unc13c Dnaaf4 Fam81a Myzap Tcf12 Mns1 Pigb Tex9 Lipc Rfx7 Rnf111 Mindy2 Rbm4b Aqp9 Myo1e NA NA Pygo1 NA NA
ccp_trial_3_saline_dist_mm	16.2	2	0	0.0	0.00	1.0e+00	Snx13 Ankmy2
Trabecular tissue density	16.4	25	1	1.2	-0.94	7.7e-89	Nfia Tm2d1 Patj Kank4 Usp1 Dock7 Angptl3 Atg4c Alg6 Itgb3bp Efcab7 Pgm1 Ube2u RGD1560146 Hook1 Ror1 Cyp2j4 Cyp2j10 L1td1 Rsl24d1 Ccpg1 AC142458.1 NA NA NA
tautz: manual_spc7	13.2	3	0	0.0	-1.00	1.0e-06	Lcmt1 Coq7 Ccp110
tautz: manual_spc15	15.0	1	0	0.0	0.00	1.0e+00	Adat2
tautz: manual_mpc3	13.4	2	0	0.0	0.00	1.0e+00	Mttp Trmt10a
tautz: manual_mpc10	14.9	13	0	0.0	1.00	1.6e-27	Ankrd50 NEWGENE_1309446 Dcun1d1 Mccc1 RGD1565989 Qrfpr Anxa5 Trpc3 RGD1359508 Larp1b AABR07010085.2 NA NA
tautz: manual_mpc14	28.2	1	1	1.2	0.00	1.0e+00	Snx16
tautz: manual_mpc12	13.0	2	0	0.0	0.00	1.0e+00	Snx13 Ankmy2
tautz: manual_spc4	13.2	3	0	0.0	0.00	1.0e+00	Snx16 Pag1 Zbtb10
tautz: manual_mpc9	15.8	14	0	0.0	-1.00	2.2e-29	Rap1gap2 Mnt Dph1 Rtn4rl1 Wdr81 Slc43a2 Pitpna Crk Smyd4 Sgsm2 Scarf1 Doc2b NA Ccdc92b
tautz: manual_spc20	14.2	8	0	0.0	-0.86	3.4e-05	Snx16 RGD1565989 Jade1 Qrfpr Anxa5 Bbs7 Trpc3 Larp1b
tautz: manual_spc3	18.0	1	0	0.0	0.00	1.0e+00	Snx16
tautz: manual_mpc6	15.8	1	0	0.0	0.00	1.0e+00	Snx16
tautz: manual_mpc11	14.4	1	0	0.0	0.00	1.0e+00	Snx16
punishment	20.7	3	1	1.2	1.00	7.4e-08	Slc35a1 RGD1359108 Snx16
Weight adjusted by age	50.2	1	1	1.2	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	2.12	3.7
Adipose	alternative TSS	39	2.42	4.2
Adipose	gene expression	146	1.76	3.5
Adipose	isoform ratio	51	1.81	3.6
Adipose	intron excision ratio	22	0.75	2.9
Adipose	mRNA stability	47	1.36	3.3
BLA	alternative polyA	21	1.75	3.6
BLA	alternative TSS	14	1.67	3.4
BLA	gene expression	109	1.80	3.5
BLA	isoform ratio	34	1.94	3.5
BLA	intron excision ratio	50	1.67	3.1
BLA	mRNA stability	34	1.68	3.5
Brain	alternative polyA	36	1.79	3.8
Brain	alternative TSS	23	1.34	3.4
Brain	gene expression	145	1.60	3.5
Brain	isoform ratio	58	1.84	3.5
Brain	intron excision ratio	88	1.63	3.3
Brain	mRNA stability	76	1.74	3.5
Eye	alternative polyA	5	2.79	3.5
Eye	alternative TSS	1	0.42	3.3
Eye	gene expression	20	1.78	3.4
Eye	isoform ratio	4	1.13	3.3
Eye	intron excision ratio	14	2.28	3.5
Eye	mRNA stability	5	2.15	3.5
IL	alternative polyA	22	3.61	4.1
IL	alternative TSS	4	1.39	3.7
IL	gene expression	56	1.54	3.4
IL	isoform ratio	22	2.79	3.7
IL	intron excision ratio	16	1.66	3.2
IL	mRNA stability	22	1.98	3.5
LHb	alternative polyA	9	1.57	3.6
LHb	alternative TSS	9	2.59	4.1
LHb	gene expression	59	1.84	3.4
LHb	isoform ratio	13	1.73	3.3
LHb	intron excision ratio	10	0.97	2.6
LHb	mRNA stability	13	1.26	3.4
Liver	alternative polyA	29	1.93	3.6
Liver	alternative TSS	21	1.39	3.2
Liver	gene expression	110	1.53	3.3
Liver	isoform ratio	36	1.51	3.3
Liver	intron excision ratio	57	1.30	3.2
Liver	mRNA stability	39	1.59	3.4
NAcc	alternative polyA	9	1.73	3.3
NAcc	alternative TSS	5	1.47	2.7
NAcc	gene expression	47	1.43	3.3
NAcc	isoform ratio	22	2.97	4.0
NAcc	intron excision ratio	10	1.05	2.9
NAcc	mRNA stability	22	2.03	3.7
NAcc2	alternative polyA	20	1.81	3.6
NAcc2	alternative TSS	13	1.78	3.6
NAcc2	gene expression	102	1.91	3.6
NAcc2	isoform ratio	30	1.95	3.5
NAcc2	intron excision ratio	38	1.44	3.1
NAcc2	mRNA stability	30	1.68	3.7
OFC	alternative polyA	11	1.88	3.5
OFC	alternative TSS	6	1.88	3.1
OFC	gene expression	71	1.92	3.4
OFC	isoform ratio	18	2.21	3.4
OFC	intron excision ratio	23	2.29	3.5
OFC	mRNA stability	17	1.57	3.7
PL	alternative polyA	18	3.01	3.8
PL	alternative TSS	6	1.94	3.7
PL	gene expression	61	1.64	3.4
PL	isoform ratio	19	2.18	3.7
PL	intron excision ratio	15	1.44	3.1
PL	mRNA stability	22	1.91	3.7
PL2	alternative polyA	28	2.23	3.7
PL2	alternative TSS	19	2.03	3.7
PL2	gene expression	120	1.88	3.5
PL2	isoform ratio	43	2.33	3.6
PL2	intron excision ratio	50	1.59	3.2
PL2	mRNA stability	42	1.72	3.5

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