Hub : Traits

sol weight in grams

Project: lionikas_2014

1137 significantly associated models · 198 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	2	45435209	47498986	4	1	1.2e-09	1.9e-08	5.1e-01	99	Mocs2
2	2	110161447	113607123	4	1	3.3e-09	6.8e-10	7.8e-50	-478	Slc2a2
3	2	113624043	118238955	13	4	1.2e-09	7.4e-10	1.0e+00	100	Mfn1 Ccdc39 Egfem1 NA
4	4	17825992	20728817	4	1	8.1e-12	7.4e-12	1.0e+00	100	Cacna2d1
5	5	16490911	18501601	2	1	1.2e-07	8.1e-08	1.0e+00	100	Penk
6	5	32364125	34085103	2	1	1.0e-07	4.8e-08	1.0e+00	100	Cpne3
7	5	137682119	138752373	1	1	1.6e-10	1.6e-02	8.6e-11	-625	Stk40
8	6	49976875	52971202	5	2	1.3e-08	2.0e-09	4.0e-02	88	Ahr Twist1
9	7	6527566	11123596	112	9	1.0e-08	6.1e-08	1.0e+00	100	Nfic Ncln Map2k2 Zfr2 Cbarp Diras1 Apc2 Giot1 AC094643.2
10	8	69336832	77140861	42	8	4.2e-14	6.6e-14	1.0e+00	100	Anxa2 Tmod2 Rab27a Rsl24d1 Adam10 Bnip2 Unc13c Fam81a
11	8	102533918	104393934	4	1	1.7e-07	4.1e-08	1.0e+00	100	Amotl2
12	20	5086090	6657065	5	4	8.3e-08	6.8e-08	1.0e+00	100	Spdef Taf11 Ilrun NA

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
body_g	4.6	24	0	0.0	1.00	3.3e-107	Atp6v0d2 Cep63 Amotl2 Rab6b Ice2 Stk40 Rab27a Rsl24d1 Ccpg1 Adam10 Aldh1a2 Bnip2 Dnaaf4 Fam81a Myzap Mns1 Nedd4 Pigb Rnf111 Mindy2 Aqp9 Myo1e NA Pygo1
dissection: UMAP 3 of all traits	7.4	5	0	0.0	-1.00	3.3e-04	Spdef Taf11 Ilrun NA NA
dissection: PC 2 of all traits	6.8	40	0	0.0	-0.95	6.1e-46	Mier2 Plpp2 Snx13 Ncln Bsg Fgf22 Rnf126 Palm R3hdm4 Kiss1r Wdr18 Abca7 Gpx4 Sbno2 Pcsk4 Abhd17a Btbd2 Mob3a Ap3d1 NA Dapk3 Atcay Zfr2 Matk Cbarp Pwwp3a Ndufs7 Gamt Rps15 Polrmt Mknk2 Prtn3 Reep6 Cfd Apc2 Plk5 Slc39a3 Zfp709l1 NA NA
glucose_mg_dl	24.2	1	1	2.9	0.00	1.0e+00	Stk40
EDL weight in grams	5.7	138	28	82.4	1.00	0.0e+00	Mier2 Plpp2 Nfic Ncln Gna11 Tle2 Tle6 Sirt6 Ankrd24 Theg Odf3l2 Bsg Hcn2 Fgf22 Rnf126 Palm Ice2 Anxa2 R3hdm4 Kiss1r Wdr18 Grin3b Abca7 Arhgap45 Polr2e Gpx4 Sbno2 Midn Efna2 Pcsk4 Rexo1 Abhd17a Scamp4 Csnk1g2 Btbd2 Mob3a Ap3d1 Sf3a2 Lsm7 NA Gadd45b NA Sgta Map2k2 Zbtb7a Dapk3 Atcay Zfr2 Matk Mrpl54 Apba3 Tjp3 Pip5k1c Tbxa2r Hmg20b Cbarp Pwwp3a Ndufs7 Gamt Rps15 Polrmt Atp8b3 Stk40 Lmnb2 Plppr3 Mbd3 Mknk2 Diras1 Prtn3 Gzmm Dazap1 Izumo4 Creb3l3 Tmprss9 Dot1l Lingo3 Jsrp1 Reep6 Cfd NA Klf16 Apc2 Plk5 Mfsd12 NA Slc39a3 NA Tcf3 Giot1 Rab27a Rsl24d1 Ccpg1os AC094643.2 Ccpg1 Cgnl1 Adam10 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Zfp280d Bnip2 Mir628 Unc13c Dnaaf4 Fam81a Myzap Tcf12 Mns1 Sppl2b Nedd4 Pigb Tex9 Lipc Rfx7 Rnf111 Mindy2 Aqp9 Myo1e NA NA Adat3 NA NA NA NA NA NA Pygo1 NA Zfp709l1 NA NA NA NA NA Zfp347
TA weight in grams	11.9	42	35	102.9	0.99	1.2e-218	Hdac9 Snx13 Onecut1 Leo1 Ice2 Anxa2 Tmod2 Twist1 Tmod3 Rab27a Rsl24d1 Ccpg1os Ccpg1 Cgnl1 Adam10 Khdc3 AC142458.1 Wdr72 Aldh1a2 Prtg Bnip2 Mir628 Unc13c Dnaaf4 Fam81a Myzap Tcf12 Mns1 Nedd4 Pigb Tex9 Lipc Rfx7 Rnf111 Mindy2 Aqp9 Myo1e NA NA Pygo1 NA NA
light_reinforcement_lr_active	9.7	1	0	0.0	0.00	1.0e+00	Apc2
reaction_time_corr	12.8	2	0	0.0	0.00	1.0e+00	Cpne3 Atp6v0d2
reaction_time_leftcorr	12.8	2	0	0.0	0.00	1.0e+00	Cpne3 Atp6v0d2
pavca_mi_d3_magazine_ncs	20.8	1	0	0.0	0.00	1.0e+00	Stk40
pavca_mi_d1_avg_lev_lat	12.3	1	0	0.0	0.00	1.0e+00	Stk40
Total cortical area	11.9	4	0	0.0	-1.00	3.4e-04	Spdef Taf11 Ilrun NA
Trabecular tissue density	12.6	10	0	0.0	1.00	1.3e-32	Rab27a Rsl24d1 Ccpg1os Ccpg1 Khdc3 Prtg Dnaaf4 Pigb Tex9 NA
tautz: manual_spc21	17.1	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_spc14	16.5	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_mpc4	14.8	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_mpc10	24.5	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_mpc5	23.1	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_mpc14	11.2	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_mpc12	13.0	2	0	0.0	0.00	1.0e+00	Snx13 Stk40
tautz: manual_mcs	17.3	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_spc4	18.0	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_spc10	80.6	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_spc11	85.1	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_spc6	40.1	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_mpc17	13.2	1	0	0.0	0.00	1.0e+00	Stk40
tautz: manual_spc1	31.5	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_spc18	46.6	1	1	2.9	0.00	1.0e+00	Stk40
tautz: manual_mpc11	17.2	1	0	0.0	0.00	1.0e+00	Stk40

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	0.66	2.8
Adipose	alternative TSS	11	0.68	2.8
Adipose	gene expression	57	0.69	2.9
Adipose	isoform ratio	25	0.89	2.8
Adipose	intron excision ratio	14	0.48	3.2
Adipose	mRNA stability	22	0.64	2.8
BLA	alternative polyA	8	0.67	3.1
BLA	alternative TSS	7	0.83	2.9
BLA	gene expression	53	0.87	2.9
BLA	isoform ratio	20	1.14	3.1
BLA	intron excision ratio	24	0.80	3.0
BLA	mRNA stability	29	1.43	3.0
Brain	alternative polyA	15	0.75	3.0
Brain	alternative TSS	7	0.41	3.1
Brain	gene expression	71	0.78	2.9
Brain	isoform ratio	27	0.85	3.0
Brain	intron excision ratio	44	0.81	3.0
Brain	mRNA stability	31	0.71	2.8
Eye	alternative polyA	0	0.00	2.9
Eye	alternative TSS	0	0.00	2.9
Eye	gene expression	7	0.62	3.0
Eye	isoform ratio	5	1.41	3.3
Eye	intron excision ratio	5	0.82	2.9
Eye	mRNA stability	3	1.29	2.6
IL	alternative polyA	9	1.48	3.3
IL	alternative TSS	6	2.09	3.1
IL	gene expression	28	0.77	2.9
IL	isoform ratio	4	0.51	2.7
IL	intron excision ratio	4	0.41	2.7
IL	mRNA stability	12	1.08	3.0
LHb	alternative polyA	4	0.70	2.9
LHb	alternative TSS	1	0.29	2.9
LHb	gene expression	22	0.69	2.9
LHb	isoform ratio	6	0.80	2.7
LHb	intron excision ratio	8	0.78	2.8
LHb	mRNA stability	6	0.58	3.0
Liver	alternative polyA	12	0.80	2.6
Liver	alternative TSS	3	0.20	2.7
Liver	gene expression	46	0.64	2.8
Liver	isoform ratio	12	0.50	2.6
Liver	intron excision ratio	27	0.62	2.9
Liver	mRNA stability	15	0.61	2.8
NAcc	alternative polyA	0	0.00	2.5
NAcc	alternative TSS	3	0.88	2.8
NAcc	gene expression	21	0.64	2.9
NAcc	isoform ratio	9	1.21	3.0
NAcc	intron excision ratio	2	0.21	2.6
NAcc	mRNA stability	12	1.11	3.0
NAcc2	alternative polyA	2	0.18	3.0
NAcc2	alternative TSS	11	1.51	3.2
NAcc2	gene expression	53	0.99	3.0
NAcc2	isoform ratio	18	1.17	3.1
NAcc2	intron excision ratio	15	0.57	2.9
NAcc2	mRNA stability	16	0.90	3.0
OFC	alternative polyA	2	0.34	2.6
OFC	alternative TSS	7	2.19	3.8
OFC	gene expression	32	0.86	3.0
OFC	isoform ratio	4	0.49	2.7
OFC	intron excision ratio	5	0.50	3.5
OFC	mRNA stability	11	1.02	2.9
PL	alternative polyA	4	0.67	3.0
PL	alternative TSS	2	0.65	3.0
PL	gene expression	33	0.89	2.9
PL	isoform ratio	5	0.57	2.8
PL	intron excision ratio	7	0.67	3.0
PL	mRNA stability	13	1.13	3.2
PL2	alternative polyA	9	0.72	2.9
PL2	alternative TSS	7	0.75	3.1
PL2	gene expression	56	0.88	2.9
PL2	isoform ratio	12	0.65	2.9
PL2	intron excision ratio	20	0.63	3.0
PL2	mRNA stability	22	0.90	2.9

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