Hub : Traits

Soleus weight

Muscle

Tags: Physiology · Muscle

Project: lionikas_2014

12 loci · 37 genes with independent associations · 685 total associated genes

Significant Loci

#	Chr	Start pos	End pos	# assoc genes	# joint models	Best TWAS P	Best GWAS P	Cond GWAS P	Joint genes
1	chr2	45805476	47511335	15	6	3.47e-09	1.92e-08	2.69e-13	Itga1 Mocs2 Pelo
2	chr2	109920085	112309017	6	1	1.71e-08	1.46e-09	6.05e-03	Pld1
3	chr2	113625967	117667018	43	1	8.08e-10	7.39e-10	1.00e+00	Ccdc39
4	chr4	18046243	20728817	7	1	8.13e-12	7.40e-12	1.00e+00	Cacna2d1
5	chr5	26491462	27887585	1	1	1.64e-07	1.26e-07	1.00e+00	LOC120102834
6	chr5	32364125	33884913	2	1	6.78e-08	4.78e-08	1.95e-01	Cpne3
7	chr5	137680740	138752373	3	1	1.38e-07	1.59e-02	5.01e-01	Stk40
8	chr6	50925291	52322886	4	1	1.27e-08	2.04e-09	6.83e-03	Hdac9
9	chr7	6527566	11994279	431	11	3.46e-11	6.11e-08	1.00e+00	Brd4 Kiss1r LOC103690119 LOC130046242 Mier2 Plekhj1 Spmap2 Tbxa2r Timm13 Zfp347
10	chr8	69362619	78060378	156	11	1.10e-13	6.58e-14	1.00e+00	Adam10 Aqp9 Ccpg1 LOC103693133 LOC120094195 LOC120094204 Myzap Pierce2 Rab27a Tmod2 Wdr72
11	chr8	102517155	104287494	9	1	3.69e-08	4.15e-08	1.00e+00	Cep63
12	chr20	5086090	6587967	8	1	1.26e-07	6.79e-08	1.05e-01	Snrpc

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	6.66	163	8	21.6	0.99	0.00e+00	Abca7 Abhd17a Adam10 Adamtsl5 Adat3 Aldh1a2 Amh Ankrd24 Ap3d1 Apba3 Apc2 Arhgap45 Arid3a Atcay Atp8b3 Bnip2 Brd4 Bsg Btbd2 C2cd4c Cbarp Ccpg1 Celf5 Cfd Cgnl1 Cirbp Creb3l3 Csnk1g2 Dapk3 Dazap1 Diras1 Dnaaf4 Dot1l Efna2 Fam174c Fam81a Fgf22 Gadd45b Gamt Giot1 Gipc3 Gna11 Gng7 Gpx4 Grin3b Gtf2a2 Gzmm Hcn2 Hdac9 Hmg20b Ice2 Izumo4 Jsrp1 Khdc3 Kiss1r Klf16 Lingo3 Lmnb2 LOC100125368 LOC100360470 LOC100909682 LOC100910577 LOC100912823 LOC102549817 LOC102550657 LOC102552420 LOC102553301 LOC103690119 LOC103693133 LOC103693140 LOC108351405 LOC108351595 LOC120093530 LOC120093532 LOC120093770 LOC120093772 LOC120093775 LOC120094195 LOC120094201 LOC120094202 LOC120094203 LOC120094204 LOC130046242 Lsm7 Map2k2 Matk Mbd3 Mex3d Mfsd12 Midn Mier2 Mindy2 Mir628 Misp Mknk2 Mob3a Mrpl54 Myo1e Myzap Ncln Ndufs7 Nedd4 Nfic Oaz1 Palm Pcsk4 Pierce2 Pigb Pip5k1c Plekhj1 Plk5 Plpp2 Plppr3 Polr2e Polrmt Prss57 Prtg Prtn3 Ptbp1 Pwwp3a Pygo1 R3hdm4 Rab27a Reep6 Rexo1 RGD1359127 Rnf111 Rnf126 Rpl37a-ps11 Rps15 Rsl24d1 Sbno2 Scamp4 Sf3a2 Sgta Shc2 Sirt6 Slc39a3 Smim24 Spmap2 Sppl2b Stk11 Tbxa2r Tcf12 Tcf3 Tex9 Thop1 Timm13 Tjp3 Tle2 Tle5 Tle6 Tmem259 Tmprss9 Unc13c Wdr18 Wdr72 Zbtb7a Zfp347 Zfp709l1 Zfp873 Zfr2 Znf624l
Body weight	4.67	32	0	0	1	3.83e-193	Adam10 Aldh1a2 Amotl2 Aqp9 Bnip2 Ccpg1 Cep63 Cgnl1 Cpne3 Dnaaf4 Fam81a Gtf2a2 Lipc LOC103693133 LOC120094195 LOC120094201 LOC120094203 LOC120094204 Mindy2 Myo1e Myzap Nedd4 Pigb Polr2m Prtg Pygo1 Rnf111 Rpl37a-ps11 Rsl24d1 Sltm Tcf12 Tex9
Epididymis fat weight	14.35	4	4	10.8	-1	6.68e-11	Ilrun LOC103694391 Snrpc Spdef
Glucose	19.8	1	1	2.7	0	1.00e+00	Stk40
Tail length	8.24	4	1	2.7	1	1.24e-11	Ilrun LOC103694391 Snrpc Spdef
Length with tail	5.63	4	0	0	1	2.71e-09	Ilrun LOC103694391 Snrpc Spdef
Liver weight, right	15.64	4	3	8.1	1	7.50e-10	Ilrun LOC103694391 Snrpc Spdef
Extensor digitorum longus weight	6.14	151	38	102.7	1	0.00e+00	Abca7 Abhd17a Adam10 Adat3 Aldh1a2 Ankrd24 Ap3d1 Apba3 Apc2 Aqp9 Arid3a Atcay Atp8b3 Bnip2 Bsg Btbd2 C2cd4c Cbarp Ccpg1 Celf5 Cfd Cgnl1 Cirbp Csnk1g2 Dapk3 Dazap1 Diras1 Dnaaf4 Dot1l Efna2 Fam174c Fam81a Fgf22 Gamt Giot1 Gipc3 Gna11 Gng7 Gpx4 Gtf2a2 Gzmm Hcn2 Hmg20b Ice2 Izumo4 Jsrp1 Khdc3 Kiss1r Klf16 Lipc Lmnb2 LOC100125368 LOC100360470 LOC100909682 LOC100910577 LOC100912823 LOC102549817 LOC102550657 LOC102552420 LOC102553301 LOC103693133 LOC103693140 LOC108351405 LOC120093530 LOC120093532 LOC120093775 LOC120094195 LOC120094201 LOC120094202 LOC120094203 LOC120094204 LOC130046242 Lsm7 Map2k2 Matk Mbd3 Mex3d Mfsd12 Midn Mier2 Mindy2 Mir628 Misp Mknk2 Mob3a Mrpl54 Myo1e Myzap Ncln Ndufs7 Nedd4 Nfic Oaz1 Palm Pcsk4 Pierce2 Pigb Pip5k1c Plekhj1 Plk5 Plpp2 Plppr3 Polr2m Polrmt Prss57 Prtg Prtn3 Ptbp1 Pwwp3a Pygo1 R3hdm4 Rab27a Reep6 Rexo1 RGD1359127 Rnf111 Rnf126 Rpl37a-ps11 Rps15 Rsl24d1 Sbno2 Scamp4 Sf3a2 Sgta Sirt6 Slc39a3 Sltm Smim24 Spmap2 Stk11 Stk40 Tbxa2r Tcf12 Tex9 Thop1 Timm13 Tjp3 Tle5 Tle6 Tmem259 Tmprss9 Unc13c Wdr18 Wdr72 Zbtb7a Zfp280d Zfp347 Zfp709l1 Zfp873 Zfr2 Znf624l
Tibialis anterior weight	11.66	49	39	105.4	0.99	0.00e+00	Adam10 Aldh1a2 Aqp9 Atosa Bnip2 Ccpg1 Cgnl1 Dnaaf4 Fam81a Gnb5 Gtf2a2 Hdac9 Ice2 Khdc3 Leo1 Lipc LOC100912347 LOC103693133 LOC103693140 LOC120094195 LOC120094201 LOC120094202 LOC120094203 LOC120094204 Lysmd2 Mindy2 Mir628 Myo1e Myo5c Myzap Nedd4 Onecut1 Pierce2 Pigb Polr2m Prtg Pygo1 Rab27a Rnf111 Rpl37a-ps11 Rsl24d1 Sltm Tcf12 Tex9 Tmod2 Tmod3 Unc13c Wdr72 Zfp280d
Patch foraging total patch changes 18 sec	19.73	1	0	0	0	1.00e+00	Stk40
Locomotor testing rearing	13.62	1	0	0	0	1.00e+00	Stk40
Reaction time number correct	13.08	2	0	0	0	1.00e+00	Cpne3 Wwp1
Reaction time trials correct on left	13.08	2	0	0	0	1.00e+00	Cpne3 Wwp1
Reaction time trials on left	12.41	2	0	0	0	1.00e+00	Cpne3 Wwp1
Reaction time trials completed	12.41	2	0	0	0	1.00e+00	Cpne3 Wwp1
Reaction time trials AUC	12.58	2	0	0	0	1.00e+00	Cpne3 Wwp1
Incentive salience index mean	15.71	1	0	0	0	1.00e+00	Stk40
Time in novel zone, NPP test	17.13	2	0	0	0	1.00e+00	Pld1 Tnik
Bone volume	15.12	1	1	2.7	0	1.00e+00	Stk40
Bone: trabecular tissue density	12.9	10	0	0	1	9.13e-41	Ccpg1 Dnaaf4 LOC103693140 Nedd4 Pierce2 Pigb Prtg Rab27a Rsl24d1 Tex9
Se content in liver	14.26	1	0	0	0	1.00e+00	Snrpc
Sr content in liver	70.03	1	1	2.7	0	1.00e+00	Stk40

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	30	0.8	2.86
Adipose	alternative TSS	23	0.7	2.79
Adipose	gene expression	61	0.7	2.83
Adipose	isoform ratio	28	0.6	2.85
Adipose	intron excision ratio	9	0.3	3.16
Adipose	mRNA stability	28	0.6	2.87
BLA	alternative polyA	20	0.9	3.22
BLA	alternative TSS	22	1.2	2.92
BLA	gene expression	50	0.7	2.94
BLA	isoform ratio	34	1.1	2.97
BLA	intron excision ratio	22	0.7	3.18
BLA	mRNA stability	19	0.8	3.06
Brain	alternative polyA	22	0.6	3.02
Brain	alternative TSS	40	1	3.03
Brain	gene expression	64	0.6	2.89
Brain	isoform ratio	34	0.6	2.92
Brain	intron excision ratio	35	0.6	3.09
Brain	mRNA stability	28	0.5	2.83
Eye	alternative polyA	0	0	3.12
Eye	alternative TSS	7	1.8	3.58
Eye	gene expression	7	0.6	3.1
Eye	isoform ratio	12	2.1	3.17
Eye	intron excision ratio	9	1	3.24
Eye	mRNA stability	3	0.8	2.84
IL	alternative polyA	4	0.4	3.06
IL	alternative TSS	6	0.9	2.6
IL	gene expression	35	0.8	2.86
IL	isoform ratio	7	0.6	2.85
IL	intron excision ratio	6	0.5	2.75
IL	mRNA stability	8	0.6	2.94
LHb	alternative polyA	11	1	3
LHb	alternative TSS	4	0.7	3.25
LHb	gene expression	28	0.8	2.93
LHb	isoform ratio	10	0.8	2.97
LHb	intron excision ratio	7	0.6	2.81
LHb	mRNA stability	7	0.6	2.81
Liver	alternative polyA	13	0.5	2.68
Liver	alternative TSS	9	0.3	2.78
Liver	gene expression	44	0.6	2.83
Liver	isoform ratio	24	0.6	2.84
Liver	intron excision ratio	24	0.5	2.85
Liver	mRNA stability	14	0.5	2.83
NAcc	alternative polyA	16	0.5	3.02
NAcc	alternative TSS	19	0.7	3.05
NAcc	gene expression	57	0.7	2.98
NAcc	isoform ratio	35	0.8	3.04
NAcc	intron excision ratio	38	0.8	2.91
NAcc	mRNA stability	20	0.6	2.96
OFC	alternative polyA	3	0.3	2.73
OFC	alternative TSS	9	1.3	3.02
OFC	gene expression	28	0.7	2.92
OFC	isoform ratio	8	0.6	2.85
OFC	intron excision ratio	8	0.7	3.12
OFC	mRNA stability	11	0.8	3.05
PL	alternative polyA	24	0.7	3.01
PL	alternative TSS	37	1.1	3.1
PL	gene expression	56	0.6	2.85
PL	isoform ratio	45	0.9	3.03
PL	intron excision ratio	23	0.4	2.82
PL	mRNA stability	25	0.6	2.97
pVTA	alternative polyA	12	0.7	3.09
pVTA	alternative TSS	15	1.1	3.02
pVTA	gene expression	34	0.6	2.93
pVTA	isoform ratio	13	0.6	2.96
pVTA	intron excision ratio	19	0.6	2.91
pVTA	mRNA stability	11	0.8	3.04
RMTg	alternative polyA	9	1.5	3.49
RMTg	alternative TSS	2	0.4	2.71
RMTg	gene expression	12	0.7	3
RMTg	isoform ratio	6	0.9	2.95
RMTg	intron excision ratio	1	0.1	3.08
RMTg	mRNA stability	7	1.1	2.92