Hub : Traits

Bone: endosteal perimeter

Tags: Physiology · Bone

Project: r01_doug_adams

4 loci · 11 genes with independent associations · 291 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	chr10	88157669	96755402	277	8	5.03e-13	1.30e-11	NaN	Abca9 Bptf Marchf10 Mettl2 Psmd12 Rgs9 Strada
2	chr10	97001015	99093851	11	1	5.61e-12	4.24e-13	1.33e-03	LOC102547233
3	chr10	102999385	104180892	2	1	1.67e-07	2.49e-05	4.22e-01	Cyth1
4	chr20	53722628	54429288	1	1	4.95e-13	2.52e-01	1.00e+00	LOC103694460

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	7.33	7	1	9.1	-0.54	1.04e-01	Axin2 Cep112 LOC103694460 LOC120095197 Map2k6 Prkar1a Wipi1
Body weight	4.73	22	1	9.1	0.97	4.86e-40	Abca6 Abca9 Apoh Arsg C10h17orf58 Cyb561 Dcaf7 Ddx5 LOC102550334 LOC103694460 LOC108352143 LOC120095199 LOC120095200 Map2k6 Marchf10 Mettl2 Mrc2 Nsf Prkar1a Rgs9 Tanc2 Wipi1
Epididymis fat weight	10.03	1	0	0	0	1.00e+00	Axin2
Left kidney weight	15.24	1	1	9.1	0	1.00e+00	LOC103694460
Right kidney weight	12.61	1	1	9.1	0	1.00e+00	LOC103694460
Tail length	5.89	1	0	0	0	1.00e+00	Abca9
Liver weight, left	10.61	1	0	0	0	1.00e+00	LOC103694460
Liver weight, right	23.79	1	1	9.1	0	1.00e+00	LOC103694460
Retroperitoneal fat weight	29.13	1	1	9.1	0	1.00e+00	LOC103694460
Intraocular pressure	24.4	1	1	9.1	0	1.00e+00	LOC103694460
Extensor digitorum longus weight	5.06	14	1	9.1	-0.88	6.40e-08	Ace Axin2 C10h17orf58 Ccdc47 Dcaf7 Ddx5 Icam2 Kcnh6 Kpna2 LOC103694460 LOC120095197 Map3k3 Smarcd2 Tex2
Tibialis anterior weight	11.7	1	1	9.1	0	1.00e+00	LOC103694460
Tibia length	5.79	1	0	0	0	1.00e+00	Afmid
Patch foraging indifference point 0 sec	12.96	1	0	0	0	1.00e+00	LOC103694460
Patch foraging total patch changes 0 sec	12.64	1	0	0	0	1.00e+00	LOC103694460
Patch foraging total patch changes 6 sec	10.88	2	0	0	0	1.00e+00	Arsg LOC102550334
Condit. Reinf. active minus inactive responses	12.9	2	0	0	0	1.00e+00	C10h17orf58 Ccdc47
Condit. Reinf. active responses	11.93	2	0	0	0	1.00e+00	C10h17orf58 Tex2
Pavlov. Cond. index score	15.43	1	0	0	0	1.00e+00	LOC103694460
Pavlov. Cond. magazine entry number	20.26	1	0	0	0	1.00e+00	LOC103694460
Pavlov. Cond. intertrial magazine entries	14.84	36	0	0	1	5.14e-197	Ace Bptf C10h17orf58 Cactin-ps2 Cep95 Dcaf7 Ddx42 Ddx5 Ern1 Helz Icam2 Kcnh6 Kpna2 Limd2 LOC102546698 LOC108352143 LOC120095195 LOC120095301 Map3k3 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Polg2 Prr29 Psmd12 Scn4a Smurf2 Snord104 Strada Taco1 Tanc2 Tcam1 Tex2 Tlk2
Pavlov. Cond. response bias	13.13	1	0	0	0	1.00e+00	LOC103694460
Intermittent access total locomotion	14.32	1	0	0	1	4.47e-04	Psmd12
Short access day 10 total locomotion	14.6	13	0	0	1	1.69e-30	C10h17orf58 Cep95 Ddx42 Ddx5 Ern1 Icam2 LOC120095301 Milr1 Nol11 Pecam1 Scn4a Strada Tex2
Bone surface	11.01	32	3	27.3	0.99	8.93e-73	Abca5 Abca9 Ace Arsg Cactin-ps2 Ccdc47 Cyb561 Dcaf7 Ddx5 Fam20a Gna13 Icam2 Kcnh6 Kcnj16 Kcnj2 Limd2 LOC102547233 LOC120095204 LOC120095206 Map2k6 Map3k3 Marchf10 Milr1 Prkar1a Scn4a Slc16a6 Smarcd2 Strada Taco1 Tanc2 Tlk2 Wipi1
Bone volume	10.5	13	0	0	1	7.65e-36	Abca8 Abca9 Ace Ccdc47 Dcaf7 Icam2 Kcnj16 Kcnj2 Map2k6 Map3k3 Scn4a Smarcd2 Wipi1
Bone: cortical apparent density	12.1	1	0	0	0	1.00e+00	Tanc2
Bone: cortical porosity	23.02	23	5	45.5	0.99	1.70e-84	Ace Cactin-ps2 Ccdc47 Crhr1 Cyb561 Dcaf7 Icam2 Kcnh6 Limd2 LOC103694460 LOC108352143 LOC120095188 LOC120095191 Map3k3 Marchf10 Mettl2 Mrc2 Scn4a Strada Taco1 Tanc2 Tex2 Tlk2
Bone: cortical porosity	20.15	8	0	0	1	1.32e-71	Crhr1 Cyb561 Icam2 Kcnh6 LOC120095188 Marchf10 Mettl2 Mrc2
Bone: cortical thickness	11.59	28	4	36.4	-0.99	4.49e-93	Abca5 Abca8 Abca8a Abca9 Arsg Axin2 Cep95 Ddx5 Fam20a Kcnj16 Kcnj2 LOC100912202 LOC102547233 LOC102549521 LOC102550782 LOC120095197 LOC120095203 LOC120095204 LOC120095206 Map2k6 Pecam1 Prkar1a Prkca Psmd12 Rgs9 Slc16a6 Smurf2 Wipi1
Bone: endosteal estimation	15.25	85	78	709.1	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Crhr1 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC100912202 LOC102546698 LOC102547233 LOC102549521 LOC102549596 LOC102550334 LOC102550782 LOC103693474 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC108352227 LOC120095186 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095210 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Nsf Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmd12 Rgs9 Scn4a Slc16a6 Smarcd2 Smurf2 Snord104 Strada Taco1 Tanc2 Tcam1 Tex2 Tlk2 Wipi1
Bone: marrow area	14.89	85	78	709.1	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Crhr1 Cyb561 Cyth1 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC100912202 LOC102546698 LOC102547233 LOC102549521 LOC102549596 LOC102550334 LOC102550782 LOC103693474 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC108352227 LOC120095186 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Nsf Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmd12 Rgs9 Scn4a Slc16a6 Smarcd2 Smurf2 Snord104 Strada Taco1 Tanc2 Tcam1 Tex2 Tlk2 Wipi1
Bone: maximum diameter	10.03	17	1	9.1	1	3.21e-47	Ccdc47 Cyb561 Helz Kcnh6 Kcnj16 Kcnj2 LOC102547233 LOC102549596 LOC103693474 LOC103694460 LOC108352143 Map3k3 Marchf10 Pitpnc1 Rgs9 Smarcd2 Taco1
Bone: minimum diameter	12.8	78	48	436.4	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Crhr1 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC102546698 LOC102550334 LOC102550782 LOC103694460 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC108352227 LOC120095186 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Nsf Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmd12 Rgs9 Scn4a Smarcd2 Smurf2 Snord104 Strada Taco1 Tanc2 Tcam1 Tex2 Tlk2 Wipi1
Bone: periosteal estimation	10.95	78	40	363.6	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Crhr1 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC102546698 LOC102547233 LOC102549596 LOC102550334 LOC102550782 LOC103693474 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC108352227 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmd12 Rgs9 Scn4a Smarcd2 Smurf2 Snord104 Strada Taco1 Tanc2 Tex2 Tlk2 Wipi1
Bone: periosteal perimeter	11.41	27	0	0	0.99	2.03e-144	Abca6 Abca8 Abca8a Abca9 Arsg Axin2 Ccdc47 Crhr1 Cyb561 Fam20a Icam2 Kcnh6 LOC102550334 LOC103694460 LOC108352143 LOC120095188 LOC120095200 LOC120095203 LOC120095204 Map3k3 Marchf10 Mettl2 Mrc2 Prkar1a Rgs9 Smarcd2 Wipi1
Cu content in liver	43.87	1	1	9.1	0	1.00e+00	LOC103694460
Fe content in liver	26.96	1	1	9.1	0	1.00e+00	LOC103694460
K content in liver	46.75	1	1	9.1	0	1.00e+00	LOC103694460
Rb content in liver	81.33	1	1	9.1	0	1.00e+00	LOC103694460
Sr content in liver	22.24	1	0	0	0	1.00e+00	LOC103694460

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	14	0.4	2.01
Adipose	alternative TSS	13	0.4	2.04
Adipose	gene expression	24	0.3	2
Adipose	isoform ratio	15	0.3	2.02
Adipose	intron excision ratio	4	0.1	2.3
Adipose	mRNA stability	12	0.3	2.01
BLA	alternative polyA	11	0.5	2.19
BLA	alternative TSS	4	0.2	2.14
BLA	gene expression	27	0.4	2.13
BLA	isoform ratio	8	0.3	2.01
BLA	intron excision ratio	6	0.2	2.09
BLA	mRNA stability	14	0.6	2.19
Brain	alternative polyA	15	0.4	2.07
Brain	alternative TSS	19	0.5	2.16
Brain	gene expression	30	0.3	2.04
Brain	isoform ratio	24	0.4	2.08
Brain	intron excision ratio	13	0.2	2.14
Brain	mRNA stability	16	0.3	2.01
Eye	alternative polyA	0	0	2.16
Eye	alternative TSS	7	1.8	2.5
Eye	gene expression	3	0.2	2.08
Eye	isoform ratio	1	0.2	1.99
Eye	intron excision ratio	0	0	1.97
Eye	mRNA stability	1	0.3	2.04
IL	alternative polyA	4	0.4	2.28
IL	alternative TSS	2	0.3	1.94
IL	gene expression	17	0.4	2.08
IL	isoform ratio	3	0.2	1.99
IL	intron excision ratio	2	0.2	2.17
IL	mRNA stability	6	0.4	2.04
LHb	alternative polyA	4	0.4	2.19
LHb	alternative TSS	5	0.8	2.16
LHb	gene expression	13	0.4	2.07
LHb	isoform ratio	1	0.1	1.9
LHb	intron excision ratio	1	0.1	1.96
LHb	mRNA stability	5	0.4	2.13
Liver	alternative polyA	10	0.4	2.23
Liver	alternative TSS	9	0.3	1.98
Liver	gene expression	22	0.3	2.01
Liver	isoform ratio	18	0.5	2.08
Liver	intron excision ratio	13	0.3	2.1
Liver	mRNA stability	10	0.3	2
NAcc	alternative polyA	16	0.5	2.05
NAcc	alternative TSS	8	0.3	2.14
NAcc	gene expression	27	0.3	2.06
NAcc	isoform ratio	14	0.3	2
NAcc	intron excision ratio	9	0.2	2.03
NAcc	mRNA stability	17	0.5	2.15
OFC	alternative polyA	2	0.2	1.99
OFC	alternative TSS	1	0.1	2.09
OFC	gene expression	11	0.3	2.13
OFC	isoform ratio	2	0.1	1.97
OFC	intron excision ratio	0	0	1.97
OFC	mRNA stability	2	0.1	2.03
PL	alternative polyA	17	0.5	2.2
PL	alternative TSS	15	0.5	2.18
PL	gene expression	33	0.4	2.06
PL	isoform ratio	13	0.3	2.09
PL	intron excision ratio	8	0.1	2.03
PL	mRNA stability	15	0.4	2.07
pVTA	alternative polyA	5	0.3	2.15
pVTA	alternative TSS	10	0.8	2.22
pVTA	gene expression	18	0.3	2.17
pVTA	isoform ratio	2	0.1	2
pVTA	intron excision ratio	4	0.1	2.1
pVTA	mRNA stability	6	0.4	2.22
RMTg	alternative polyA	1	0.2	2.04
RMTg	alternative TSS	0	0	1.97
RMTg	gene expression	7	0.4	2.11
RMTg	isoform ratio	1	0.2	2.19
RMTg	intron excision ratio	2	0.2	2.01
RMTg	mRNA stability	5	0.8	2.35