Hub : Traits

Bone: periosteal estimation

Tags: Physiology · Bone

Project: r01_doug_adams

6 loci · 16 genes with independent associations · 93 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	chr3	44152620	45549784	1	1	3.12e-08	3.71e-02	4.51e-06	Ly75
2	chr7	128215412	131793143	23	3	6.21e-08	1.29e-07	1.00e+00	Ccdc65 LOC100362820 Tuba1a
3	chr10	89723294	95835187	64	9	3.03e-09	2.01e-08	1.00e+00	Ccdc47 Cyb561 Kcnh6 LOC120095197 LOC120095203 Prkca Psmd12 Rgs9
4	chr10	97001015	98453432	2	1	1.74e-07	1.60e-08	2.91e-02	LOC103693474
5	chr16	256182	2058130	2	1	2.03e-07	1.90e-07	1.00e+00	Anxa11
6	chr16	2999353	4396663	1	1	1.74e-08	6.90e-10	1.21e-02	Wnt5a

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	4.88	9	0	0	1	1.94e-32	Asb8 Cacnb3 Ccdc65 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Body weight	6.22	14	7	43.8	0.99	2.17e-34	Asb8 C10h17orf58 Cacnb3 Ccdc65 Cyb561 Kcnh3 LOC100362820 LOC120093830 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Length without tail	7.35	12	0	0	1	1.77e-46	Asb8 Cacnb3 Ccdc65 Kcnh3 LOC120093830 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Retroperitoneal fat weight	8.85	1	1	6.2	0	1.00e+00	Ly75
Intraocular pressure	10.88	1	0	0	0	1.00e+00	Pfkm
Extensor digitorum longus weight	4.66	23	0	0	0.29	5.04e-02	Ace Asb8 C10h17orf58 Cacnb3 Ccdc47 Ccdc65 Dcaf7 Ddx42 Icam2 Kcnh3 Kcnh6 LOC108352150 LOC120093830 Pfkm Prkag1 Scn4a Slc48a1 Strada Taco1 Tanc2 Tuba1a Tuba1b Zfp641
Tibia length	7.8	12	0	0	1	1.57e-39	Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Food consumed during 24 hour testing period	11.76	1	0	0	0	1.00e+00	Ly75
Water consumed over 24 hours	19.18	1	0	0	0	1.00e+00	Ly75
Patch foraging indifference point 0 sec	8.38	7	0	0	1	1.40e-20	C10h17orf58 Cep112 Helz Kpna2 Pitpnc1 Prkca Psmd12
Patch foraging total patch changes 0 sec	8.36	5	0	0	1	4.33e-08	C10h17orf58 Helz Pitpnc1 Prkca Psmd12
Patch foraging total patch changes 18 sec	13.09	1	0	0	0	1.00e+00	Ly75
Patch foraging total patch changes 6 sec	9.43	2	0	0	1	4.59e-05	Cep112 LOC120095200
Reaction time mean minus median	9.87	1	0	0	0	1.00e+00	Zfp641
Reaction time mean minus median AUC	17.14	1	0	0	0	1.00e+00	Ly75
Reaction time mean	9.87	1	0	0	0	1.00e+00	Ly75
Reaction time mean AUC	10.73	1	0	0	0	1.00e+00	Ly75
Reaction time omissions	9.88	10	0	0	-1	9.04e-38	Asb8 Cacnb3 Ccdc65 Kcnh3 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Std. dev. reaction times	14.29	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	13.16	6	1	6.2	0.99	5.70e-07	Abca9 Ace C10h17orf58 Ccdc47 Dcaf7 Ly75
Condit. Reinf. active responses	11.34	8	1	6.2	0.99	9.09e-11	Ace C10h17orf58 Ccdc47 Helz Ly75 Pitpnc1 Rgs9 Wipi1
Condit. Reinf. lever reinforcers received	12.08	3	1	6.2	0.99	1.16e-02	C10h17orf58 Ly75 Rgs9
Pavlov. Cond. change in total contacts	11.21	1	0	0	0	1.00e+00	Ly75
Pavlov. Cond. intertrial magazine entries	12.83	19	0	0	1	4.48e-65	Ace Bptf C10h17orf58 Ccdc47 Dcaf7 Ddx42 Helz Icam2 Kpna2 Limd2 LOC108352143 Map3k3 Marchf10 Psmd12 Scn4a Smurf2 Strada Taco1 Tanc2
Intermittent access total locomotion	12.63	5	0	0	1	2.78e-28	C10h17orf58 Helz Kpna2 Pitpnc1 Psmd12
Short access day 10 total infusions	12.05	1	0	0	0	1.00e+00	C10h17orf58
Short access day 10 total locomotion	12.8	7	0	0	1	6.90e-26	Ace C10h17orf58 Helz LOC108352143 Pitpnc1 Psmd12 Taco1
Locomotion distance, session 3	14.48	1	0	0	0	1.00e+00	Ly75
Stereotopy head waving bouts, day 7	23.7	1	0	0	0	1.00e+00	Ly75
Stereotopy head waving duration, day 7	21.6	1	0	0	0	1.00e+00	Ly75
Locomotion velocity, session 8	13.06	1	0	0	0	1.00e+00	Wnt5a
Degree of sensitization stereotypy	38.66	1	1	6.2	0	1.00e+00	Ly75
Condit. Reinf. active minus inactive responses	16.76	1	0	0	0	1.00e+00	Ly75
Condit. Reinf. active responses	13.63	1	0	0	0	1.00e+00	Ly75
Incentive salience index mean	15.42	1	0	0	0	1.00e+00	Ly75
Total zone transitions, hab. session 2	19.52	1	0	0	0	1.00e+00	Ly75
Total locomotion distance, hab. session 2	24.97	1	1	6.2	0	1.00e+00	Ly75
Locomotion velocity, hab. session 2	19.99	1	1	6.2	0	1.00e+00	Ly75
Bone: apparent density	11.02	13	1	6.2	0.99	2.28e-32	Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Zfp641
Bone surface	11.96	31	2	12.5	0.99	2.08e-59	Ace Asb8 Bptf Cacnb3 Ccdc47 Ccdc65 Cyb561 Dcaf7 Ddx42 Icam2 Kcnh3 Kcnh6 Limd2 LOC100362820 LOC108352143 LOC120093830 LOC120095188 Ly75 Map3k3 Marchf10 Pfkm Prkag1 Scn4a Slc48a1 Smurf2 Strada Taco1 Tanc2 Tuba1a Tuba1b Zfp641
Bone volume	10	25	1	6.2	0.99	2.45e-50	Ace Asb8 Cacnb3 Ccdc47 Ccdc65 Dcaf7 Ddx42 Icam2 Kcnh3 Kcnh6 Limd2 LOC100362820 LOC120093830 Ly75 Map3k3 Pfkm Prkag1 Scn4a Slc48a1 Strada Taco1 Tanc2 Tuba1a Tuba1b Zfp641
Bone: connectivity density	9.93	7	1	6.2	0.99	4.13e-08	Cacnb3 Ccdc65 Kcnh3 LOC120093830 Ly75 Prkag1 Tuba1a
Bone: cortical apparent density	14.27	2	0	0	0	1.00e+00	LOC120095188 Ly75
Bone: cortical area	11.25	16	0	0	1	2.04e-58	Anxa11 Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: cortical porosity	17.42	16	2	12.5	0.99	1.47e-27	Ace Ccdc47 Cyb561 Dcaf7 Ddx42 Icam2 Kcnh6 Limd2 LOC108352143 LOC120095188 Map3k3 Marchf10 Scn4a Strada Taco1 Tanc2
Bone: cortical porosity	15.59	9	0	0	0.99	1.32e-08	Ccdc47 Cyb561 Icam2 Kcnh6 Limd2 LOC120095188 Marchf10 Taco1 Tanc2
Bone: cortical thickness	10.34	1	0	0	0	1.00e+00	Prkca
Bone: cortical tissue density	17.88	1	0	0	0	1.00e+00	Ly75
Bone: elastic work	15.82	1	0	0	0	1.00e+00	Ly75
Bone: endosteal estimation	15.57	57	40	250	0.99	7.17e-122	Abca9 Ace Anxa11 Arsg Asb8 Axin2 Bptf C10h17orf58 Cacnb3 Cacng4 Cacng5 Ccdc47 Ccdc65 Cep112 Cyb561 Dcaf7 Ddx42 Fam20a Helz Icam2 Kcnh3 Kcnh6 Kpna2 Limd2 LOC100362820 LOC102547233 LOC103693474 LOC108352143 LOC108352150 LOC108352151 LOC120093830 LOC120095188 LOC120095197 LOC120095200 LOC120095203 LOC120097392 Ly75 Map3k3 Marchf10 Nol11 Pfkm Pitpnc1 Prkag1 Prkca Psmd12 Rgs9 Scn4a Slc48a1 Smurf2 Strada Taco1 Tanc2 Tuba1a Tuba1b Wipi1 Wnt5a Zfp641
Bone: endosteal perimeter	15.7	53	40	250	0.99	6.15e-122	Abca9 Ace Arsg Asb8 Axin2 Bptf C10h17orf58 Cacnb3 Cacng4 Cacng5 Ccdc47 Ccdc65 Cep112 Cyb561 Dcaf7 Ddx42 Fam20a Helz Icam2 Kcnh3 Kcnh6 Kpna2 Limd2 LOC100362820 LOC102547233 LOC103693474 LOC108352143 LOC108352150 LOC108352151 LOC120093830 LOC120095188 LOC120095197 LOC120095200 LOC120095203 Map3k3 Marchf10 Nol11 Pfkm Pitpnc1 Prkag1 Prkca Psmd12 Rgs9 Scn4a Slc48a1 Smurf2 Strada Taco1 Tanc2 Tuba1a Tuba1b Wipi1 Zfp641
Bone: final force	11.01	16	1	6.2	0.99	1.72e-31	Anxa11 Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: final moment	11.61	16	1	6.2	0.98	2.58e-27	Anxa11 Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: marrow area	15.19	57	40	250	0.99	3.58e-122	Abca9 Ace Anxa11 Arsg Asb8 Axin2 Bptf C10h17orf58 Cacnb3 Cacng4 Cacng5 Ccdc47 Ccdc65 Cep112 Cyb561 Dcaf7 Ddx42 Fam20a Helz Icam2 Kcnh3 Kcnh6 Kpna2 Limd2 LOC100362820 LOC102547233 LOC103693474 LOC108352143 LOC108352150 LOC108352151 LOC120093830 LOC120095188 LOC120095197 LOC120095200 LOC120095203 LOC120097392 Ly75 Map3k3 Marchf10 Nol11 Pfkm Pitpnc1 Prkag1 Prkca Psmd12 Rgs9 Scn4a Slc48a1 Smurf2 Strada Taco1 Tanc2 Tuba1a Tuba1b Wipi1 Wnt5a Zfp641
Bone: maximum diameter	8.45	28	0	0	1	2.79e-62	Ace C10h17orf58 Cacng4 Ccdc47 Cep112 Cyb561 Dcaf7 Ddx42 Helz Icam2 Kcnh6 Limd2 LOC102547233 LOC103693474 LOC108352143 LOC108352150 LOC120095188 LOC120095197 Map3k3 Marchf10 Pitpnc1 Psmd12 Rgs9 Scn4a Strada Taco1 Tanc2 Wipi1
Bone: maximum force	14.25	17	3	18.8	1	8.40e-46	Anxa11 Asb8 Cacnb3 Ccdc65 Helz Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: maximum moment	14.63	17	3	18.8	1	1.34e-39	Anxa11 Asb8 Cacnb3 Ccdc65 Helz Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: minimum diameter	13.8	55	32	200	1	5.04e-159	Abca9 Ace Anxa11 Arsg Asb8 Axin2 Bptf C10h17orf58 Cacnb3 Cacng4 Cacng5 Ccdc47 Ccdc65 Cep112 Cyb561 Dcaf7 Ddx42 Fam20a Helz Icam2 Kcnh3 Kcnh6 Kpna2 Limd2 LOC100362820 LOC108352143 LOC108352150 LOC108352151 LOC120093830 LOC120095188 LOC120095197 LOC120095200 LOC120095203 LOC120097392 Ly75 Map3k3 Marchf10 Nol11 Pfkm Pitpnc1 Prkag1 Prkca Psmd12 Rgs9 Scn4a Slc48a1 Smurf2 Strada Taco1 Tanc2 Tuba1a Tuba1b Wipi1 Wnt5a Zfp641
Bone: periosteal perimeter	10.53	40	0	0	1	6.25e-87	Abca9 Ace Arsg Asb8 Axin2 C10h17orf58 Cacnb3 Ccdc47 Ccdc65 Cyb561 Dcaf7 Ddx42 Fam20a Icam2 Kcnh3 Kcnh6 Limd2 LOC100362820 LOC108352143 LOC120093830 LOC120095188 LOC120095200 LOC120095203 Map3k3 Marchf10 Pfkm Pitpnc1 Prkag1 Prkca Rgs9 Scn4a Slc48a1 Strada Taco1 Tanc2 Tuba1a Tuba1b Wipi1 Wnt5a Zfp641
Bone: post-yield work	11.13	1	0	0	0	1.00e+00	LOC100362820
Bone: stiffness	16.77	16	12	75	1	5.91e-40	Anxa11 Asb8 Cacnb3 Ccdc65 Kcnh3 LOC100362820 LOC120093830 LOC120097392 Ly75 Pfkm Prkag1 Slc48a1 Tuba1a Tuba1b Wnt5a Zfp641
Bone: trabecular number	22.6	2	1	6.2	0	1.00e+00	Ly75 Tuba1a
Bone: trabecular spacing	60.24	1	1	6.2	0	1.00e+00	Ly75
Bone: trabecular thickness	29.94	2	1	6.2	0	1.00e+00	Ddx42 Ly75
Rest time, locomotor task time 1	12.3	1	0	0	0	1.00e+00	Ly75
Distance moved, locomotor task time 1	13.8	1	0	0	0	1.00e+00	Ly75
Weight adjusted by age	20.87	1	0	0	0	1.00e+00	Ly75
Locomotion in novel chamber	34.01	1	1	6.2	0	1.00e+00	Ly75
Food seeking constrained by brief footshock	13.79	1	0	0	0	1.00e+00	Ly75
Run reversals in cocaine runway, females	21.72	1	0	0	0	1.00e+00	Ly75
Mg content in liver	13.79	1	0	0	0	1.00e+00	Ly75
Mn content in liver	32.26	1	1	6.2	0	1.00e+00	Ly75
Na content in liver	12.24	1	0	0	0	1.00e+00	Ly75
Sr content in liver	14.16	1	0	0	0	1.00e+00	Ly75
Zn content in liver	12.81	1	0	0	0	1.00e+00	Ly75

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	5	0.1	2.07
Adipose	alternative TSS	3	0.1	2.06
Adipose	gene expression	9	0.1	2.01
Adipose	isoform ratio	5	0.1	2.02
Adipose	intron excision ratio	0	0	2.24
Adipose	mRNA stability	2	0	2.02
BLA	alternative polyA	3	0.1	2.26
BLA	alternative TSS	0	0	2.1
BLA	gene expression	5	0.1	2.14
BLA	isoform ratio	3	0.1	1.99
BLA	intron excision ratio	4	0.1	2.02
BLA	mRNA stability	1	0	2.14
Brain	alternative polyA	4	0.1	2.13
Brain	alternative TSS	2	0	2.1
Brain	gene expression	6	0.1	2.01
Brain	isoform ratio	3	0.1	2.07
Brain	intron excision ratio	3	0.1	2.01
Brain	mRNA stability	3	0.1	1.98
Eye	alternative polyA	0	0	2.04
Eye	alternative TSS	0	0	1.92
Eye	gene expression	1	0.1	2.02
Eye	isoform ratio	1	0.2	2.12
Eye	intron excision ratio	0	0	1.87
Eye	mRNA stability	0	0	1.78
IL	alternative polyA	1	0.1	2.29
IL	alternative TSS	1	0.2	1.81
IL	gene expression	7	0.2	2.14
IL	isoform ratio	1	0.1	1.97
IL	intron excision ratio	0	0	2.2
IL	mRNA stability	1	0.1	2.14
LHb	alternative polyA	0	0	2.21
LHb	alternative TSS	0	0	2.03
LHb	gene expression	4	0.1	2.08
LHb	isoform ratio	0	0	1.96
LHb	intron excision ratio	0	0	1.96
LHb	mRNA stability	1	0.1	2.12
Liver	alternative polyA	6	0.2	2.08
Liver	alternative TSS	1	0	1.95
Liver	gene expression	3	0	2.02
Liver	isoform ratio	4	0.1	2.06
Liver	intron excision ratio	1	0	2.05
Liver	mRNA stability	3	0.1	2.01
NAcc	alternative polyA	2	0.1	2.07
NAcc	alternative TSS	0	0	2.17
NAcc	gene expression	9	0.1	2.04
NAcc	isoform ratio	4	0.1	2.04
NAcc	intron excision ratio	0	0	2.05
NAcc	mRNA stability	6	0.2	2.12
OFC	alternative polyA	0	0	2.03
OFC	alternative TSS	0	0	2.14
OFC	gene expression	5	0.1	2.13
OFC	isoform ratio	1	0.1	1.94
OFC	intron excision ratio	0	0	2.03
OFC	mRNA stability	1	0.1	2.07
PL	alternative polyA	2	0.1	2.12
PL	alternative TSS	1	0	2.19
PL	gene expression	7	0.1	2.1
PL	isoform ratio	3	0.1	2.11
PL	intron excision ratio	4	0.1	2.06
PL	mRNA stability	5	0.1	2.06
pVTA	alternative polyA	2	0.1	2.28
pVTA	alternative TSS	1	0.1	2.16
pVTA	gene expression	0	0	2.15
pVTA	isoform ratio	1	0	2.04
pVTA	intron excision ratio	0	0	2.14
pVTA	mRNA stability	1	0.1	2.14
RMTg	alternative polyA	0	0	2.1
RMTg	alternative TSS	0	0	2.31
RMTg	gene expression	0	0	2.06
RMTg	isoform ratio	0	0	2.25
RMTg	intron excision ratio	0	0	1.81
RMTg	mRNA stability	0	0	2.1