Hub : Traits

Bone: minimum diameter

Tags: Physiology · Bone

Project: r01_doug_adams

3 loci · 11 genes with independent associations · 106 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	chr1	234616020	236013208	3	1	6.75e-08	5.59e-08	1.00e+00	Exoc6
2	chr10	89400319	95911835	102	9	2.80e-09	2.31e-08	NaN	Arsg Bptf Fam20a Helz Icam2 Kcnh6 Psmd12 Rgs9 Taco1
3	chr16	2113611	3511944	1	1	1.58e-07	4.48e-08	3.89e-02	Erc2

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
Body weight	3.98	11	0	0	1	7.75e-27	C10h17orf58 Cyb561 Dcaf7 Ddx42 Ddx5 Icam2 Marchf10 Mettl2 Milr1 Mrc2 Tex2
Length with tail	3.67	1	0	0	0	1.00e+00	Ddx5
Extensor digitorum longus weight	4.11	8	0	0	-1	2.30e-08	C10h17orf58 Ccdc47 Dcaf7 Icam2 Kcnh6 Strada Taco1 Tanc2
Patch foraging indifference point 0 sec	8.48	5	0	0	1	2.14e-15	C10h17orf58 Ddx5 Helz Pitpnc1 Psmd12
Patch foraging total patch changes 0 sec	8.41	5	0	0	1	5.76e-08	C10h17orf58 Ddx5 Helz Pitpnc1 Psmd12
Patch foraging total patch changes 6 sec	9.56	3	0	0	1	1.30e-05	Cep112 LOC102550334 LOC120095200
Condit. Reinf. active minus inactive responses	11.86	3	0	0	0	1.00e+00	Abca9 C10h17orf58 Ccdc47
Condit. Reinf. active responses	10.36	11	0	0	1	4.42e-20	Arsg C10h17orf58 Ccdc47 Fam20a Helz Icam2 LOC108352148 Pitpnc1 Rgs9 Tex2 Wipi1
Condit. Reinf. lever reinforcers received	9.64	3	0	0	0	1.00e+00	C10h17orf58 Rgs9 Tex2
Pavlov. Cond. intertrial magazine entries	13.7	30	0	0	1	5.60e-109	Ace Bptf C10h17orf58 Ccdc47 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Helz Icam2 Limd2 LOC108352143 LOC120095195 LOC120095301 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Pecam1 Polg2 Psmd12 Scn4a Smurf2 Strada Taco1 Tanc2 Tex2
Intermittent access total locomotion	12.5	11	0	0	1	9.57e-39	C10h17orf58 Ddx42 Ddx5 Icam2 LOC120095301 Milr1 Pitpnc1 Psmd12 Scn4a Taco1 Tex2
Short access day 10 total infusions	12.35	1	0	0	0	1.00e+00	C10h17orf58
Short access day 10 total locomotion	13.28	21	0	0	1	1.03e-72	Ace Bptf C10h17orf58 Cep95 Ddx42 Ddx5 Ern1 Helz Icam2 LOC108352143 LOC120095195 LOC120095301 Milr1 Pecam1 Pitpnc1 Polg2 Psmd12 Scn4a Strada Taco1 Tex2
One hour access (0.3 mA shock)	12.73	1	0	0	0	1.00e+00	Exoc6
Bone surface	9.42	22	0	0	1	2.20e-59	Ace Bptf Ccdc47 Cyb561 Dcaf7 Ddx42 Ddx5 Fam20a Icam2 Kcnh6 Limd2 LOC108352143 LOC120095188 Map3k3 Marchf10 Milr1 Pecam1 Scn4a Smurf2 Strada Taco1 Tanc2
Bone volume	8.94	13	0	0	1	7.35e-35	Ace Ccdc47 Dcaf7 Fam20a Icam2 Kcnh6 Limd2 Map3k3 Milr1 Scn4a Strada Taco1 Tanc2
Bone: cortical apparent density	10.51	3	0	0	0	1.00e+00	Cyb561 Marchf10 Mettl2
Bone: cortical area	10.31	1	0	0	0	1.00e+00	Erc2
Bone: cortical porosity	18.49	17	4	36.4	0.99	5.17e-33	Ace Ccdc47 Cyb561 Dcaf7 Icam2 Kcnh6 Limd2 LOC108352143 LOC120095188 Map3k3 Marchf10 Mettl2 Mrc2 Scn4a Strada Taco1 Tanc2
Bone: cortical porosity	17.52	11	0	0	0.99	4.22e-16	Cyb561 Dcaf7 Icam2 Kcnh6 Limd2 LOC120095188 Marchf10 Mettl2 Mrc2 Taco1 Tanc2
Bone: cortical thickness	7.97	1	0	0	0	1.00e+00	Fam20a
Bone: cortical tissue density	10.57	3	0	0	0	1.00e+00	Cyb561 Marchf10 Mettl2
Bone: endosteal estimation	16.72	50	48	436.4	1	3.36e-181	Abca6 Abca9 Ace Arsg Axin2 Bptf C10h17orf58 Cacng4 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Erc2 Ern1 Exoc6 Fam20a Helz Icam2 Kcnh6 Limd2 LOC102550334 LOC108352143 LOC108352148 LOC120095188 LOC120095195 LOC120095200 LOC120095203 LOC120095301 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Psmd12 Rgs9 Scn4a Smurf2 Strada Taco1 Tanc2 Tex2 Wipi1
Bone: endosteal perimeter	18.65	49	48	436.4	1	4.45e-195	Abca6 Abca9 Ace Arsg Axin2 Bptf C10h17orf58 Cacng4 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Exoc6 Fam20a Helz Icam2 Kcnh6 Limd2 LOC102550334 LOC108352143 LOC108352148 LOC120095188 LOC120095195 LOC120095200 LOC120095203 LOC120095301 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Psmd12 Rgs9 Scn4a Smurf2 Strada Taco1 Tanc2 Tex2 Wipi1
Bone: final force	11.54	1	0	0	0	1.00e+00	Erc2
Bone: final moment	12.78	1	0	0	0	1.00e+00	Erc2
Bone: marrow area	16.27	50	47	427.3	1	8.73e-182	Abca6 Abca9 Ace Arsg Axin2 Bptf C10h17orf58 Cacng4 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Erc2 Ern1 Exoc6 Fam20a Helz Icam2 Kcnh6 Limd2 LOC102550334 LOC108352143 LOC108352148 LOC120095188 LOC120095195 LOC120095200 LOC120095203 LOC120095301 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Psmd12 Rgs9 Scn4a Smurf2 Strada Taco1 Tanc2 Tex2 Wipi1
Bone: maximum diameter	8.61	27	0	0	1	1.22e-64	Ace C10h17orf58 Ccdc47 Cyb561 Dcaf7 Exoc6 Fam20a Helz Icam2 Kcnh6 Limd2 LOC108352143 LOC108352148 LOC120095188 Map3k3 Marchf10 Mettl2 Mrc2 Pitpnc1 Psmd12 Rgs9 Scn4a Strada Taco1 Tanc2 Tex2 Wipi1
Bone: maximum force	13.18	2	1	9.1	0	1.00e+00	Erc2 Helz
Bone: maximum moment	13.44	2	1	9.1	0	1.00e+00	Erc2 Helz
Bone: periosteal estimation	12.73	50	32	290.9	1	4.83e-212	Abca6 Abca9 Ace Arsg Axin2 Bptf C10h17orf58 Cacng4 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Erc2 Ern1 Exoc6 Fam20a Helz Icam2 Kcnh6 Limd2 LOC102550334 LOC108352143 LOC108352148 LOC120095188 LOC120095195 LOC120095200 LOC120095203 LOC120095301 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Psmd12 Rgs9 Scn4a Smurf2 Strada Taco1 Tanc2 Tex2 Wipi1
Bone: periosteal perimeter	10.34	33	0	0	1	1.17e-90	Abca6 Abca9 Ace Arsg Axin2 C10h17orf58 Ccdc47 Cyb561 Dcaf7 Ddx5 Exoc6 Fam20a Icam2 Kcnh6 Limd2 LOC102550334 LOC108352143 LOC108352148 LOC120095188 LOC120095200 LOC120095203 Map3k3 Marchf10 Mettl2 Mrc2 Pitpnc1 Prkar1a Rgs9 Scn4a Strada Taco1 Tanc2 Wipi1
Bone: stiffness	12.32	1	0	0	0	1.00e+00	Erc2
Se content in liver	24.14	1	1	9.1	-1	2.02e-04	Exoc6

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	3	0.1	1.84
Adipose	alternative TSS	6	0.2	1.83
Adipose	gene expression	8	0.1	1.85
Adipose	isoform ratio	5	0.1	1.8
Adipose	intron excision ratio	3	0.1	2.03
Adipose	mRNA stability	3	0.1	1.8
BLA	alternative polyA	1	0	2.05
BLA	alternative TSS	2	0.1	1.85
BLA	gene expression	7	0.1	1.95
BLA	isoform ratio	1	0	1.83
BLA	intron excision ratio	2	0.1	1.83
BLA	mRNA stability	2	0.1	1.95
Brain	alternative polyA	4	0.1	1.94
Brain	alternative TSS	0	0	1.9
Brain	gene expression	4	0	1.84
Brain	isoform ratio	8	0.1	1.88
Brain	intron excision ratio	1	0	1.87
Brain	mRNA stability	2	0	1.8
Eye	alternative polyA	2	0.7	1.97
Eye	alternative TSS	0	0	1.92
Eye	gene expression	0	0	1.82
Eye	isoform ratio	1	0.2	2.01
Eye	intron excision ratio	0	0	1.88
Eye	mRNA stability	0	0	1.71
IL	alternative polyA	2	0.2	2.18
IL	alternative TSS	1	0.2	1.63
IL	gene expression	5	0.1	1.88
IL	isoform ratio	1	0.1	1.76
IL	intron excision ratio	0	0	1.75
IL	mRNA stability	2	0.1	1.89
LHb	alternative polyA	0	0	1.97
LHb	alternative TSS	2	0.3	1.82
LHb	gene expression	3	0.1	1.89
LHb	isoform ratio	1	0.1	1.79
LHb	intron excision ratio	0	0	1.71
LHb	mRNA stability	1	0.1	1.9
Liver	alternative polyA	4	0.2	1.94
Liver	alternative TSS	4	0.1	1.83
Liver	gene expression	2	0	1.88
Liver	isoform ratio	5	0.1	1.88
Liver	intron excision ratio	2	0	1.97
Liver	mRNA stability	3	0.1	1.86
NAcc	alternative polyA	3	0.1	1.91
NAcc	alternative TSS	0	0	1.87
NAcc	gene expression	13	0.2	1.84
NAcc	isoform ratio	3	0.1	1.8
NAcc	intron excision ratio	0	0	1.81
NAcc	mRNA stability	5	0.2	1.92
OFC	alternative polyA	2	0.2	2.01
OFC	alternative TSS	0	0	1.8
OFC	gene expression	2	0	1.9
OFC	isoform ratio	3	0.2	1.71
OFC	intron excision ratio	0	0	1.68
OFC	mRNA stability	0	0	1.87
PL	alternative polyA	4	0.1	2.03
PL	alternative TSS	2	0.1	1.92
PL	gene expression	9	0.1	1.9
PL	isoform ratio	3	0.1	1.87
PL	intron excision ratio	2	0	1.78
PL	mRNA stability	5	0.1	1.89
pVTA	alternative polyA	0	0	2.01
pVTA	alternative TSS	1	0.1	1.86
pVTA	gene expression	3	0.1	1.95
pVTA	isoform ratio	0	0	1.79
pVTA	intron excision ratio	2	0.1	1.89
pVTA	mRNA stability	1	0.1	1.86
RMTg	alternative polyA	0	0	1.66
RMTg	alternative TSS	0	0	1.77
RMTg	gene expression	0	0	1.8
RMTg	isoform ratio	0	0	1.87
RMTg	intron excision ratio	1	0.1	1.71
RMTg	mRNA stability	1	0.2	2.09