Hub : Traits

Bone: marrow area

Tags: Physiology · Bone

Project: r01_doug_adams

2 loci · 13 genes with independent associations · 256 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	89400319	96755402	245	7	4.81e-14	5.31e-13	NaN	LOC120095197 LOC120095203 Milr1 Prkar1a Prkca Psmd12 Snord104
2	chr10	97001015	98746667	11	6	9.64e-14	5.37e-16	6.24e-265	LOC102547233 LOC102549596 LOC103693474

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	5.76	8	0	0	-1	4.57e-13	Axin2 Cep112 Fam20a LOC120095197 Map2k6 Prkar1a Prkca Wipi1
Body weight	4.31	18	0	0	0.95	5.19e-19	Abca6 Abca9 Apoh Arsg C10h17orf58 Cep112 Cyb561 Dcaf7 LOC102550334 LOC120095199 LOC120095200 Map2k6 Marchf10 Mettl2 Prkar1a Prkca Rgs9 Wipi1
Tail length	5.89	1	0	0	0	1.00e+00	Abca9
Extensor digitorum longus weight	5.4	10	1	7.7	-0.99	3.45e-10	Ace C10h17orf58 Ccdc47 Dcaf7 Ddx5 Icam2 Kcnh6 LOC108352151 Psmc5 Scn4a
Patch foraging indifference point 0 sec	9.6	1	0	0	0	1.00e+00	Prkca
Patch foraging total patch changes 0 sec	9.55	1	0	0	0	1.00e+00	Prkca
Patch foraging total patch changes 6 sec	10.79	1	0	0	0	1.00e+00	Arsg
Locomotor testing rearing	9.97	1	0	0	0	1.00e+00	LOC120095206
Condit. Reinf. active minus inactive responses	12.93	1	0	0	0	1.00e+00	Ccdc47
Condit. Reinf. active responses	11.41	3	0	0	0	1.00e+00	C10h17orf58 Icam2 Tex2
Pavlov. Cond. intertrial magazine entries	14.56	32	0	0	1	2.15e-176	Ace Bptf C10h17orf58 Cactin-ps2 Ccdc47 Cep95 Dcaf7 Ddx42 Ddx5 Ern1 Icam2 Kcnh6 Limd2 LOC102546698 LOC108352143 LOC120095195 LOC120095301 Map3k3 Milr1 Mrc2 Nol11 Pecam1 Polg2 Prr29 Psmd12 Scn4a Smurf2 Snord104 Strada Taco1 Tanc2 Tex2
Intermittent access total locomotion	14.06	3	0	0	1	3.23e-08	C10h17orf58 Ddx42 Psmd12
Short access day 10 total locomotion	14.45	14	0	0	1	1.67e-31	C10h17orf58 Cep95 Ddx42 Ddx5 Ern1 Icam2 LOC120095301 Milr1 Nol11 Pecam1 Scn4a Strada Taco1 Tex2
Bone surface	10.68	33	2	15.4	0.99	1.81e-85	Abca5 Abca9 Ace Arsg Cactin-ps2 Ccdc47 Cyb561 Dcaf7 Ddx5 Fam20a Gna13 Icam2 Kcnh6 Kcnj16 Kcnj2 Limd2 LOC102547233 LOC120095191 LOC120095204 LOC120095206 Map2k6 Map3k3 Marchf10 Milr1 Prkar1a Psmc5 Scn4a Slc16a6 Strada Taco1 Tanc2 Tlk2 Wipi1
Bone volume	10.17	15	0	0	1	4.50e-43	Abca9 Ace Ccdc47 Dcaf7 Fam20a Icam2 Kcnh6 Kcnj16 Kcnj2 Limd2 Map2k6 Map3k3 Scn4a Taco1 Wipi1
Bone: cortical porosity	20.49	21	4	30.8	0.99	2.05e-37	Ace Cactin-ps2 Ccdc47 Cyb561 Dcaf7 Icam2 Kcnh6 Limd2 LOC108352143 LOC120095188 LOC120095191 Marchf10 Mettl2 Mrc2 Psmc5 Scn4a Strada Taco1 Tanc2 Tex2 Tlk2
Bone: cortical porosity	19.44	7	0	0	1	8.94e-18	Cyb561 Icam2 Kcnh6 LOC120095188 Marchf10 Mettl2 Mrc2
Bone: cortical thickness	11.62	32	4	30.8	-0.99	3.15e-97	Abca5 Abca8 Abca8a Abca9 Arsg Axin2 Bptf Cep95 Ddx42 Ddx5 Fam20a Kcnj16 Kcnj2 LOC100912202 LOC102547233 LOC102549521 LOC102550782 LOC120095197 LOC120095203 LOC120095204 LOC120095206 Map2k6 Pecam1 Pitpnc1 Prkar1a Prkca Psmd12 Rgs9 Slc16a6 Smurf2 Tex2 Wipi1
Bone: endosteal estimation	16.52	79	79	607.7	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 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 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmc5 Psmd12 Rgs9 Scn4a Slc16a6 Smurf2 Snord104 Strada Taco1 Tanc2 Tex2 Tlk2 Wipi1
Bone: endosteal perimeter	16.86	79	78	600	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 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 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmc5 Psmd12 Rgs9 Scn4a Slc16a6 Smurf2 Snord104 Strada Taco1 Tanc2 Tex2 Tlk2 Wipi1
Bone: maximum diameter	9.71	17	0	0	1	8.53e-51	Ccdc47 Cyb561 Dcaf7 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 LOC102547233 LOC102549596 LOC103693474 LOC108352143 LOC120095188 Marchf10 Pitpnc1 Rgs9 Taco1
Bone: minimum diameter	13.03	71	47	361.5	0.99	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC102546698 LOC102550334 LOC102550782 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmd12 Rgs9 Scn4a Smurf2 Snord104 Strada Taco1 Tanc2 Tex2 Tlk2 Wipi1
Bone: periosteal estimation	11.04	77	40	307.7	1	0.00e+00	Abca5 Abca6 Abca8 Abca8a Abca9 Ace Apoh Arsg Axin2 Bptf C10h17orf58 Cacng4 Cacng5 Cactin-ps2 Ccdc47 Cep112 Cep95 Cyb561 Dcaf7 Ddx42 Ddx5 Ern1 Fam20a Gna13 Helz Icam2 Kcnh6 Kcnj16 Kcnj2 Kpna2 Limd2 LOC102546698 LOC102547233 LOC102549596 LOC102550334 LOC102550782 LOC103693474 LOC108352143 LOC108352148 LOC108352150 LOC108352151 LOC120095188 LOC120095191 LOC120095195 LOC120095197 LOC120095199 LOC120095200 LOC120095203 LOC120095204 LOC120095206 LOC120095301 Map2k6 Map3k3 Marchf10 Mettl2 Milr1 Mrc2 Nol11 Pecam1 Pitpnc1 Polg2 Prkar1a Prkca Prr29 Psmc5 Psmd12 Rgs9 Scn4a Slc16a6 Smurf2 Snord104 Strada Taco1 Tanc2 Tex2 Tlk2 Wipi1
Bone: periosteal perimeter	10.87	23	0	0	1	3.20e-84	Abca6 Abca8 Abca8a Abca9 Arsg Axin2 Ccdc47 Cyb561 Fam20a Icam2 Kcnh6 LOC108352143 LOC120095188 LOC120095200 LOC120095203 LOC120095204 Map2k6 Marchf10 Mettl2 Mrc2 Prkar1a Rgs9 Wipi1
Latency to leave start box in cocaine runway, F	14.14	1	0	0	0	1.00e+00	Abca5

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	14	0.4	2.06
Adipose	alternative TSS	11	0.3	2.1
Adipose	gene expression	21	0.2	2.05
Adipose	isoform ratio	18	0.4	2.1
Adipose	intron excision ratio	4	0.1	2.6
Adipose	mRNA stability	9	0.2	2.05
BLA	alternative polyA	11	0.5	2.32
BLA	alternative TSS	4	0.2	2.2
BLA	gene expression	23	0.3	2.19
BLA	isoform ratio	4	0.1	2.16
BLA	intron excision ratio	3	0.1	2.22
BLA	mRNA stability	8	0.3	2.24
Brain	alternative polyA	15	0.4	2.19
Brain	alternative TSS	19	0.5	2.26
Brain	gene expression	20	0.2	2.07
Brain	isoform ratio	18	0.3	2.17
Brain	intron excision ratio	8	0.1	2.24
Brain	mRNA stability	11	0.2	2.03
Eye	alternative polyA	0	0	2.05
Eye	alternative TSS	7	1.8	2.45
Eye	gene expression	4	0.3	2.14
Eye	isoform ratio	1	0.2	2.12
Eye	intron excision ratio	0	0	2.11
Eye	mRNA stability	0	0	1.97
IL	alternative polyA	4	0.4	2.55
IL	alternative TSS	1	0.2	1.86
IL	gene expression	13	0.3	2.18
IL	isoform ratio	2	0.2	2.21
IL	intron excision ratio	0	0	2.47
IL	mRNA stability	5	0.4	2.09
LHb	alternative polyA	4	0.4	2.4
LHb	alternative TSS	4	0.7	2.29
LHb	gene expression	11	0.3	2.15
LHb	isoform ratio	1	0.1	2.12
LHb	intron excision ratio	1	0.1	2.16
LHb	mRNA stability	3	0.2	2.18
Liver	alternative polyA	10	0.4	2.27
Liver	alternative TSS	9	0.3	2.09
Liver	gene expression	16	0.2	2.08
Liver	isoform ratio	19	0.5	2.21
Liver	intron excision ratio	14	0.3	2.2
Liver	mRNA stability	8	0.3	2.09
NAcc	alternative polyA	14	0.5	2.2
NAcc	alternative TSS	6	0.2	2.21
NAcc	gene expression	23	0.3	2.1
NAcc	isoform ratio	10	0.2	2.14
NAcc	intron excision ratio	3	0.1	2.19
NAcc	mRNA stability	15	0.5	2.18
OFC	alternative polyA	0	0	2.15
OFC	alternative TSS	0	0	2.29
OFC	gene expression	9	0.2	2.19
OFC	isoform ratio	2	0.1	2.16
OFC	intron excision ratio	0	0	2.34
OFC	mRNA stability	1	0.1	2.04
PL	alternative polyA	12	0.4	2.18
PL	alternative TSS	12	0.4	2.29
PL	gene expression	28	0.3	2.15
PL	isoform ratio	9	0.2	2.22
PL	intron excision ratio	4	0.1	2.2
PL	mRNA stability	12	0.3	2.1
pVTA	alternative polyA	5	0.3	2.37
pVTA	alternative TSS	9	0.7	2.39
pVTA	gene expression	12	0.2	2.24
pVTA	isoform ratio	2	0.1	2.21
pVTA	intron excision ratio	2	0.1	2.34
pVTA	mRNA stability	3	0.2	2.2
RMTg	alternative polyA	1	0.2	2.33
RMTg	alternative TSS	0	0	2.2
RMTg	gene expression	3	0.2	2.18
RMTg	isoform ratio	0	0	2.37
RMTg	intron excision ratio	2	0.2	2.09
RMTg	mRNA stability	6	1	2.29