Hub : Traits

Bone: endosteal perimeter

Tags: Physiology · Bone

Project: r01_doug_adams

3 loci · 9 genes with independent associations · 69 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	10	87823507	96755402	67	7	8.86e-13	1.30e-11	NaN	Cacng5 Wipi1 Map2k6 Marchf10 Strada Cep95 Prkar1a
2	10	99794956	101075728	1	1	8.71e-08	2.08e-06	7.31e-47	Cd300lf
3	10	102999385	104282175	1	1	2.24e-07	2.49e-05	6.03e-02	Cep295nl

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	5.18	6	0	0	-1	1.05e-09	Slc16a6 Cacng4 Prkca Cep112 AABR07030647.1 Prkar1a
Body weight	4.39	15	0	0	1	1.54e-47	Amz2 Apoh Wipi1 Arsg Mettl2 Mrc2 Marchf10 Cyb561 ENSRNOG00000043295 Abca6 Prkar1a Abca9 Map3k3 ENSRNOG00000065020 ENSRNOG00000067823
Epididymis fat weight	7.18	1	0	0	0	1.00e+00	Slc16a6
Extensor digitorum longus weight	4.98	12	1	11.1	-0.99	1.25e-13	Kcnh6 Ccdc47 Ddx42 Smarcd2 Tex2 Kpna2 Dcaf7 ENSRNOG00000043295 Bptf ENSRNOG00000062516 ENSRNOG00000063680 Pecam1
Indifference point 0 sec	10.04	1	0	0	0	1.00e+00	ENSRNOG00000067823
Delay discounting total patch changes 6 sec	11.3	2	0	0	1	2.91e-05	Wipi1 Prkar1a
Condit. Reinf. active minus inactive responses	12.63	2	0	0	0	1.00e+00	Ccdc47 Dcaf7
Condit. Reinf. active responses	11.6	4	0	0	1	1.35e-04	Kpna2 ENSRNOG00000043295 Gna13 Pecam1
Pavlov. Cond. intertrial magazine entries	14.62	33	0	0	0.99	1.37e-160	Psmd12 Mettl2 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Icam2 Limd2 Ddx5 Dcaf7 ENSRNOG00000043295 Bptf Tanc2 AC133055.1 Snord104 Prr29 Map3k3 Ace ENSRNOG00000062516 ENSRNOG00000063680 Pecam1 ENSRNOG00000067362
Intermittent access total locomotion	14.16	6	0	0	0.14	7.93e-01	Psmd12 Helz ENSRNOG00000043295 ENSRNOG00000067362 ENSRNOG00000067823 ENSRNOG00000069533
Short access day 10 total locomotion	14.72	13	0	0	1	3.14e-22	Strada Scn4a Kpna2 Icam2 Ddx5 Dcaf7 ENSRNOG00000043295 AC133055.1 Ace ENSRNOG00000062516 ENSRNOG00000063680 Pecam1 ENSRNOG00000067823
Bone surface	10.63	28	2	22.2	0.99	1.88e-79	Slc16a6 Arsg Fam20a Kcnj16 Mrc2 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Cep95 Icam2 Ddx5 Dcaf7 ENSRNOG00000043295 Prkar1a Tanc2 Abca9 Prr29 Map3k3 Ace Gna13 ENSRNOG00000063680 Kcnj2 ENSRNOG00000065020
Bone volume	10.08	14	0	0	1	3.02e-44	Kcnj16 Kcnh6 Taco1 Ccdc47 Ddx42 Smarcd2 Scn4a Dcaf7 Prkar1a Abca9 Map3k3 Ace ENSRNOG00000063680 Kcnj2
Bone: cortical apparent density	11.91	1	0	0	0	1.00e+00	Marchf10
Bone: cortical porosity	20.77	18	5	55.6	0.99	2.77e-49	Lyzl6 Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace ENSRNOG00000063680 ENSRNOG00000066876
Bone: cortical porosity	19.51	9	0	0	1	7.53e-32	Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Strada Ccdc47 Ddx42 ENSRNOG00000063680
Bone: cortical thickness	11.86	25	4	44.4	-0.99	6.55e-73	Psmd12 Helz Cacng4 Prkca Wipi1 Fam20a Abca8 Abca8a Map2k6 Kcnj16 Scn4a Tex2 Cep95 Smurf2 Icam2 Ddx5 Cep295nl Bptf Prkar1a Abca9 Prr29 Kcnj2 ENSRNOG00000065020 Pecam1 Pitpnc1
Bone: cortical tissue density	11.63	1	0	0	0	1.00e+00	Marchf10
Bone: endosteal estimation	15.47	69	61	677.8	1	0.00e+00	Slc16a6 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cd300lf Cep112 Icam2 Limd2 Ddx5 Cep295nl AABR07030647.1 Dcaf7 Prp2l1 ENSRNOG00000043295 Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace ENSRNOG00000062516 Gna13 ENSRNOG00000063680 Kcnj2 ENSRNOG00000065020 Pecam1 ENSRNOG00000066876 ENSRNOG00000067362 ENSRNOG00000067823 Pitpnc1 ENSRNOG00000069533
Bone: marrow area	15.12	69	61	677.8	1	0.00e+00	Slc16a6 Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cd300lf Cep112 Icam2 Limd2 Ddx5 Cep295nl AABR07030647.1 Dcaf7 Prp2l1 ENSRNOG00000043295 Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace ENSRNOG00000062516 Gna13 ENSRNOG00000063680 Kcnj2 ENSRNOG00000065020 Pecam1 ENSRNOG00000066876 ENSRNOG00000067362 ENSRNOG00000067823 Pitpnc1 ENSRNOG00000069533
Bone: maximum diameter	8.92	20	0	0	1	4.97e-57	Kcnj16 Mrc2 Marchf10 Cyb561 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Kpna2 Dcaf7 ENSRNOG00000043295 AABR07030630.1 Prr29 Map3k3 Ace ENSRNOG00000063680 Kcnj2 ENSRNOG00000067362
Bone: minimum diameter	13.04	65	40	444.4	1	0.00e+00	Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 Dcaf7 Prp2l1 ENSRNOG00000043295 Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace ENSRNOG00000062516 Gna13 ENSRNOG00000063680 Kcnj2 ENSRNOG00000065020 Pecam1 ENSRNOG00000066876 ENSRNOG00000067362 ENSRNOG00000067823 Pitpnc1 ENSRNOG00000069533
Bone: periosteal estimation	11.12	64	36	400	1	0.00e+00	Amz2 Psmd12 Helz Cacng4 Cacng5 Prkca Lyzl6 Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Kcnj16 Crhr1 Mettl2 Mrc2 Marchf10 Cyb561 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Ftsj3 Smarcd2 Tcam1 Scn4a Ern1 Tex2 Polg2 Cep95 Smurf2 Kpna2 Cep112 Icam2 Limd2 Ddx5 AABR07030647.1 Dcaf7 ENSRNOG00000043295 Abca6 Bptf Prkar1a AABR07030630.1 Tanc2 AC133055.1 Snord104 Abca9 Prr29 Map3k3 Ace ENSRNOG00000062516 Gna13 ENSRNOG00000063680 Kcnj2 ENSRNOG00000065020 Pecam1 ENSRNOG00000067362 ENSRNOG00000067823 Pitpnc1 ENSRNOG00000069533
Bone: periosteal perimeter	11.04	30	0	0	0.99	1.49e-78	Apoh Rgs9 Wipi1 Arsg Fam20a Abca8 Abca8a Map2k6 Crhr1 Mrc2 Marchf10 Cyb561 Kcnh6 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Tex2 Kpna2 Dcaf7 Abca6 Prkar1a AABR07030630.1 Abca9 Map3k3 Ace ENSRNOG00000063680 ENSRNOG00000065020 ENSRNOG00000067823
Latency to leave start box in cocaine runway, F	14.5	1	0	0	0	1.00e+00	Map2k6

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	14	0.7	2.14
Adipose	alternative TSS	0	0	1.82
Adipose	gene expression	26	0.3	2.02
Adipose	isoform ratio	7	0.2	1.97
Adipose	intron excision ratio	6	0.2	2.24
Adipose	mRNA stability	13	0.4	2.05
BLA	alternative polyA	5	0.4	2.07
BLA	alternative TSS	8	1	2.22
BLA	gene expression	30	0.5	2.16
BLA	isoform ratio	5	0.3	2.01
BLA	intron excision ratio	5	0.2	1.99
BLA	mRNA stability	8	0.4	2.09
Brain	alternative polyA	8	0.4	2.05
Brain	alternative TSS	15	0.9	2.16
Brain	gene expression	29	0.3	2.05
Brain	isoform ratio	12	0.4	2.08
Brain	intron excision ratio	14	0.3	2.09
Brain	mRNA stability	8	0.2	1.97
Eye	alternative polyA	0	0	1.96
Eye	alternative TSS	0	0	1.84
Eye	gene expression	5	0.4	2.3
Eye	isoform ratio	0	0	1.78
Eye	intron excision ratio	3	0.5	2.01
Eye	mRNA stability	0	0	1.96
IL	alternative polyA	0	0	2.11
IL	alternative TSS	1	0.3	1.98
IL	gene expression	12	0.3	2.08
IL	isoform ratio	1	0.1	2.12
IL	intron excision ratio	1	0.1	2
IL	mRNA stability	3	0.3	1.99
LHb	alternative polyA	0	0	2.05
LHb	alternative TSS	3	0.9	2.22
LHb	gene expression	8	0.2	2.05
LHb	isoform ratio	1	0.1	1.95
LHb	intron excision ratio	1	0.1	1.99
LHb	mRNA stability	7	0.7	2.13
Liver	alternative polyA	5	0.3	1.94
Liver	alternative TSS	11	0.7	2.05
Liver	gene expression	21	0.3	2.02
Liver	isoform ratio	6	0.3	1.94
Liver	intron excision ratio	16	0.4	2.16
Liver	mRNA stability	7	0.3	1.97
NAcc	alternative polyA	6	0.5	2.07
NAcc	alternative TSS	1	0.1	1.85
NAcc	gene expression	28	0.4	2.12
NAcc	isoform ratio	2	0.1	1.95
NAcc	intron excision ratio	4	0.1	1.97
NAcc	mRNA stability	13	0.6	2.13
OFC	alternative polyA	2	0.3	2.07
OFC	alternative TSS	0	0	1.73
OFC	gene expression	13	0.4	2.16
OFC	isoform ratio	2	0.2	1.96
OFC	intron excision ratio	0	0	2.19
OFC	mRNA stability	4	0.4	2.14
PL	alternative polyA	8	0.6	2.25
PL	alternative TSS	7	0.6	2.04
PL	gene expression	34	0.5	2.13
PL	isoform ratio	2	0.1	1.93
PL	intron excision ratio	6	0.2	1.99
PL	mRNA stability	14	0.5	2.09