Hub : Traits

Bone: periosteal estimation

Tags: Physiology · Bone

Project: r01_doug_adams

4 loci · 11 genes with independent associations · 62 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	7	128200675	130977246	22	4	3.99e-08	1.29e-07	1.00e+00	Asb8 Tuba1b Hdac7 Fkbp11
2	10	89561948	96071622	36	5	6.11e-09	2.01e-08	NaN	Psmd12 Apoh Dcaf7 AABR07030630.1 Map3k3
3	16	558324	2117247	3	1	1.65e-07	1.90e-07	1.16e-133	Ppif
4	16	2999353	4396663	1	1	2.62e-07	6.90e-10	4.44e-04	Wnt5a

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	4.81	21	0	0	1	4.40e-46	Asb8 Tuba1c Zfp641 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Body weight	6.27	28	19	172.7	0.99	1.85e-45	Ccdc47 Asb8 Kpna2 Tuba1c Cep112 Zfp641 ENSRNOG00000043295 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Map3k3 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000067823 ENSRNOG00000069732 Fkbp11
Length without tail	7.74	22	0	0	1	1.16e-57	Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Intraocular pressure	11.19	4	0	0	-1	1.94e-07	Zfp641 Tmem106c Hdac7 Pfkm
Extensor digitorum longus weight	4.58	32	2	18.2	0.39	1.78e-03	Kcnh6 Taco1 Ccdc47 Ddx42 Asb8 Smarcd2 Kpna2 Tuba1c Zfp641 Dcaf7 ENSRNOG00000043295 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Tibia length	7.72	22	4	36.4	1	1.15e-54	Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Indifference point 0 sec	8.83	4	0	0	1	7.78e-07	Psmd12 ENSRNOG00000043295 ENSRNOG00000067823 ENSRNOG00000069533
Delay discounting total patch changes 0 sec	8.7	2	0	0	0	1.00e+00	ENSRNOG00000043295 ENSRNOG00000067823
Delay discounting total patch changes 6 sec	9.28	2	0	0	0	1.00e+00	Cep112 ENSRNOG00000067823
Reaction time mean minus median	10.51	1	0	0	0	1.00e+00	Fkbp11
Reaction time omissions	10.48	19	0	0	-1	6.94e-51	Asb8 Tuba1c Zfp641 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Hdac7 Pfkm Ccdc65 Rapgef3 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Condit. Reinf. active minus inactive responses	11.65	5	0	0	1	1.75e-08	Ccdc47 Kpna2 Dcaf7 ENSRNOG00000043295 ENSRNOG00000063680
Condit. Reinf. active responses	10.82	5	0	0	1	8.88e-08	Wipi1 Fam20a Kpna2 Dcaf7 ENSRNOG00000043295
Condit. Reinf. lever reinforcers received	9.77	2	0	0	0	1.00e+00	Kpna2 ENSRNOG00000043295
Pavlov. Cond. intertrial magazine entries	12.96	19	0	0	1	3.58e-81	Psmd12 Mrc2 Taco1 Strada Ccdc47 Ddx42 Scn4a Icam2 Ddx5 Dcaf7 ENSRNOG00000043295 Bptf Tanc2 Prr29 Map3k3 Ace ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000069533
Intermittent access total locomotion	12.94	8	0	0	1	4.43e-22	Psmd12 Helz Cacng5 Icam2 ENSRNOG00000043295 ENSRNOG00000067362 ENSRNOG00000067823 ENSRNOG00000069533
Short access day 10 total infusions	12.19	1	0	0	0	1.00e+00	ENSRNOG00000043295
Short access day 10 total locomotion	13.1	7	0	0	1	2.76e-21	Psmd12 Taco1 Icam2 Ddx5 ENSRNOG00000043295 Bptf ENSRNOG00000067823
Locomotion velocity, session 8	15.27	1	0	0	0	1.00e+00	Wnt5a
Bone: apparent density	10.46	22	0	0	1	2.11e-56	Asb8 Tuba1c Zfp641 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone surface	11.31	41	0	0	1	7.51e-98	Psmd12 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Tuba1c Icam2 Ddx5 Zfp641 Dcaf7 ENSRNOG00000043295 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone volume	9.27	35	0	0	1	3.80e-94	Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Tuba1c Icam2 Zfp641 Dcaf7 Spats2 Tanc2 Prph Slc48a1 Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: connectivity density	8.84	5	0	0	1	1.07e-06	Tuba1b Adcy6 Hdac7 Ccdc65 ENSRNOG00000061607
Bone: cortical apparent density	11.03	1	0	0	0	1.00e+00	Cacng4
Bone: cortical area	10.94	26	0	0	1	7.68e-89	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: cortical porosity	17.1	12	2	18.2	1	3.61e-28	Mrc2 Kcnh6 Taco1 Ccdc47 Ddx42 Scn4a Dcaf7 Tanc2 Prr29 Map3k3 Ace ENSRNOG00000063680
Bone: cortical porosity	14.95	6	0	0	1	1.52e-05	Mrc2 Kcnh6 Taco1 Ccdc47 Ddx42 ENSRNOG00000063680
Bone: cortical thickness	9.06	5	0	0	-1	7.72e-08	Psmd12 Cacng4 Prkca Map2k6 AABR07030630.1
Bone: cortical tissue density	10.49	1	0	0	0	1.00e+00	Cacng4
Bone: endosteal estimation	14.8	62	35	318.2	0.98	1.53e-134	Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 ENSRNOG00000043295 Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000067620 ENSRNOG00000067823 ENSRNOG00000069533 ENSRNOG00000069732 Fkbp11
Bone: endosteal perimeter	15.68	58	36	327.3	0.99	2.18e-127	Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Smurf2 Kpna2 Tuba1c Cep112 Icam2 Ddx5 Zfp641 Dcaf7 ENSRNOG00000043295 Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000067620 ENSRNOG00000067823 ENSRNOG00000069533 ENSRNOG00000069732 Fkbp11
Bone: final force	10.4	26	0	0	1	3.06e-79	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: final moment	10.42	26	0	0	1	3.20e-75	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: marrow area	14.44	62	35	318.2	0.98	1.73e-134	Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 ENSRNOG00000043295 Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000067620 ENSRNOG00000067823 ENSRNOG00000069533 ENSRNOG00000069732 Fkbp11
Bone: maximum diameter	8.29	23	0	0	1	5.25e-67	Psmd12 Prkca Fam20a Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Smarcd2 Scn4a Kpna2 Icam2 Dcaf7 ENSRNOG00000043295 AABR07030630.1 Tanc2 Prr29 Map3k3 Ace ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000069533
Bone: maximum force	14.29	26	5	45.5	1	3.28e-79	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: maximum moment	14.16	26	7	63.6	1	8.83e-72	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: minimum diameter	13.58	62	31	281.8	1	8.38e-183	Psmd12 Helz Cacng4 Cacng5 Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Ppif Tmem254 Scn4a Smurf2 Kpna2 Wnt5a Tuba1c Cep112 Icam2 Ddx5 Zfp641 Zcchc24 Dcaf7 ENSRNOG00000043295 Bptf Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067362 ENSRNOG00000067620 ENSRNOG00000067823 ENSRNOG00000069533 ENSRNOG00000069732 Fkbp11
Bone: periosteal perimeter	10.49	47	0	0	1	4.77e-106	Prkca Apoh Rgs9 Wipi1 Fam20a Map2k6 Mrc2 Kcnh6 Taco1 Strada Ccdc47 Ddx42 Asb8 Smarcd2 Scn4a Kpna2 Tuba1c Icam2 Zfp641 Dcaf7 ENSRNOG00000043295 Prkar1a AABR07030630.1 Spats2 Tanc2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Prr29 Map3k3 Kmt2d ENSRNOG00000061607 Ace ENSRNOG00000063058 ENSRNOG00000063680 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: post-yield work	9.98	3	0	0	1	1.00e-04	Tuba1b ENSRNOG00000061607 Fkbp11
Bone: stiffness	16.35	26	22	200	1	1.15e-62	Asb8 Ppif Tmem254 Wnt5a Tuba1c Zfp641 Zcchc24 Spats2 Prph Slc48a1 Tmem106c Tuba1b Cacnb3 Adcy6 Fkbp11 Hdac7 Pfkm Ccdc65 Rapgef3 Kansl2 Kmt2d ENSRNOG00000061607 ENSRNOG00000063058 ENSRNOG00000067620 ENSRNOG00000069732 Fkbp11
Bone: trabecular thickness	11.4	1	0	0	0	1.00e+00	Ddx42

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	7	0.3	2.16
Adipose	alternative TSS	0	0	1.94
Adipose	gene expression	16	0.2	2.01
Adipose	isoform ratio	2	0.1	1.96
Adipose	intron excision ratio	1	0	2.14
Adipose	mRNA stability	8	0.2	2.03
BLA	alternative polyA	2	0.2	1.99
BLA	alternative TSS	4	0.5	2.21
BLA	gene expression	15	0.2	2.14
BLA	isoform ratio	4	0.2	2.02
BLA	intron excision ratio	2	0.1	2.03
BLA	mRNA stability	2	0.1	2.11
Brain	alternative polyA	3	0.1	2.01
Brain	alternative TSS	4	0.2	2.25
Brain	gene expression	14	0.2	2.03
Brain	isoform ratio	5	0.2	1.99
Brain	intron excision ratio	4	0.1	2.04
Brain	mRNA stability	6	0.1	1.93
Eye	alternative polyA	0	0	2.2
Eye	alternative TSS	0	0	2.24
Eye	gene expression	0	0	2.24
Eye	isoform ratio	0	0	1.75
Eye	intron excision ratio	0	0	2.08
Eye	mRNA stability	0	0	1.99
IL	alternative polyA	0	0	2.19
IL	alternative TSS	1	0.3	1.91
IL	gene expression	1	0	2.12
IL	isoform ratio	0	0	2.13
IL	intron excision ratio	0	0	2.15
IL	mRNA stability	1	0.1	1.97
LHb	alternative polyA	0	0	2.17
LHb	alternative TSS	2	0.6	2.42
LHb	gene expression	5	0.2	2.11
LHb	isoform ratio	0	0	2.02
LHb	intron excision ratio	0	0	2.05
LHb	mRNA stability	2	0.2	2.02
Liver	alternative polyA	2	0.1	1.86
Liver	alternative TSS	0	0	2.13
Liver	gene expression	9	0.1	2.01
Liver	isoform ratio	0	0	1.92
Liver	intron excision ratio	3	0.1	2.04
Liver	mRNA stability	4	0.2	1.96
NAcc	alternative polyA	3	0.2	2.01
NAcc	alternative TSS	0	0	2.03
NAcc	gene expression	12	0.2	2.04
NAcc	isoform ratio	3	0.2	2
NAcc	intron excision ratio	0	0	2.05
NAcc	mRNA stability	6	0.3	2.1
OFC	alternative polyA	0	0	2.13
OFC	alternative TSS	0	0	1.99
OFC	gene expression	3	0.1	2.14
OFC	isoform ratio	0	0	1.98
OFC	intron excision ratio	0	0	2.06
OFC	mRNA stability	0	0	2.08
PL	alternative polyA	2	0.1	1.96
PL	alternative TSS	5	0.4	2.14
PL	gene expression	9	0.1	2.1
PL	isoform ratio	0	0	1.93
PL	intron excision ratio	1	0	2.07
PL	mRNA stability	6	0.2	2.06