Hub : Traits

Bone: cortical thickness

Tags: Physiology · Bone

Project: r01_doug_adams

6 loci · 10 genes with independent associations · 23 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	3	126323673	128419948	5	1	5.13e-09	5.49e-09	1.68e-01	Ndufaf5
2	10	91442275	92841363	1	1	1.40e-07	1.39e-06	1.04e-01	Nol11
3	10	94609547	96660473	3	1	6.52e-09	7.78e-11	3.27e-04	ENSRNOG00000065020
4	10	97108442	98504204	1	1	3.47e-09	2.01e-10	3.29e-03	Sox9
5	10	102999385	104353671	5	3	7.29e-08	7.18e-08	8.94e-16	Lgals3bp Cep295nl Afmid
6	10	105499327	107195627	8	3	7.74e-17	2.68e-10	1.96e-05	Wdr45b Znf750 Ccdc57

Pleiotropic Associations

Trait	Chi2 ratio	# genes+	# genes++	% genes++	Corr	Corr P	Genes
BMI with tail	5.37	10	1	10	0.99	6.84e-20	Lgals3bp C1qtnf1 Tasp1 Esf1 Ndufaf5 Usp36 Cep295nl Ccdc57 Afmid Nol11
BMI without tail	6.85	1	0	0	0	1.00e+00	Ccdc57
Body weight	6.09	9	4	40	0.99	9.98e-45	Tasp1 Esf1 Ndufaf5 Tbcd Znf750 Ccdc57 AABR07054000.1 Ism1 ENSRNOG00000068691
Epididymis fat weight	6.14	3	0	0	1	2.10e-05	Tasp1 Ndufaf5 Ism1
Glucose	7.72	2	0	0	0	1.00e+00	Wdr45b Narf
Left kidney weight	4.37	1	0	0	0	1.00e+00	ENSRNOG00000068691
Tail length	3.98	1	0	0	0	1.00e+00	Wdr45b
Length with tail	3.33	3	0	0	1	6.45e-06	Tasp1 Esf1 Ndufaf5
Length without tail	8.61	4	0	0	0.99	1.69e-03	Fn3k Wdr45b Narf Sectm1a
Retroperitoneal fat weight	5.95	5	3	30	0.99	5.49e-38	Tasp1 Esf1 Ndufaf5 AABR07054000.1 Ism1
Tibia length	6.83	14	4	40	0.98	1.75e-34	Tasp1 Esf1 Ndufaf5 Cep295nl Tbcd Fn3k Wdr45b Narf Sectm1a Znf750 Ccdc57 AABR07054000.1 Ism1 ENSRNOG00000068691
Delay discounting total patch changes 0 sec	7.14	1	0	0	0	1.00e+00	ENSRNOG00000065020
Delay discounting total patch changes 18 sec	9.46	1	0	0	0	1.00e+00	Ndufaf5
Delay discounting water rate 24 sec	8.59	1	0	0	0	1.00e+00	Ccdc57
Locomotor testing rearing	8.35	2	0	0	1	1.60e-04	Kcnj16 ENSRNOG00000065020
Intermitt. access day 1 inactive lever presses	11.52	1	0	0	0	1.00e+00	Sox9
Bone surface	8.89	7	0	0	-0.99	5.68e-13	Lgals3bp C1qtnf1 Kcnj16 Usp36 Cep295nl Afmid ENSRNOG00000065020
Bone volume	9.26	2	0	0	-1	2.36e-04	Kcnj16 ENSRNOG00000065020
Bone: cortical apparent density	9.47	3	0	0	1	1.16e-06	Kcnj16 Nol11 ENSRNOG00000065020
Bone: cortical area	11.1	13	3	30	0.99	3.05e-47	Tasp1 Esf1 Ndufaf5 Tbcd Fn3k Wdr45b Narf Sectm1a Znf750 Ccdc57 AABR07054000.1 Ism1 ENSRNOG00000068691
Bone: cortical thickness	12.82	7	0	0	1	1.34e-10	Lgals3bp Usp36 Cep295nl Wdr45b Narf Ccdc57 Afmid
Bone: cortical tissue density	9.12	2	0	0	1	7.44e-04	Kcnj16 Nol11
Bone: elastic work	12.25	5	0	0	0.98	1.08e-05	Sox9 Tbcd Znf750 Ccdc57 ENSRNOG00000068691
Bone: endosteal estimation	11.62	9	4	40	-0.96	2.39e-10	Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 ENSRNOG00000065020
Bone: endosteal perimeter	11.91	10	4	40	-0.98	1.06e-12	Sox9 Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 ENSRNOG00000065020
Bone: final force	18.49	5	1	10	1	2.77e-05	Tbcd Wdr45b Znf750 Ccdc57 ENSRNOG00000068691
Bone: final moment	16.14	6	1	10	0.99	1.80e-06	Sox9 Tbcd Wdr45b Znf750 Ccdc57 ENSRNOG00000068691
Bone: marrow area	11.54	9	4	40	-0.96	1.70e-10	Lgals3bp C1qtnf1 Map2k6 Kcnj16 Usp36 Cep295nl Afmid Nol11 ENSRNOG00000065020
Bone: maximum diameter	8.84	2	0	0	-0.19	7.15e-01	Kcnj16 Ccdc57
Bone: maximum force	18.25	5	2	20	0.99	6.86e-05	Tbcd Wdr45b Znf750 Ccdc57 ENSRNOG00000068691
Bone: maximum moment	18.7	5	3	30	0.99	8.13e-05	Tbcd Wdr45b Znf750 Ccdc57 ENSRNOG00000068691
Bone: minimum diameter	8.71	3	0	0	-0.12	8.02e-01	Kcnj16 Tbcd Ccdc57
Bone: periosteal estimation	9.12	4	0	0	0.03	9.43e-01	Kcnj16 Tbcd Ccdc57 ENSRNOG00000068691
Bone: periosteal perimeter	8.29	4	0	0	0.7	1.90e-01	Kcnj16 Tbcd Ccdc57 ENSRNOG00000068691
Bone: stiffness	15.53	1	0	0	0	1.00e+00	Ccdc57
Latency to leave start box in cocaine runway	10.63	1	0	0	0	1.00e+00	Ndufaf5

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	0	0	1.72
Adipose	alternative TSS	0	0	1.61
Adipose	gene expression	3	0	1.59
Adipose	isoform ratio	1	0	1.7
Adipose	intron excision ratio	2	0.1	1.69
Adipose	mRNA stability	3	0.1	1.7
BLA	alternative polyA	0	0	1.51
BLA	alternative TSS	0	0	1.6
BLA	gene expression	3	0	1.65
BLA	isoform ratio	0	0	1.69
BLA	intron excision ratio	2	0.1	1.68
BLA	mRNA stability	1	0	1.6
Brain	alternative polyA	0	0	1.66
Brain	alternative TSS	4	0.2	1.77
Brain	gene expression	6	0.1	1.65
Brain	isoform ratio	0	0	1.78
Brain	intron excision ratio	6	0.1	1.69
Brain	mRNA stability	4	0.1	1.65
Eye	alternative polyA	0	0	1.89
Eye	alternative TSS	0	0	1.56
Eye	gene expression	0	0	1.79
Eye	isoform ratio	0	0	1.67
Eye	intron excision ratio	0	0	1.64
Eye	mRNA stability	1	0.4	1.83
IL	alternative polyA	0	0	1.55
IL	alternative TSS	0	0	1.49
IL	gene expression	2	0.1	1.63
IL	isoform ratio	0	0	1.74
IL	intron excision ratio	3	0.3	1.73
IL	mRNA stability	0	0	1.65
LHb	alternative polyA	0	0	1.61
LHb	alternative TSS	0	0	1.91
LHb	gene expression	2	0.1	1.67
LHb	isoform ratio	0	0	1.8
LHb	intron excision ratio	2	0.2	1.51
LHb	mRNA stability	1	0.1	1.63
Liver	alternative polyA	0	0	1.46
Liver	alternative TSS	0	0	1.6
Liver	gene expression	3	0	1.62
Liver	isoform ratio	0	0	1.61
Liver	intron excision ratio	0	0	1.59
Liver	mRNA stability	0	0	1.65
NAcc	alternative polyA	0	0	1.56
NAcc	alternative TSS	2	0.2	1.86
NAcc	gene expression	2	0	1.66
NAcc	isoform ratio	0	0	1.67
NAcc	intron excision ratio	5	0.2	1.67
NAcc	mRNA stability	1	0	1.6
OFC	alternative polyA	0	0	1.72
OFC	alternative TSS	0	0	1.43
OFC	gene expression	3	0.1	1.71
OFC	isoform ratio	0	0	1.76
OFC	intron excision ratio	2	0.2	1.83
OFC	mRNA stability	0	0	1.63
PL	alternative polyA	0	0	1.65
PL	alternative TSS	0	0	1.69
PL	gene expression	5	0.1	1.66
PL	isoform ratio	1	0	1.71
PL	intron excision ratio	3	0.1	1.68
PL	mRNA stability	1	0	1.61