Tibia length

Tags: Physiology · Bone

Project: lionikas_2014

10 loci · 18 genes with independent associations · 421 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	186942049	189212399	2	1	1.39e-07	1.22e-07	2.33e-01	Eef1akmt2
2	chr3	37017099	38048368	1	1	1.59e-08	1.53e-02	2.30e-05	Fmnl2
3	chr3	45965821	50383141	7	1	1.02e-07	7.01e-08	4.95e-02	Fap
4	chr3	54640725	56008684	9	1	3.41e-08	2.76e-08	1.00e+00	Erich2
5	chr7	26575816	30853534	39	1	1.61e-10	9.65e-11	1.08e-02	Vezt
6	chr8	108585012	109845634	1	1	2.71e-08	1.27e-06	3.68e-13	Klhdc8b
7	chr8	110392196	112100485	2	1	1.68e-07	6.91e-07	2.83e-01	Lrrfip2
8	chr10	102999385	107195627	327	8	3.00e-15	2.53e-14	NaN	Cd7 Dnah17 Endov Lgals3bp LOC120095223 Metrnl Rbfox3
9	chr14	94418546	97682350	12	2	1.50e-08	1.24e-07	1.00e+00	Tmem17
10	chr15	47167781	49413227	21	1	1.06e-08	9.17e-09	1.00e+00	Nudt15

Pleiotropic Associations

Trait	Chi² ratio	# genes⁺	# genes⁺⁺	% genes⁺⁺	Corr	Corr P	Genes
BMI with tail	18.84	1	1	5.6	0	1.00e+00	Klhdc8b
BMI without tail	8.45	21	1	5.6	1	8.15e-63	Aatk Anapc11 Ccdc57 Fasn Fscn2 Gcgr Klhdc8b LOC102553539 LOC103693493 Lta4h Mcrip1 Mir331 Nploc4 Oxld1 Pcyt2 Rfng Slc16a3 Slc25a10 Tbcd Tspan10 Vezt
Body weight	7.43	80	21	116.7	0.96	1.14e-177	Aatk Alyref Amdhd1 Anapc11 Aspscr1 B3gntl1 Bahcc1 Baiap2 Card14 Cbx8 Ccdc137 Ccdc38 Ccdc57 Cd7 Cenpx Cep131 Cep83 Chmp6 Csnk1d Dclk3 Dcxr Eif4a3 Endov Faap100 Fasn Fgd6 Fscn2 Gaa Gcgr Gps1 Klhdc8b LOC100912167 LOC102548848 LOC102551882 LOC102551980 LOC102553539 LOC102555825 LOC103693493 LOC108352165 LOC120093556 LOC120093563 LOC120095223 LOC120095310 LOC120095311 Lrrc45 Lrrfip2 Lta4h Mafg Mcrip1 Metrnl Mir331 Mrpl12 Ndufa12 Ndufaf8 Nedd1 Npb Nploc4 Nptx1 Nr2c1 Ntn4 Oxld1 Pcyt2 Plxnc1 Ptchd3 Rbfox3 Rfng Rnf213 Sgsh Slc16a3 Slc25a10 Slc26a11 Slc38a10 Snrpf Tbcd Tmcc3 Tmem17 Tspan10 Ube2n Usp36 Vezt
Epididymis fat weight	8.72	4	0	0	-1	2.12e-06	Fign Grb14 LOC108350383 Slc4a10
Heart weight	17.24	1	0	0	0	1.00e+00	Klhdc8b
Left kidney weight	13.29	3	1	5.6	0	1.00e+00	B3gntl1 Foxk2 Klhdc8b
Right kidney weight	6.95	7	1	5.6	1	2.45e-17	Fndc3a Foxk2 Itm2b Klhdc8b Med4 Nudt15 Rcbtb2
Tail length	8.13	65	15	83.3	0.99	1.22e-234	Aatk Alyref Amdhd1 Anapc11 Aspscr1 B3gntl1 Bahcc1 Baiap2 Card14 Cbx8 Ccdc137 Ccdc38 Ccdc57 Cep131 Cep83 Chmp6 Csnk1d Eif4a3 Endov Faap100 Fasn Fgd6 Fscn2 Gaa Gcgr Gps1 Klhdc8b LOC100912167 LOC102548848 LOC102553539 LOC102555825 LOC103693493 LOC108352165 LOC120093556 LOC120093563 LOC120095223 LOC120095310 LOC120095311 Lta4h Mcrip1 Mir331 Ndufa12 Ndufaf8 Nedd1 Npb Nploc4 Nptx1 Nr2c1 Ntn4 Oxld1 Pcyt2 Plxnc1 Rfng Rnf213 Sgsh Slc16a3 Slc25a10 Slc26a11 Slc38a10 Snrpf Tbcd Tmcc3 Tspan10 Ube2n Vezt
Length with tail	12.28	43	21	116.7	0.96	3.21e-65	Aatk Amdhd1 Baiap2 Card14 Cbx8 Ccdc137 Ccdc38 Cep83 Chmp6 Dclk3 Eif4a3 Endov Fgd6 Gaa Gcgr Klhdc8b LOC100912167 LOC102548848 LOC102551272 LOC102553539 LOC108352165 LOC120093556 LOC120093563 LOC120095223 Lrrfip2 Lta4h Mir331 Ndufa12 Nedd1 Npb Nptx1 Nr2c1 Ntn4 Pcyt2 Plxnc1 Rptor Slc25a10 Slc26a11 Snrpf Tbc1d16 Tmcc3 Ube2n Vezt
Length without tail	9.11	18	2	11.1	1	2.79e-50	Amdhd1 B3gntl1 Dclk3 Dus1l Fgd6 Foxk2 LOC102553539 LOC120093563 Lta4h Mir331 Ndufa12 Nr2c1 Plxnc1 Rab40b Snrpf Tmcc3 Usp36 Vezt
Liver weight, left	13.45	1	0	0	0	1.00e+00	Klhdc8b
Liver weight, right	9.71	1	0	0	0	1.00e+00	Fmnl2
Retroperitoneal fat weight	6.31	45	0	0	0.97	6.43e-105	Aatk Alyref Anapc11 Aspscr1 B3gntl1 Bahcc1 Baiap2 Cbx8 Ccdc137 Ccdc57 Cep131 Chmp6 Eif4a3 Endov Faap100 Fign Fscn2 Gaa Gcgr Gps1 Klhdc8b LOC100912167 LOC102551882 LOC102555825 LOC103693493 LOC108350383 LOC108352165 LOC120095223 LOC120095310 LOC120095311 Mcrip1 Ndufaf8 Npb Nploc4 Oxld1 Pcyt2 Ptchd3 Rfng Rnf213 Sgsh Slc16a3 Slc25a10 Slc26a11 Slc38a10 Tspan10
Extensor digitorum longus weight	4.48	6	0	0	-1	7.23e-18	Fndc3a Itm2b Lpar6 Med4 Nudt15 Rcbtb2
Soleus weight	7.26	2	0	0	0	1.00e+00	Klhdc8b Rcbtb2
Number of licking bursts	24.53	1	1	5.6	0	1.00e+00	Klhdc8b
Food consumed during 24 hour testing period	19.17	1	0	0	0	1.00e+00	Fmnl2
Indifference point function ln k	36.38	1	1	5.6	0	1.00e+00	Klhdc8b
Indifference point function log k	36.38	1	1	5.6	0	1.00e+00	Klhdc8b
Locomotor activity	57.78	1	1	5.6	0	1.00e+00	Klhdc8b
Locomotor testing distance	64.52	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time number correct	18.64	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time trials correct on left	18.64	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time trials on left	19.51	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time omissions	23.75	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time false alarm rate	20.24	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time trials completed	19.51	1	1	5.6	0	1.00e+00	Klhdc8b
Reaction time trials AUC	20.65	1	1	5.6	0	1.00e+00	Klhdc8b
Conditioned locomotion	23.04	2	1	5.6	0	1.00e+00	Fmnl2 Klhdc8b
Cocaine response after cond. not corrected	16.6	1	0	0	0	1.00e+00	Klhdc8b
Cocaine response before conditioning	38.66	1	1	5.6	0	1.00e+00	Klhdc8b
Pavlov. Cond. magazine entry number	30	1	1	5.6	0	1.00e+00	Klhdc8b
Conditioned reinforcement - inactives	16.77	1	0	0	0	1.00e+00	Klhdc8b
Intermitt. access day 15 inactive lever presses	30.78	1	1	5.6	0	1.00e+00	Klhdc8b
Intermittent access terminal intake (last 3 days)	24.03	1	0	0	0	1.00e+00	Klhdc8b
Intermittent access total infusions	15.45	1	0	0	0	1.00e+00	Klhdc8b
Intermittent access standard deviation	16.8	1	0	0	0	1.00e+00	Klhdc8b
Cocaine induced anxiety	14.51	3	0	0	1	2.56e-05	Cd7 Cenpx Narf
Progressive ratio test 1 inactive lever presses	16.55	1	0	0	0	1.00e+00	Klhdc8b
Total sessions with >9 infusions	16	1	0	0	0	1.00e+00	Klhdc8b
Short access day 10 total inactive lever presses	101.65	1	1	5.6	0	1.00e+00	Klhdc8b
One hour access (shock baseline)	14.16	2	0	0	0	1.00e+00	LOC120093563 Plxnc1
Locomotion distance, session 1	23.98	1	1	5.6	0	1.00e+00	Klhdc8b
Locomotion distance, session 2	33.15	1	1	5.6	0	1.00e+00	Klhdc8b
Locomotion velocity, session 3	17.14	1	0	0	0	1.00e+00	Klhdc8b
Locomotion distance, session 8	52.78	1	1	5.6	0	1.00e+00	Klhdc8b
Degree of sensitization distance	24.75	1	0	0	0	1.00e+00	Klhdc8b
Condit. Reinf. active minus inactive responses	33.55	2	2	11.1	0	1.00e+00	Fmnl2 Klhdc8b
Condit. Reinf. active-inactive response ratio	23.11	2	1	5.6	0	1.00e+00	Fmnl2 Klhdc8b
Condit. Reinf. active responses	25.53	2	1	5.6	0	1.00e+00	Fmnl2 Klhdc8b
Incentive salience index mean	30.9	2	2	11.1	0	1.00e+00	Fmnl2 Klhdc8b
Time in familiar zone, hab. session 1	43.61	2	1	5.6	0	1.00e+00	Fmnl2 Klhdc8b
Time in novel zone, hab. session 1	27.89	1	1	5.6	0	1.00e+00	Fmnl2
Total zone transitions, hab. session 1	37.38	1	1	5.6	0	1.00e+00	Klhdc8b
Time in familiar zone, hab. session 2	27.1	1	1	5.6	0	1.00e+00	Klhdc8b
Total zone transitions, hab. session 2	69.58	1	1	5.6	0	1.00e+00	Klhdc8b
Total locomotion distance, hab. session 2	19.2	1	0	0	0	1.00e+00	Klhdc8b
Locomotion velocity, hab. session 2	21.15	1	1	5.6	0	1.00e+00	Klhdc8b
Novel to familiar place preference ratio	22.33	1	0	0	0	1.00e+00	Klhdc8b
Novelty place preference	20.99	1	0	0	0	1.00e+00	Klhdc8b
Time in novel zone, NPP test	17.06	1	0	0	0	1.00e+00	Klhdc8b
Total zone transitions, NPP test	106.24	1	1	5.6	0	1.00e+00	Klhdc8b
Total locomotion distance, NPP test	29.85	2	1	5.6	0	1.00e+00	Dnah17 Klhdc8b
Locomotion velocity, NPP test	51.12	1	1	5.6	0	1.00e+00	Klhdc8b
Pavlov. Cond. lever latency	16.5	1	0	0	0	1.00e+00	Fmnl2
Pavlov. Cond. change in total contacts	69.48	1	1	5.6	0	1.00e+00	Klhdc8b
Pavlov. Cond. index score	14.07	1	0	0	0	1.00e+00	Klhdc8b
Pavlov. Cond. lever-magazine prob. diff.	14.82	1	0	0	0	1.00e+00	Klhdc8b
Bone: cortical area	15.04	10	3	16.7	0.98	3.52e-11	B3gntl1 Cd7 Dus1l Foxk2 LOC102551882 LOC102551980 Lrrc45 Narf Rab40b Slc16a3
Bone: cortical thickness	15.57	19	6	33.3	0.98	4.13e-24	Afmid B3gntl1 C1qtnf1 Cbx2 Ccdc57 Cd7 Cep295nl Dus1l Engase Foxk2 Lrrc45 Narf Rab40b Rac3 Rbfox3 Slc16a3 Timp2 Usp36 Znf750
Bone: cortical thickness	14.55	1	0	0	0	1.00e+00	Foxk2
Bone: elastic work	14.17	9	0	0	1	7.87e-15	B3gntl1 Ccdc57 Cd7 Cenpx Hgs Lrrc45 Rac3 Slc16a3 Slc38a10
Bone: endosteal perimeter	8.64	2	0	0	0	1.00e+00	Pgs1 Timp2
Bone: final force	13.61	6	1	5.6	0.98	5.31e-07	B3gntl1 Cd7 Dus1l Foxk2 Lrrc45 Slc16a3
Bone: final moment	13.53	10	1	5.6	0.99	4.39e-14	B3gntl1 Ccdc57 Cd7 Dus1l Foxk2 LOC102551882 LOC102551980 Lrrc45 Ptchd3 Slc16a3
Bone: maximum diameter	9.4	9	0	0	1	1.25e-32	Afmid Birc5 C1qtnf1 Dnah17 Lgals3bp LOC100912319 Pgs1 Syngr2 Tmem235
Bone: maximum force	12.38	9	1	5.6	0.99	1.11e-14	B3gntl1 Cd7 Dus1l Foxk2 LOC102551882 LOC102551980 Lrrc45 Ptchd3 Slc16a3
Bone: maximum moment	12.09	13	1	5.6	1	1.14e-26	B3gntl1 Ccdc57 Cd7 Dus1l Foxk2 Gps1 LOC102551882 LOC102551980 Lrrc45 Metrnl Ptchd3 Slc16a3 Tbcd
Bone: periosteal estimation	8.31	1	0	0	0	1.00e+00	LOC120096689
Bone: stiffness	13.41	1	0	0	0	1.00e+00	Klhdc8b
Diff in mean of infusions in LGA sessions	16.56	1	0	0	0	1.00e+00	Slc4a10
Time to tail flick, vehicle, after self-admin	37.57	1	1	5.6	0	1.00e+00	Klhdc8b
Total heroin consumption	18.89	1	0	0	0	1.00e+00	Klhdc8b
Delay disc. indifference point, 0s delay	28.7	1	1	5.6	0	1.00e+00	Klhdc8b
Delay disc. indifference point, 4s delay	41.82	1	1	5.6	0	1.00e+00	Klhdc8b
Fecal boli incidents, locomotor time 1	16.98	1	0	0	0	1.00e+00	Klhdc8b
Rest time, locomotor task time 1	22.55	1	0	0	0	1.00e+00	Klhdc8b
Distance moved, locomotor task time 1	31.01	1	1	5.6	0	1.00e+00	Klhdc8b
Vertical activity count, locomotor time 1	49.01	1	1	5.6	0	1.00e+00	Klhdc8b
Bouts of movement, locomotor time 2	19.85	1	0	0	0	1.00e+00	Klhdc8b
Total resting periods, locomotor time 2	20.22	1	0	0	0	1.00e+00	Klhdc8b
Rest time, locomotor task time 2	25.34	1	1	5.6	0	1.00e+00	Klhdc8b
Distance moved, locomotor task time 2	42.39	1	1	5.6	0	1.00e+00	Klhdc8b
Vertical activity count, locomotor time 2	54.92	1	1	5.6	0	1.00e+00	Klhdc8b
Weight adjusted by age	30.32	1	1	5.6	0	1.00e+00	Klhdc8b
Food seeking constrained by brief footshock	13.3	2	0	0	0	1.00e+00	Itm2b Rcbtb2
Cd content in liver	20.17	1	0	0	0	1.00e+00	Klhdc8b
Fe content in liver	40.39	1	1	5.6	0	1.00e+00	Klhdc8b
Mg content in liver	15.79	1	0	0	0	1.00e+00	Klhdc8b
Na content in liver	16.36	1	0	0	0	1.00e+00	Klhdc8b
Rb content in liver	51.88	1	1	5.6	0	1.00e+00	Klhdc8b
Sr content in liver	22.41	1	0	0	0	1.00e+00	Klhdc8b

Associations by panel

Tissue	RNA modality	# hits	% hits/tests	Avg chisq
Adipose	alternative polyA	18	0.5	2.74
Adipose	alternative TSS	16	0.5	2.95
Adipose	gene expression	42	0.5	2.71
Adipose	isoform ratio	13	0.3	2.76
Adipose	intron excision ratio	13	0.4	2.85
Adipose	mRNA stability	14	0.3	2.76
BLA	alternative polyA	9	0.4	2.86
BLA	alternative TSS	12	0.6	2.91
BLA	gene expression	18	0.3	2.76
BLA	isoform ratio	9	0.3	2.87
BLA	intron excision ratio	7	0.2	2.88
BLA	mRNA stability	9	0.4	2.84
Brain	alternative polyA	8	0.2	2.77
Brain	alternative TSS	22	0.5	2.88
Brain	gene expression	28	0.3	2.72
Brain	isoform ratio	26	0.5	2.87
Brain	intron excision ratio	22	0.4	2.96
Brain	mRNA stability	17	0.3	2.74
Eye	alternative polyA	0	0	2.92
Eye	alternative TSS	0	0	2.87
Eye	gene expression	2	0.2	2.96
Eye	isoform ratio	1	0.2	2.68
Eye	intron excision ratio	6	0.7	2.57
Eye	mRNA stability	1	0.3	3.1
IL	alternative polyA	2	0.2	2.88
IL	alternative TSS	4	0.6	2.97
IL	gene expression	10	0.2	2.76
IL	isoform ratio	4	0.3	2.82
IL	intron excision ratio	2	0.2	2.93
IL	mRNA stability	7	0.5	2.85
LHb	alternative polyA	0	0	2.89
LHb	alternative TSS	1	0.2	2.51
LHb	gene expression	8	0.2	2.77
LHb	isoform ratio	1	0.1	2.51
LHb	intron excision ratio	2	0.2	2.69
LHb	mRNA stability	2	0.2	2.73
Liver	alternative polyA	24	0.9	3.06
Liver	alternative TSS	13	0.5	2.81
Liver	gene expression	36	0.5	2.74
Liver	isoform ratio	28	0.7	2.93
Liver	intron excision ratio	29	0.6	2.78
Liver	mRNA stability	17	0.6	2.87
NAcc	alternative polyA	14	0.5	2.88
NAcc	alternative TSS	18	0.6	3.09
NAcc	gene expression	21	0.2	2.73
NAcc	isoform ratio	18	0.4	2.99
NAcc	intron excision ratio	9	0.2	2.87
NAcc	mRNA stability	11	0.3	2.72
OFC	alternative polyA	1	0.1	2.72
OFC	alternative TSS	1	0.1	3.17
OFC	gene expression	14	0.3	2.74
OFC	isoform ratio	2	0.1	2.79
OFC	intron excision ratio	1	0.1	3.21
OFC	mRNA stability	5	0.4	2.78
PL	alternative polyA	13	0.4	2.88
PL	alternative TSS	11	0.3	2.95
PL	gene expression	25	0.3	2.77
PL	isoform ratio	20	0.4	2.94
PL	intron excision ratio	16	0.3	2.95
PL	mRNA stability	17	0.4	2.79
pVTA	alternative polyA	4	0.2	2.98
pVTA	alternative TSS	9	0.7	3.04
pVTA	gene expression	18	0.3	2.82
pVTA	isoform ratio	5	0.2	2.89
pVTA	intron excision ratio	5	0.2	2.92
pVTA	mRNA stability	8	0.5	2.86
RMTg	alternative polyA	0	0	2.74
RMTg	alternative TSS	3	0.6	2.82
RMTg	gene expression	5	0.3	2.78
RMTg	isoform ratio	3	0.5	3.11
RMTg	intron excision ratio	1	0.1	2.82
RMTg	mRNA stability	3	0.5	2.93