Abnormal bone structure

0003330

Normal Case/Contol ^ⓘ

Sibling Case/Control ^ⓘ

Links

Sex Split

Interactive Plot

Statistics

Case	Control
79972	380222

Phenotype Definition

Any anomaly in the composite material or the layered arrangement of the bony skeleton. [HPO:probinson]

Top SNP Information

Location	SNP	Gene	Ref>Alt	Alt in Case	Alt in Control	Chi-square	P-value	Odds ratio
chr15:48426484	rs1426654	SLC24A5	A>G	4266	23260	66.76	3.072e-16	0.8713
chr6:170242949	rs9396958	-	T>C	2418	13696	61.8	3.799e-15	0.8399
chr2:3313043	rs73133173	EIPR1	A>C	2153	12310	61.49	4.444e-15	0.8318
chr1:29783282	rs6676357	-	T>C	1447	8607	61.33	4.819e-15	0.8001
chr2:211717706	rs12995612	-	C>G	2480	13992	60.97	5.786e-15	0.8426
chr6:22050187	rs1736507	-	C>A	2166	12347	60.23	8.437e-15	0.8338
chr2:26113913	rs78404020	-	A>G	2061	11756	57.16	4.026e-14	0.8341
chr16:86042597	rs8051812	-	A>G	3330	18275	57.09	4.153e-14	0.8661
chr1:236085940	rs12038310	-	C>T	2298	12978	57.0	4.362e-14	0.8421
chr15:48392165	rs1834640	-	A>G	4988	26636	55.73	8.33e-14	0.8897
chr3:50070763	rs7621352	RBM6	A>C	78778	383282	50.04	1.505e-12	0.9628
chr10:37096493	rs12412437	-	C>A	3486	18893	49.53	1.953e-12	0.8772
chr9:9860780	rs2147065	PTPRD	T>C	3090	16877	49.47	2.01e-12	0.8704
chr11:44843134	rs11038167	TSPAN18	A>C	1541	8908	49.46	2.02e-12	0.8231
chr9:91202260	rs4433238	-	G>A	4729	25154	49.04	2.511e-12	0.8936
chr1:35815123	rs12043750	ZMYM4	C>T	4037	21657	48.69	3.001e-12	0.886
chr3:50108792	rs3774734	RBM6	A>C	74589	348381	48.43	3.43e-12	1.038
chr3:50129399	Affx-22412948	RBM6	C>T	81269	394987	48.4	3.481e-12	0.9634
chr3:50174848	rs7642934	-	G>A	79961	388857	47.73	4.886e-12	0.9636
chr3:49936102	rs2230590	MST1R	C>T	81316	395076	47.27	6.176e-12	0.9638
chr3:50070763	rs7621352	RBM6	A>C	73482	356567	47.91	4.462e-12	0.9625
chr3:49936102	rs2230590	MST1R	C>T	76015	368260	44.39	2.685e-11	0.9639
chr3:49902544	rs9821675	CAMKV	A>G	81593	381257	42.1	8.693e-11	1.036
chr3:50129399	Affx-22412948	RBM6	C>T	75064	363558	41.92	9.52e-11	0.9649
chr3:50108792	rs3774734	RBM6	A>C	72291	337128	41.43	1.223e-10	1.036
chr3:49924940	rs1062633	MST1R	C>T	75708	366551	41.23	1.352e-10	0.9651
chr3:50174848	rs7642934	-	G>A	74670	361751	40.35	2.125e-10	0.9655
chr3:49834571	rs6809879	CDHR4	A>G	28790	131892	40.22	2.271e-10	1.047
chr3:49899795	rs3796386	CAMKV	G>A	69146	322215	40.02	2.513e-10	1.036
chr3:49949071	rs868891	MON1A	A>G	69724	325134	38.37	5.849e-10	1.035
chr3:50153356	rs1138536	RBM5	C>T	70773	330261	37.44	9.437e-10	1.035
chr3:49817450	rs9829155	IP6K1	T>C	28961	132903	36.23	1.755e-09	1.044
chr3:49941436	rs2280406	-	G>A	81952	383424	36.1	1.873e-09	1.034
chr3:50062878	rs13071931	RBM6	G>A	41385	191302	36.08	1.892e-09	1.039
chr3:50144951	rs1061474	RBM5	C>T	70726	330170	35.05	3.219e-09	1.033
chr3:49808274	rs62262730	IP6K1	T>G	28607	131408	33.84	5.982e-09	1.043
chr3:50174025	rs2189691	-	T>C	43986	203949	31.62	1.873e-08	1.035
chr7:2028968	rs34809719	MAD1L1	G>T	28817	141546	31.16	2.382e-08	0.9609
chr3:50176739	Affx-22413417	-	C>A	41694	193240	30.39	3.531e-08	1.035
chr7:1978002	rs56259105	MAD1L1	T>C	28993	142309	30.06	4.188e-08	0.9617

Location	SNP	Gene	Ref>Alt	Alt in Case	Alt in Control	Chi-square	P-value	Odds ratio
chr2:157108393	rs4664804	-	T>C	16657	36608	26.76	2.309e-07	0.9503
chr5:53771189	rs62354517	-	A>G	53629	110139	25.15	5.309e-07	1.032
chr1:191249774	rs76855352	-	C>T	2173	5170	24.28	8.309e-07	0.8809
chr14:49485194	rs17279640	-	C>A	1870	3415	23.78	1.081e-06	1.151
chr4:156638073	rs3796587	GUCY1A1	C>G	30124	65221	23.76	1.094e-06	0.9632
chr1:241704748	rs2050513	KMO	C>A	28007	60714	23.67	1.143e-06	0.9622
chr11:79093294	rs553692	TENM4	T>G	76653	163522	23.05	1.579e-06	0.9719
chr10:37096493	rs12412437	-	C>A	3486	8049	22.61	1.989e-06	0.9072
chr13:112348972	rs12430744	-	G>C	71326	152198	22.58	2.017e-06	0.9718
chr4:68102416	rs4860240	-	T>C	4231	9670	21.9	2.868e-06	0.9163
chr9:91202260	rs4433238	-	G>A	4729	10755	21.71	3.178e-06	0.9208
chr3:50070763	rs7621352	RBM6	A>C	78778	167820	21.65	3.279e-06	0.9728
chr7:15898572	rs17428455	-	T>G	24527	49801	21.47	3.603e-06	1.04
chr2:138006655	rs16838442	THSD7B	C>T	4194	9580	21.43	3.668e-06	0.9169
chr3:49834571	rs6809879	CDHR4	A>G	30198	61593	21.23	4.073e-06	1.036
chr15:80533732	rs68014311	CTXND1	A>C	17637	38524	20.95	4.715e-06	0.957
chr7:40928113	rs10276497	-	G>T	78590	167330	20.85	4.958e-06	0.9733
chr1:191286162	rs12172717	-	C>A	2245	5283	20.82	5.054e-06	0.8908
chr3:49936102	rs2230590	MST1R	C>T	81316	173022	20.69	5.394e-06	0.9734
chr1:103379918	rs3753841	COL11A1	A>G	66084	141136	20.67	5.444e-06	0.9728
chr12:69019993	rs17120790	RAP1B	A>G	32975	67057	24.66	6.825e-07	1.038
chr4:156638073	rs3796587	GUCY1A1	C>G	28847	62372	23.38	1.331e-06	0.9626
chr3:50070763	rs7621352	RBM6	A>C	73482	156418	22.91	1.695e-06	0.9712
chr14:49485194	rs17279640	-	C>A	1843	3371	22.35	2.273e-06	1.148
chr3:49936102	rs2230590	MST1R	C>T	76015	161614	21.83	2.985e-06	0.9719
chr19:4505445	rs16989695	PLIN4	A>G	77755	160590	21.63	3.301e-06	1.029
chr1:181147387	rs7523183	-	G>A	49665	106270	21.42	3.685e-06	0.9701
chr1:181146814	rs10797677	-	A>G	50999	109073	21.11	4.346e-06	0.9705
chr11:79093294	rs553692	TENM4	T>G	73004	155365	20.51	5.924e-06	0.9727
chr1:103379918	rs3753841	COL11A1	A>G	60844	129811	20.5	5.972e-06	0.972
chr3:49902544	rs9821675	CAMKV	A>G	81593	168749	20.19	7.007e-06	1.028
chr19:46387344	rs11550348	IRF2BP1	G>A	19409	42179	19.94	7.984e-06	0.9595
chr3:49834571	rs6809879	CDHR4	A>G	28790	58632	19.9	8.178e-06	1.036
chr4:133326621	rs79004738	-	G>A	5963	13365	19.56	9.748e-06	0.9322
chr5:53771189	rs62354517	-	A>G	52004	106878	19.53	9.887e-06	1.029
chr3:49924940	rs1062633	MST1R	C>T	75708	160806	19.45	1.034e-05	0.9734
chr18:43303089	rs10460032	SLC14A1	G>A	25452	55007	19.44	1.038e-05	0.9641
chr13:91971967	rs7981508	-	A>T	17974	36267	19.37	1.074e-05	1.044
chr4:178064403	rs12639921	-	T>G	18173	36691	19.11	1.231e-05	1.043
chr3:50129399	Affx-22412948	RBM6	C>T	75064	159467	18.93	1.355e-05	0.9738

Associated Diseases ^ⓘ

ID	Name	Top Correlation
ICD: E559	Vitamin D deficiency, unspecified	1/20
ICD: M159	Polyarthrosis, unspecified	5/20
ICD: M161	Other primary coxarthrosis	2/20
ICD: M189	Arthrosis of first carpometacarpal joint, unspecified	2/20
ICD: M1994	Arthrosis, unspecified (Hand)	2/20
ICD: M1997	Arthrosis, unspecified (Ankle and foot)	2/20
ICD: M819	Osteoporosis, unspecified	2/20

ID	Name	Top Correlation
ICD-10: C349	Bronchus or lung, unspecified	0/20
ICD-10: C795	Secondary malignant neoplasm of bone and bone marrow	0/20
ICD-10: G560	Carpal tunnel syndrome	0/20
ICD-10: G960	Cerebrospinal fluid leak	0/20
ICD-10: H809	Otosclerosis, unspecified	0/20
ICD-10: J180	Bronchopneumonia, unspecified	0/20
ICD-10: J942	Haemothorax	0/20
ICD-10: K092	Other cysts of jaw	0/20
ICD-10: L578	Other skin changes due to chronic exposure to nonionising radiation	0/20
ICD-10: M130	Polyarthritis, unspecified	0/20
ICD-10: M167	Other secondary coxarthrosis	0/20
ICD-10: M180	Primary arthrosis of first carpometacarpal joints, bilateral	0/20
ICD-10: M181	Other primary arthrosis of first carpometacarpal joint	0/20
ICD-10: M190	Primary arthrosis of other joints	0/20
ICD-10: M1995	Arthrosis, unspecified (Pelvic region and thigh)	0/20
ICD-10: M1996	Arthrosis, unspecified-Lower leg	0/20
ICD-10: M1998	Arthrosis, unspecified (Other)	0/20
ICD-10: M1999	Arthrosis, unspecified (Site unspecified)	0/20
ICD-10: M241	Other articular cartilage disorders	0/20
ICD-10: M254	Effusion of joint	0/20
ICD-10: M4692	Inflammatory spondylopathy, unspecified (Cervical region)	0/20
ICD-10: M4696	Inflammatory spondylopathy, unspecified (Lumbar region)	0/20
ICD-10: M4699	Inflammatory spondylopathy, unspecified (Site unspecified)	0/20
ICD-10: M512	Other specified intervertebral disk displacement	0/20
ICD-10: M513	Other specified intervertebral disk degeneration	0/20
ICD-10: M659	Synovitis and tenosynovitis, unspecified	0/20
ICD-10: M671	Other contracture of tendon (sheath)	0/20
ICD-10: M706	Trochanteric bursitis	0/20
ICD-10: M722	Plantar fascial fibromatosis	0/20
ICD-10: M75	Shoulder lesions	0/20
ICD-10: M754	Impingement syndrome of shoulder	0/20
ICD-10: M770	Medial epicondylitis	0/20
ICD-10: M796	Pain in limb	0/20
ICD-10: M8090	Unspecified osteoporosis with pathological fracture (Multiple sites)	0/20
ICD-10: M8098	Unspecified osteoporosis with pathological fracture (Other)	0/20
ICD-10: M814	Drug-induced osteoporosis	0/20
ICD-10: M8140	Drug-induced osteoporosis (Multiple sites)	0/20
ICD-10: M82	Osteoporosis in diseases classified elsewhere	0/20
ICD-10: M899	Disorder of bone, unspecified	0/20
ICD-10: M9075	Fracture of bone in neoplastic disease (Pelvic region and thigh)	0/20
ICD-10: M9078	Fracture of bone in neoplastic disease (Other)	0/20
ICD-10: M940	Chondrocostal junction syndrome [Tietze]	0/20
ICD-10: M960	Pseudarthrosis after fusion or arthrodesis	0/20
ICD-10: N328	Other specified disorders of bladder	0/20
ICD-10: N872	Severe cervical dysplasia, not elsewhere classified	0/20
ICD-10: N879	Dysplasia of cervix uteri, unspecified	0/20
ICD-10: O40	Polyhydramnios	0/20
ICD-10: O48	Prolonged pregnancy	0/20
ICD-10: R238	Other and unspecified skin changes	0/20
ICD-10: R601	Generalised oedema	0/20
ICD-10: R900	Intracranial space-occupying lesion	0/20
ICD-10: T390	Salicylates	0/20
ICD-10: Y86	Sequelae of other accidents	0/20

Abnormal bone structure

0003330

Normal Case/Contol ⓘ

Sibling Case/Control ⓘ

Links

Statistics

Phenotype Definition

Top SNP Information Show Normal Table Show Sibling SNP

Associated Diseases ⓘ Shared SNP diseases No shared SNP diseases

Normal Case/Contol ^ⓘ

Sibling Case/Control ^ⓘ

Top SNP Information

Associated Diseases ^ⓘ