Variant report

Variant	nsv1020137
Chromosome Location	chr9:12164023-12305664
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr9:12292536-12292567	H1-hESC	embryonic stem cell:	n/a	n/a
2	BACH1	chr9:12170667-12170713	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr9:12230772-12231081	GM12878	blood:	n/a	n/a
4	CEBPB	chr9:12180768-12180970	IMR90	lung:	n/a	n/a
5	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
6	CEBPB	chr9:12195470-12195708	H1-hESC	embryonic stem cell:	n/a	chr9:12195611-12195622
7	CEBPB	chr9:12195488-12195695	K562	blood:	n/a	chr9:12195611-12195622
8	CEBPB	chr9:12195456-12195797	HepG2	liver:	n/a	chr9:12195611-12195622
9	CEBPB	chr9:12193945-12194181	A549	lung:	n/a	chr9:12194071-12194082 chr9:12194071-12194084
10	CEBPB	chr9:12195471-12195788	IMR90	lung:	n/a	chr9:12195611-12195622
11	CEBPB	chr9:12208833-12209071	HepG2	liver:	n/a	chr9:12208898-12208909 chr9:12208899-12208908 chr9:12208897-12208910
12	CTCF	chr9:12231143-12231170	GM20000	blood:	n/a	n/a
13	CTCF	chr9:12215488-12215552	GM13977	blood:	n/a	n/a
14	CTCF	chr9:12195560-12195710	HEK293	kidney:	n/a	n/a
15	CTCF	chr9:12210677-12210803	Kidney_OC	kidney:	n/a	n/a
16	CTCF	chr9:12230966-12231007	Kidney_OC	kidney:	n/a	n/a
17	CTCF	chr9:12195600-12195750	HCPEpiC	choroid plexus:	n/a	n/a
18	CTCF	chr9:12219074-12219108	GM10248	blood:	n/a	n/a
19	CTCF	chr9:12210667-12210803	GM10248	blood:	n/a	n/a
20	CTCF	chr9:12195560-12195710	HMF	breast:	n/a	n/a
21	CTCF	chr9:12195560-12195710	AoAF	blood vessel:	n/a	n/a
22	CTCF	chr9:12219290-12219372	GM13976	blood:	n/a	n/a
23	CTCF	chr9:12224065-12224152	GM13976	blood:	n/a	n/a
24	CTCF	chr9:12264400-12264550	HFF	foreskin:	n/a	n/a
25	CTCF	chr9:12195520-12195670	HMF	breast:	n/a	n/a
26	CTCF	chr9:12180880-12181030	GM12878	blood:	n/a	n/a
27	CTCF	chr9:12195600-12195750	NHEK	skin:	n/a	n/a
28	CTCF	chr9:12180880-12181030	HEK293	kidney:	n/a	n/a
29	CUX1	chr9:12230853-12230855	GM12878	blood:	n/a	n/a
30	E2F4	chr9:12208242-12208320	MCF10A-Er-Src	breast:	n/a	n/a
31	E2F4	chr9:12185683-12185754	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F6	chr9:12246607-12246944	H1-hESC	embryonic stem cell:	n/a	n/a
33	FOS	chr9:12185838-12186217	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
34	FOS	chr9:12183409-12183596	MCF10A-Er-Src	breast:	n/a	chr9:12183552-12183561 chr9:12183551-12183560
35	FOS	chr9:12185877-12186243	HUVEC	blood vessel:	n/a	chr9:12186008-12186019
36	FOS	chr9:12228774-12228990	MCF10A-Er-Src	breast:	n/a	chr9:12228868-12228879 chr9:12228870-12228877 chr9:12228872-12228881 chr9:12228873-12228880 chr9:12228870-12228882 chr9:12228871-12228881 chr9:12228872-12228880
37	FOS	chr9:12185825-12186238	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
38	FOS	chr9:12185897-12186081	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
39	FOS	chr9:12185825-12186224	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
40	FOS	chr9:12183392-12183690	MCF10A-Er-Src	breast:	n/a	chr9:12183552-12183561 chr9:12183551-12183560
41	FOSL2	chr9:12261384-12261559	HepG2	liver:	n/a	n/a
42	GATA2	chr9:12169256-12169499	SH-SY5Y	brain:	n/a	n/a
43	IRF3	chr9:12230497-12230498	GM12878	blood:	n/a	n/a
44	JUN	chr9:12164113-12164366	HepG2	liver:	n/a	chr9:12164249-12164258 chr9:12164248-12164261
45	JUN	chr9:12183467-12183667	HepG2	liver:	n/a	chr9:12183552-12183561 chr9:12183499-12183512 chr9:12183551-12183560
46	JUN	chr9:12226650-12226850	HepG2	liver:	n/a	chr9:12226797-12226810
47	JUND	chr9:12228831-12228889	H1-hESC	embryonic stem cell:	n/a	chr9:12228868-12228879 chr9:12228870-12228877 chr9:12228872-12228881 chr9:12228870-12228881 chr9:12228873-12228880 chr9:12228870-12228882 chr9:12228871-12228881 chr9:12228872-12228880
48	JUND	chr9:12226631-12226897	HepG2	liver:	n/a	n/a
49	JUND	chr9:12164081-12164391	HepG2	liver:	n/a	chr9:12164249-12164258
50	JUND	chr9:12183411-12183693	HepG2	liver:	n/a	chr9:12183552-12183561 chr9:12183550-12183561 chr9:12183551-12183560

No.	Distal block	Cell Line	Cell type
1	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
2	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
3	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
4	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
5	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TYRP1-4	chr9:12287320-12288238	NONHSAT130222

Variant related genes	Relation type
ENSG00000231491	TF binding region
ENSG00000224935	TF binding region
RNU2-47P	TF binding region
ENSG00000261226	chromatin interactions

Extended variants
information (count: 2171 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:2171 , 50 per page) page: 1 2 3 4 5 6 7 ... 44

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558306385	chr9:12164042-12164043	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs540403365	chr9:12164057-12164058	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs113669855	chr9:12164059-12164060	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs560225471	chr9:12164081-12164082	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs534963082	chr9:12164113-12164114	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs529190658	chr9:12164127-12164128	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs372658338	chr9:12164162-12164163	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs145195916	chr9:12164172-12164173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs375569986	chr9:12164173-12164174	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs540091362	chr9:12164175-12164176	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs149130779	chr9:12164177-12164178	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs577104331	chr9:12164187-12164188	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs545383058	chr9:12164196-12164197	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs369623633	chr9:12164272-12164273	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs571639001	chr9:12164279-12164280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs565163436	chr9:12164326-12164327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs575676909	chr9:12164335-12164336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs34021111	chr9:12164340-12164341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs34474068	chr9:12164378-12164379	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs544732694	chr9:12164386-12164387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs561437337	chr9:12164388-12164389	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs537024111	chr9:12164406-12164407	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs530318467	chr9:12164408-12164409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs547273042	chr9:12164412-12164413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs145170267	chr9:12164470-12164471	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs556980862	chr9:12164478-12164479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs187291354	chr9:12164542-12164543	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs73406672	chr9:12164545-12164546	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs192686621	chr9:12164565-12164566	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs79647299	chr9:12164586-12164587	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs145790882	chr9:12164632-12164633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs567874493	chr9:12164707-12164708	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs533729884	chr9:12164793-12164794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs553730511	chr9:12164838-12164839	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs577045271	chr9:12164849-12164850	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs374123683	chr9:12164855-12164856	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs558876219	chr9:12164954-12164955	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs575570114	chr9:12164974-12164975	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs16928478	chr9:12164986-12164987	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs561374933	chr9:12165003-12165004	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs184668996	chr9:12165006-12165007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs540824320	chr9:12165010-12165011	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs560559021	chr9:12165021-12165022	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148017820	chr9:12165029-12165030	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs10960502	chr9:12165072-12165073	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs62536620	chr9:12165106-12165107	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs562458867	chr9:12165138-12165139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs7024240	chr9:12165146-12165147	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs547822804	chr9:12165197-12165198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs567813273	chr9:12165199-12165200	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
Disorders of sex development	21048976	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Cancer	20164920	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Type 2 diabetes	21526130	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12161400-12167200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:12161600-12164800	Enhancers	Brain Germinal Matrix	brain
3	chr9:12162800-12166400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:12162800-12166600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:12164000-12164200	Enhancers	Fetal Brain Female	brain
6	chr9:12164200-12166200	Weak transcription	Fetal Brain Female	brain
7	chr9:12165800-12166400	Enhancers	Brain Substantia Nigra	brain
8	chr9:12166200-12166400	Enhancers	Fetal Brain Female	brain
9	chr9:12166400-12167000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:12166600-12167000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:12191600-12192000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr9:12191600-12192000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:12191800-12192000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:12192000-12200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:12200400-12200600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:12200400-12200800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:12200400-12202000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr9:12200600-12201000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr9:12200800-12201200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:12201200-12204400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:12204400-12204800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:12212600-12213000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:12212600-12213600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:12212800-12214000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:12213000-12213400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:12213000-12213800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr9:12213400-12214200	Enhancers	Brain Germinal Matrix	brain
28	chr9:12213400-12214400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:12213800-12214200	Enhancers	Brain Hippocampus Middle	brain
30	chr9:12221800-12222000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:12222000-12224400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:12224200-12224600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:12224200-12225000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr9:12224200-12225000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr9:12224400-12224800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr9:12224400-12224800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:12231000-12231400	Enhancers	Liver	Liver
38	chr9:12231200-12231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:12231400-12233400	Weak transcription	Liver	Liver
40	chr9:12231600-12232000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:12233400-12233800	Enhancers	Liver	Liver
42	chr9:12235200-12235600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:12241200-12242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr9:12241400-12243200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr9:12241600-12242000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:12241600-12242000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr9:12241600-12242000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:12241600-12242000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr9:12241600-12242000	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr9:12242600-12242800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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