Variant report

Variant	nsv872635
Chromosome Location	chr1:188813880-188870483
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	ATF1	chr1:188818322-188818328	K562	blood:	n/a	n/a
2	BRCA1	chr1:188857430-188857935	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr1:188833745-188833994	HepG2	liver:	n/a	n/a
4	CEBPB	chr1:188861142-188861475	Hela-S3	cervix:	n/a	chr1:188861298-188861309
5	CEBPB	chr1:188861151-188861446	A549	lung:	n/a	chr1:188861298-188861309
6	CEBPB	chr1:188857462-188857804	IMR90	lung:	n/a	n/a
7	CEBPB	chr1:188861120-188861477	IMR90	lung:	n/a	chr1:188861298-188861309
8	CEBPB	chr1:188861165-188861434	K562	blood:	n/a	chr1:188861298-188861309
9	CEBPB	chr1:188861237-188861445	H1-hESC	embryonic stem cell:	n/a	chr1:188861298-188861309
10	CEBPB	chr1:188861137-188861478	HepG2	liver:	n/a	chr1:188861298-188861309
11	CEBPB	chr1:188857286-188858045	Hela-S3	cervix:	n/a	n/a
12	CEBPB	chr1:188854862-188855129	HepG2	liver:	n/a	chr1:188854961-188854974 chr1:188854963-188854974 chr1:188854961-188854972 chr1:188854961-188854974
13	CEBPB	chr1:188845139-188845339	HepG2	liver:	n/a	chr1:188845215-188845226 chr1:188845214-188845227
14	CHD2	chr1:188857543-188857987	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:188844030-188844110	GM13976	blood:	n/a	n/a
16	CTCF	chr1:188847422-188847457	Kidney_OC	kidney:	n/a	n/a
17	CTCF	chr1:188827164-188827243	GM10266	blood:	n/a	n/a
18	CTCF	chr1:188866946-188866995	Lung_OC	lung:	n/a	n/a
19	E2F4	chr1:188863616-188863912	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr1:188859185-188859360	MCF10A-Er-Src	breast:	n/a	n/a
21	EP300	chr1:188857333-188857989	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr1:188862368-188862984	MCF-7	breast:	n/a	n/a
23	EP300	chr1:188857367-188857999	SK-N-SH_RA	brain:	n/a	n/a
24	EP300	chr1:188857339-188858091	Hela-S3	cervix:	n/a	n/a
25	EP300	chr1:188857328-188858092	SK-N-SH	brain:	n/a	n/a
26	EP300	chr1:188862410-188863143	MCF-7	breast:	n/a	n/a
27	FOS	chr1:188841615-188841822	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr1:188841592-188841856	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr1:188841651-188841753	MCF10A-Er-Src	breast:	n/a	n/a
30	FOS	chr1:188841665-188841799	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr1:188857504-188857992	Hela-S3	cervix:	n/a	n/a
32	FOS	chr1:188857594-188857890	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr1:188857660-188857877	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr1:188857510-188857983	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr1:188820676-188820818	MCF10A-Er-Src	breast:	n/a	n/a
36	FOS	chr1:188857514-188857925	MCF10A-Er-Src	breast:	n/a	n/a
37	FOSL2	chr1:188857392-188858061	SK-N-SH	brain:	n/a	n/a
38	FOXM1	chr1:188862409-188863117	MCF-7	breast:	n/a	n/a
39	FOXM1	chr1:188862457-188863041	MCF-7	breast:	n/a	n/a
40	GATA3	chr1:188836700-188837200	SK-N-SH	brain:	n/a	chr1:188836974-188836990 chr1:188836724-188836731 chr1:188836928-188836944 chr1:188836926-188836947 chr1:188836933-188836940 chr1:188836933-188836940 chr1:188836933-188836940 chr1:188836922-188836939 chr1:188836931-188836940 chr1:188837080-188837087
41	GATA3	chr1:188857431-188858067	A549	lung:	n/a	n/a
42	GATA3	chr1:188838232-188838314	SH-SY5Y	brain:	n/a	n/a
43	GATA3	chr1:188836689-188837241	SK-N-SH	brain:	n/a	chr1:188836974-188836990 chr1:188836724-188836731 chr1:188836928-188836944 chr1:188836926-188836947 chr1:188836933-188836940 chr1:188836933-188836940 chr1:188836933-188836940 chr1:188836922-188836939 chr1:188836931-188836940 chr1:188837080-188837087
44	GATA3	chr1:188862192-188863262	MCF-7	breast:	n/a	n/a
45	GATA3	chr1:188855544-188855930	MCF-7	breast:	n/a	chr1:188855795-188855804 chr1:188855797-188855804 chr1:188855792-188855808 chr1:188855795-188855805 chr1:188855797-188855804 chr1:188855790-188855811 chr1:188855797-188855804 chr1:188855792-188855808 chr1:188855699-188855711 chr1:188855701-188855710 chr1:188855796-188855804 chr1:188855797-188855807 chr1:188855701-188855708
46	GATA3	chr1:188857517-188858053	MCF-7	breast:	n/a	n/a
47	GATA3	chr1:188857179-188858286	SK-N-SH	brain:	n/a	n/a
48	GATA3	chr1:188855573-188856008	SH-SY5Y	brain:	n/a	chr1:188855795-188855804 chr1:188855797-188855804 chr1:188855792-188855808 chr1:188855795-188855805 chr1:188855797-188855804 chr1:188855790-188855811 chr1:188855797-188855804 chr1:188855792-188855808 chr1:188855699-188855711 chr1:188855701-188855710 chr1:188855796-188855804 chr1:188855797-188855807 chr1:188855701-188855708
49	GATA3	chr1:188862364-188863046	MCF-7	breast:	n/a	n/a
50	GATA3	chr1:188855555-188855794	MCF-7	breast:	n/a	chr1:188855699-188855711 chr1:188855701-188855710 chr1:188855701-188855708

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:188826823-188826873	HMEC	breast:	n/a
2	chr1:188826823-188826873	AG09309	skin:	n/a
3	chr1:188826889-188826939	AG09319	gingival:	n/a
4	chr1:188826823-188826873	GM12892	blood:	n/a
5	chr1:188826823-188826873	PrEC	prostate:	n/a
6	chr1:188826823-188826873	AG04450	lung:	fetal
7	chr1:188826889-188826939	SKMC	muscle:	n/a
8	chr1:188826889-188826939	AG10803	skin:	n/a
9	chr1:188826889-188826939	GM12891	blood:	n/a
10	chr1:188826823-188826873	SK-N-SH	brain:	n/a
11	chr1:188826823-188826873	SKMC	muscle:	n/a
12	chr1:188826823-188826873	RPTEC	kidney:	n/a
13	chr1:188826823-188826873	AG04449	skin:	fetal
14	chr1:188826889-188826939	HCF	heart:	n/a
15	chr1:188826823-188826873	H1-hESC	embryonic stem cell:	embryo
16	chr1:188826823-188826873	NT2-D1	testis:	n/a
17	chr1:188826889-188826939	K562	blood:	n/a
18	chr1:188826823-188826873	PFSK-1	brain:	n/a
19	chr1:188826889-188826939	HEK293	kidney:	embryo
20	chr1:188826889-188826939	HMEC	breast:	n/a
21	chr1:188826823-188826873	HIPEpiC	eye:	n/a
22	chr1:188826889-188826939	Hela-S3	cervix:	n/a
23	chr1:188826823-188826873	Hepatocyte	liver:	n/a
24	chr1:188826823-188826873	SK-N-MC	brain:	n/a
25	chr1:188826823-188826873	MCF-7	breast:	n/a
26	chr1:188826889-188826939	NHBE	bronchial:	n/a
27	chr1:188826823-188826873	A549	lung:	n/a
28	chr1:188826889-188826939	HUVEC	blood vessel:	n/a
29	chr1:188826889-188826939	HRPEpiC	eye:	n/a
30	chr1:188826823-188826873	NH-A	brain:	n/a
31	chr1:188826889-188826939	HepG2	liver:	n/a
32	chr1:188826823-188826873	MCF10A-Er-Src	breast:	n/a
33	chr1:188826889-188826939	HRE	kidney:	n/a
34	chr1:188826889-188826939	SK-N-MC	brain:	n/a
35	chr1:188826889-188826939	Caco-2	colon:	n/a
36	chr1:188826889-188826939	NHDF-neo	bronchial:	n/a
37	chr1:188826823-188826873	HEK293	kidney:	embryo
38	chr1:188826889-188826939	PFSK-1	brain:	n/a
39	chr1:188826889-188826939	T-47D	breast:	n/a
40	chr1:188826889-188826939	AoSMC	blood vessel:	n/a
41	chr1:188826889-188826939	IMR90	lung:	fetal
42	chr1:188826823-188826873	SK-N-SH_RA	brain:	n/a
43	chr1:188826823-188826873	HCM	heart:	n/a
44	chr1:188826823-188826873	HUVEC	blood vessel:	n/a
45	chr1:188826889-188826939	HPAEpiC	pulmonary alveolar:	n/a
46	chr1:188826823-188826873	GM06990	blood:	n/a
47	chr1:188826823-188826873	T-47D	breast:	n/a
48	chr1:188826889-188826939	BE2_C	brain:	n/a
49	chr1:188826889-188826939	LNCaP	prostate:	n/a
50	chr1:188826889-188826939	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:188401580..188402198-chr1:188862429..188863519,3	MCF-7	breast:
2	chr1:188846061..188848491-chr1:188851171..188853585,2	MCF-7	breast:
3	chr1:188846061..188848491-chr1:188851171..188853585,2	MCF-7	breast:
4	chr1:188866159..188868933-chr1:188870871..188872423,2	MCF-7	breast:
5	chr1:188788862..188791265-chr1:188817309..188819818,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM5C-2	chr1:188856372-188856565	XLOC_001129
2	lnc-PLA2G4A-17	chr1:188860643-188860786	refGeneNc_416_NR_033922
3	lnc-FAM5C-2	chr1:188838608-188838879	XLOC_001129

Variant related genes	Relation type
ENSG00000238054	TF binding region
LINC01035	TF binding region
ENSG00000238054	CpG island
LINC01035	CpG island
KIAA0494	miRNA target sites

Extended variants
information (count: 657 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:657 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6692563	chr1:188813880-188813881	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs562197374	chr1:188813882-188813883	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs142923360	chr1:188813936-188813937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs76113908	chr1:188813952-188813953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs373274833	chr1:188813964-188813965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs565116457	chr1:188813965-188813966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs374195628	chr1:188814006-188814007	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs143525695	chr1:188814007-188814008	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs137924413	chr1:188814024-188814025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs148058472	chr1:188814043-188814044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs550422941	chr1:188814052-188814053	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs558789292	chr1:188814134-188814135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs11809624	chr1:188814137-188814138	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs535688284	chr1:188814167-188814168	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs74366095	chr1:188814223-188814224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567864541	chr1:188814224-188814225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs533598551	chr1:188814225-188814226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs182389400	chr1:188814309-188814310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs576735983	chr1:188814320-188814321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs545798606	chr1:188814321-188814322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs556447800	chr1:188814330-188814331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs576387615	chr1:188814335-188814336	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs542085054	chr1:188814459-188814460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs11810928	chr1:188814484-188814485	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs113078457	chr1:188814560-188814561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs149450815	chr1:188814564-188814565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs6686153	chr1:188814572-188814573	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs564345482	chr1:188814580-188814581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs187026740	chr1:188814619-188814620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs202187874	chr1:188814622-188814623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549893138	chr1:188814653-188814654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs190386402	chr1:188814654-188814655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs529543110	chr1:188814660-188814661	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs75946456	chr1:188814667-188814668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs549171340	chr1:188814674-188814675	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs143955154	chr1:188814690-188814691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs55913641	chr1:188814697-188814698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs533654642	chr1:188814735-188814736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs547438983	chr1:188814747-188814748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs570430568	chr1:188814769-188814770	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs539453243	chr1:188814770-188814771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs115467597	chr1:188814787-188814788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs182940484	chr1:188814811-188814812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs111344635	chr1:188814812-188814813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs114371819	chr1:188814831-188814832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs549441340	chr1:188814834-188814835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs572241895	chr1:188814908-188814909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs139885645	chr1:188815024-188815025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs113484706	chr1:188815056-188815057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs578029101	chr1:188815077-188815078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	20688739	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21611746	CNVD
Myelofibrosis	22110671	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17899364	CNVD
Non-small cell lung cancer	19010865	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:188813000-188815600	Weak transcription	Pancreas	Pancrea
2	chr1:188815600-188816000	ZNF genes & repeats	Pancreas	Pancrea
3	chr1:188815800-188816000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:188819600-188820400	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:188820400-188821400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:188820600-188820800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:188823800-188824200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:188823800-188824600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:188824200-188824600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:188826600-188826800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:188826600-188827000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:188826600-188827200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:188826800-188827000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:188827000-188827200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:188835000-188835400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:188846600-188847200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:188846600-188847600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:188854400-188855000	Enhancers	Hela-S3	cervix
19	chr1:188855000-188855800	Weak transcription	Hela-S3	cervix
20	chr1:188855800-188856400	Enhancers	Hela-S3	cervix
21	chr1:188856400-188857600	Flanking Active TSS	Hela-S3	cervix
22	chr1:188857200-188858000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:188857600-188859200	Weak transcription	Hela-S3	cervix
24	chr1:188859200-188859600	Enhancers	Hela-S3	cervix
25	chr1:188869600-188869800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:188869800-188872000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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