Variant report

Variant	nsv516072
Chromosome Location	chr1:189835520-189878594
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	chr1:189869294-189869344	K562	blood:	n/a	n/a
2	ATF1	chr1:189849426-189849494	K562	blood:	n/a	n/a
3	CEBPB	chr1:189837043-189837350	A549	lung:	n/a	n/a
4	CEBPB	chr1:189864108-189864385	IMR90	lung:	n/a	chr1:189864217-189864230 chr1:189864219-189864228 chr1:189864217-189864228 chr1:189864219-189864228 chr1:189864219-189864228 chr1:189864218-189864229 chr1:189864219-189864228
5	CEBPB	chr1:189864066-189864360	HepG2	liver:	n/a	chr1:189864217-189864230 chr1:189864219-189864228 chr1:189864217-189864228 chr1:189864219-189864228 chr1:189864219-189864228 chr1:189864218-189864229 chr1:189864219-189864228
6	CHD1	chr1:189867799-189867825	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr1:189845480-189845630	GM12872	blood:	n/a	n/a
8	CTCF	chr1:189867531-189867571	Kidney_OC	kidney:	n/a	n/a
9	CUX1	chr1:189862299-189862379	GM12878	blood:	n/a	n/a
10	E2F4	chr1:189860844-189860979	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr1:189849056-189849988	SK-N-SH	brain:	n/a	n/a
12	EP300	chr1:189849288-189849583	SK-N-SH_RA	brain:	n/a	n/a
13	EP300	chr1:189849300-189849593	SK-N-SH_RA	brain:	n/a	n/a
14	ESR1	chr1:189852112-189852468	ECC-1	luminal epithelium:	n/a	n/a
15	ESR1	chr1:189852207-189852492	ECC-1	luminal epithelium:	n/a	n/a
16	FOS	chr1:189843012-189843091	MCF10A-Er-Src	breast:	n/a	n/a
17	FOXA2	chr1:189838530-189838813	A549	lung:	n/a	n/a
18	GATA2	chr1:189849212-189849890	SH-SY5Y	brain:	n/a	n/a
19	GATA3	chr1:189860873-189860897	SH-SY5Y	brain:	n/a	n/a
20	GATA3	chr1:189849146-189849886	SH-SY5Y	brain:	n/a	n/a
21	GATA3	chr1:189849213-189849838	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr1:189855011-189855427	SH-SY5Y	brain:	n/a	chr1:189855250-189855271 chr1:189855257-189855264 chr1:189855257-189855264 chr1:189855257-189855264
23	GATA3	chr1:189849154-189849914	SK-N-SH	brain:	n/a	n/a
24	GATA3	chr1:189846984-189847039	SH-SY5Y	brain:	n/a	n/a
25	JUN	chr1:189863367-189863468	K562	blood:	n/a	n/a
26	JUND	chr1:189860639-189860927	HepG2	liver:	n/a	chr1:189860829-189860838
27	KAP1	chr1:189857690-189858077	K562	blood:	n/a	n/a
28	MAFF	chr1:189873780-189873880	K562	blood:	n/a	n/a
29	MAFF	chr1:189843875-189844190	HepG2	liver:	n/a	chr1:189844027-189844045
30	MAFF	chr1:189877261-189877565	K562	blood:	n/a	n/a
31	MAFF	chr1:189877274-189877610	HepG2	liver:	n/a	n/a
32	MAFF	chr1:189873697-189874000	HepG2	liver:	n/a	n/a
33	MAFF	chr1:189843938-189844138	K562	blood:	n/a	chr1:189844027-189844045
34	MAFK	chr1:189877272-189877601	HepG2	liver:	n/a	chr1:189877436-189877450 chr1:189877438-189877449 chr1:189877437-189877448
35	MAFK	chr1:189842959-189843287	HepG2	liver:	n/a	n/a
36	MAFK	chr1:189843861-189844222	IMR90	lung:	n/a	chr1:189844029-189844044
37	MAFK	chr1:189873817-189873937	Hela-S3	cervix:	n/a	n/a
38	MAFK	chr1:189877252-189877572	Hela-S3	cervix:	n/a	chr1:189877436-189877450 chr1:189877438-189877449 chr1:189877437-189877448
39	MAFK	chr1:189877343-189877508	H1-hESC	embryonic stem cell:	n/a	chr1:189877436-189877450 chr1:189877438-189877449 chr1:189877437-189877448
40	MAFK	chr1:189844009-189844059	K562	blood:	n/a	chr1:189844029-189844044
41	MAFK	chr1:189846511-189846761	HepG2	liver:	n/a	chr1:189846624-189846639
42	MAFK	chr1:189873689-189874002	IMR90	lung:	n/a	n/a
43	MAFK	chr1:189843900-189844198	HepG2	liver:	n/a	chr1:189844029-189844044
44	MAFK	chr1:189877265-189877634	HepG2	liver:	n/a	chr1:189877436-189877450 chr1:189877438-189877449 chr1:189877437-189877448
45	MAFK	chr1:189842153-189842373	HepG2	liver:	n/a	n/a
46	MAFK	chr1:189877250-189877621	IMR90	lung:	n/a	chr1:189877436-189877450 chr1:189877438-189877449 chr1:189877437-189877448
47	MAFK	chr1:189842993-189843263	HepG2	liver:	n/a	n/a
48	MAFK	chr1:189873733-189873977	HepG2	liver:	n/a	n/a
49	MAFK	chr1:189846527-189846689	HepG2	liver:	n/a	chr1:189846624-189846639
50	MAFK	chr1:189843863-189844216	HepG2	liver:	n/a	chr1:189844029-189844044

No.	Distal block	Cell Line	Cell type
1	chr1:189813747..189815721-chr1:189850350..189852733,2	K562	blood:
2	chr1:189853792..189857239-chr1:189857756..189861653,3	MCF-7	breast:
3	chr1:189853792..189857239-chr1:189857756..189861653,3	MCF-7	breast:
4	chr1:189844299..189845892-chr1:189850457..189852405,2	MCF-7	breast:
5	chr1:189117678..189120245-chr1:189847842..189850269,2	K562	blood:
6	chr1:189844299..189845892-chr1:189850457..189852405,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM5C-1	chr1:189837131-189837342	XLOC_001130
2	lnc-FAM5C-1	chr1:189837457-189837658	XLOC_001130

Variant related genes	Relation type
ENSG00000238270	TF binding region

Extended variants
information (count: 567 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:567 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs76409883	chr1:189837138-189837139	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs192172254	chr1:189837270-189837271	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs539430908	chr1:189837296-189837297	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs140367905	chr1:189837311-189837312	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs576639672	chr1:189837322-189837323	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs542533090	chr1:189837360-189837361	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs562108283	chr1:189837363-189837364	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs2292762	chr1:189837364-189837365	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs541081582	chr1:189837374-189837375	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs564239928	chr1:189837400-189837401	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs184566649	chr1:189837430-189837431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs149466366	chr1:189837476-189837477	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs549751365	chr1:189837527-189837528	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs563360673	chr1:189837531-189837532	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs531468779	chr1:189837595-189837596	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs189430616	chr1:189837612-189837613	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs55845245	chr1:189837640-189837641	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs2944690	chr1:189837652-189837653	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs547652341	chr1:189837653-189837654	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs6697981	chr1:189837770-189837771	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs149884792	chr1:189837772-189837773	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs189113727	chr1:189838539-189838540	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs551013062	chr1:189838583-189838584	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs557894233	chr1:189838630-189838631	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs577823736	chr1:189838636-189838637	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs543462768	chr1:189838740-189838741	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs557999029	chr1:189838747-189838748	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs557423578	chr1:189838764-189838765	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs574090404	chr1:189838770-189838771	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs573239014	chr1:189838783-189838784	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs534107449	chr1:189838786-189838787	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs542991622	chr1:189838790-189838791	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs559515412	chr1:189838794-189838795	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs527556150	chr1:189838809-189838810	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs564446977	chr1:189838810-189838811	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs11805759	chr1:189839800-189839801	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs571591003	chr1:189839826-189839827	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs3005710	chr1:189839840-189839841	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs551126064	chr1:189839877-189839878	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs368751896	chr1:189839905-189839906	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs370536147	chr1:189839943-189839944	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs190193281	chr1:189839953-189839954	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs553195318	chr1:189839983-189839984	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs577169186	chr1:189840069-189840070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs529085671	chr1:189840083-189840084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs533894612	chr1:189840085-189840086	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs3005711	chr1:189840086-189840087	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs67606262	chr1:189840105-189840106	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs75195188	chr1:189840109-189840110	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs577985769	chr1:189840129-189840130	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:88)

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
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
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
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Lung adenocarcinoma	17086460	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Pancreatic cancer	17952125	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189837200-189837600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:189839800-189841000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:189840000-189841000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:189840000-189841200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:189840400-189840600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:189844400-189845000	Enhancers	Fetal Heart	heart
7	chr1:189868000-189870800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:189868200-189868400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:189868200-189869600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:189868200-189870000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:189868400-189870000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:189868600-189869200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:189868600-189870000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:189868800-189869600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:189868800-189869600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:189868800-189870000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:189869000-189869600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:189869200-189869600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:189869200-189869600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:189869400-189869800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:189869600-189870200	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:189869800-189884200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:189870200-189870600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:189870600-189871000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:189870800-189871000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:189876800-189877000	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links