Variant report

Variant	nsv548528
Chromosome Location	chr1:189636292-189675416
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	ARID3A	chr1:189655218-189655237	K562	blood:	n/a	n/a
2	ATF1	chr1:189645110-189645131	K562	blood:	n/a	n/a
3	BACH1	chr1:189660033-189660067	K562	blood:	n/a	n/a
4	BCL3	chr1:189650561-189651101	A549	lung:	n/a	n/a
5	BRCA1	chr1:189640354-189640407	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr1:189675215-189675438	HepG2	liver:	n/a	chr1:189675255-189675266
7	CEBPB	chr1:189675218-189675345	A549	lung:	n/a	chr1:189675255-189675266
8	CEBPB	chr1:189651781-189651981	A549	lung:	n/a	n/a
9	CEBPB	chr1:189646472-189646806	HepG2	liver:	n/a	n/a
10	CEBPB	chr1:189672613-189673256	IMR90	lung:	n/a	n/a
11	CEBPB	chr1:189650548-189650953	A549	lung:	n/a	n/a
12	CTCF	chr1:189647996-189648224	HepG2	liver:	n/a	n/a
13	CTCF	chr1:189648060-189648210	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr1:189648000-189648150	Caco-2	colon:	n/a	n/a
15	CTCF	chr1:189648020-189648170	HCPEpiC	choroid plexus:	n/a	n/a
16	CTCF	chr1:189642420-189642570	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr1:189648020-189648170	HCT-116	colon:	n/a	n/a
18	CTCF	chr1:189662403-189662553	A549	lung:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
19	CTCF	chr1:189662384-189662565	MCF-7	breast:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
20	CTCF	chr1:189648080-189648230	HA-sp	spinal cord:	n/a	n/a
21	CTCF	chr1:189658739-189658837	MCF-7	breast:	n/a	n/a
22	CTCF	chr1:189662360-189662510	NHEK	skin:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
23	CTCF	chr1:189662540-189662690	A549	lung:	n/a	n/a
24	CTCF	chr1:189648040-189648190	HPF	lung:	n/a	n/a
25	CTCF	chr1:189662380-189662530	HCM	heart:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
26	CTCF	chr1:189642531-189642577	ProgFib	skin:	n/a	n/a
27	CTCF	chr1:189648040-189648190	HMF	breast:	n/a	n/a
28	CTCF	chr1:189647960-189648110	GM12875	blood:	n/a	n/a
29	CTCF	chr1:189642460-189642610	HPAF	blood vessel:	n/a	n/a
30	CTCF	chr1:189648040-189648190	HEK293	kidney:	n/a	n/a
31	CTCF	chr1:189662460-189662503	LNCaP	prostate:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
32	CTCF	chr1:189648060-189648210	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr1:189658769-189658845	A549	lung:	n/a	n/a
34	CTCF	chr1:189648020-189648170	HPAF	blood vessel:	n/a	n/a
35	CTCF	chr1:189647833-189648332	MCF-7	breast:	n/a	n/a
36	CTCF	chr1:189662328-189662527	A549	lung:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
37	CTCF	chr1:189642460-189642610	SK-N-SH_RA	brain:	n/a	n/a
38	CTCF	chr1:189648040-189648190	MCF-7	breast:	n/a	n/a
39	CTCF	chr1:189647960-189648110	GM12867	blood:	n/a	n/a
40	CTCF	chr1:189642460-189642610	HMEC	breast:	n/a	n/a
41	CTCF	chr1:189648020-189648170	HCFaa	heart:	n/a	n/a
42	CTCF	chr1:189662360-189662510	AG04449	skin:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
43	CTCF	chr1:189648000-189648150	SK-N-SH_RA	brain:	n/a	n/a
44	CTCF	chr1:189648100-189648250	NHDF-neo	bronchial:	n/a	n/a
45	CTCF	chr1:189642513-189642630	Medullo	brain:	n/a	n/a
46	CTCF	chr1:189648000-189648150	HCT-116	colon:	n/a	n/a
47	CTCF	chr1:189642525-189642592	NHEK	skin:	n/a	n/a
48	CTCF	chr1:189662392-189662608	Gliobla	brain:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
49	CTCF	chr1:189662420-189662570	GM12874	blood:	n/a	chr1:189662475-189662488 chr1:189662473-189662491
50	CTCF	chr1:189647900-189648050	HVMF	connective:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:189627826..189630498-chr1:189636599..189639267,2	MCF-7	breast:
2	chr1:189624367..189627091-chr1:189650312..189652304,2	MCF-7	breast:
3	chr1:189398509..189399144-chr1:189660311..189661261,2	MCF-7	breast:
4	chr1:189672702..189674835-chr1:189679900..189682761,2	MCF-7	breast:
5	chr1:189646033..189647879-chr5:175874488..175876371,2	MCF-7	breast:
6	chr1:189627801..189630516-chr1:189640573..189642596,2	MCF-7	breast:
7	chr1:189589226..189590045-chr1:189662088..189662866,2	MCF-7	breast:
8	chr1:189398408..189399387-chr1:189661985..189662829,2	MCF-7	breast:
9	chr1:189398440..189399083-chr1:189642226..189643036,4	MCF-7	breast:

Variant related genes	Relation type
RNA5SP73	TF binding region
ENSG00000113194	chromatin interactions

Extended variants
information (count: 407 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:407 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs560227	chr1:189636292-189636293	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs543923265	chr1:189636300-189636301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs185974240	chr1:189636356-189636357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs374158452	chr1:189636360-189636361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs565058454	chr1:189636399-189636400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs147065224	chr1:189636468-189636469	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs376161061	chr1:189636496-189636497	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs190642077	chr1:189636534-189636535	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs374302611	chr1:189636566-189636567	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs552617581	chr1:189636661-189636662	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs35632900	chr1:189636664-189636665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs532218092	chr1:189636689-189636690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs181793609	chr1:189636748-189636749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs16831145	chr1:189636749-189636750	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs186558348	chr1:189636752-189636753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs147682094	chr1:189636780-189636781	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs536026542	chr1:189636794-189636795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs552880045	chr1:189636837-189636838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs189830693	chr1:189636838-189636839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs368679871	chr1:189636856-189636857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs182955763	chr1:189636904-189636905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs476454	chr1:189636930-189636931	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs141385266	chr1:189636943-189636944	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs560803774	chr1:189636949-189636950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs187917790	chr1:189636952-189636953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs540849244	chr1:189636962-189636963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs35585198	chr1:189636963-189636964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs560633871	chr1:189636988-189636989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs543444171	chr1:189636995-189636996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs552549737	chr1:189637022-189637023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs562948593	chr1:189637096-189637097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs146981326	chr1:189637105-189637106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs548700405	chr1:189637114-189637115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs568197132	chr1:189637182-189637183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs386637858	chr1:189637206-189637207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs527754388	chr1:189637219-189637220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191285681	chr1:189637221-189637222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs138106017	chr1:189637246-189637247	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569994380	chr1:189637297-189637298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs183096110	chr1:189637348-189637349	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs502008	chr1:189637421-189637422	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs568866995	chr1:189637474-189637475	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs187214350	chr1:189637475-189637476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs531084209	chr1:189637502-189637503	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs558418203	chr1:189637505-189637506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs574599946	chr1:189637597-189637598	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs540289004	chr1:189637614-189637615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs478424	chr1:189637659-189637660	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs79909315	chr1:189637733-189637734	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs114580783	chr1:189637734-189637735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

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
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189629400-189641400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:189636400-189636600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:189639200-189639400	Enhancers	A549	lung
4	chr1:189640400-189640600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:189640800-189641000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:189645000-189645400	Enhancers	Fetal Heart	heart
7	chr1:189649600-189650400	Enhancers	A549	lung
8	chr1:189650200-189651200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:189650400-189650600	Flanking Active TSS	A549	lung
10	chr1:189650400-189651000	Enhancers	HepG2	liver
11	chr1:189650600-189651000	Active TSS	A549	lung
12	chr1:189651200-189651600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:189651600-189652000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:189665400-189666400	Active TSS	Placenta	Placenta
15	chr1:189666400-189666600	Flanking Active TSS	Placenta	Placenta
16	chr1:189675200-189676200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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