Variant report

Variant	nsv963317
Chromosome Location	chr3:51931876-51938339
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	chr3:51938158-51938358	K562	blood:	n/a	n/a
2	BATF	chr3:51936393-51936677	GM12878	blood:	n/a	chr3:51936541-51936552 chr3:51936513-51936524 chr3:51936569-51936580
3	CBX3	chr3:51936380-51936729	HCT-116	colon:	n/a	n/a
4	CTCF	chr3:51932120-51932191	GM20000	blood:	n/a	n/a
5	E2F4	chr3:51936431-51936817	MCF10A-Er-Src	breast:	n/a	n/a
6	EBF1	chr3:51934161-51934428	GM12878	blood:	n/a	n/a
7	FOS	chr3:51936339-51936777	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:51936326-51936777	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:51936344-51936776	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr3:51936348-51936763	MCF10A-Er-Src	breast:	n/a	n/a
11	FOSL1	chr3:51936351-51936731	HCT-116	colon:	n/a	n/a
12	FOSL1	chr3:51936349-51936741	HCT-116	colon:	n/a	n/a
13	FOSL2	chr3:51936424-51936746	HepG2	liver:	n/a	n/a
14	FOXA1	chr3:51932206-51932529	HepG2	liver:	n/a	n/a
15	FOXA2	chr3:51932303-51932556	A549	lung:	n/a	n/a
16	JUND	chr3:51936370-51936720	HCT-116	colon:	n/a	n/a
17	JUND	chr3:51936308-51936750	HCT-116	colon:	n/a	n/a
18	MAFF	chr3:51938076-51938390	K562	blood:	n/a	chr3:51938237-51938255
19	MAFF	chr3:51938072-51938450	HepG2	liver:	n/a	chr3:51938237-51938255
20	MAFK	chr3:51938093-51938401	K562	blood:	n/a	chr3:51938239-51938255 chr3:51938239-51938250 chr3:51938240-51938251 chr3:51938238-51938252 chr3:51938239-51938250 chr3:51938244-51938253 chr3:51938240-51938251 chr3:51938239-51938254
21	MAFK	chr3:51938076-51938430	HepG2	liver:	n/a	chr3:51938239-51938255 chr3:51938239-51938250 chr3:51938240-51938251 chr3:51938238-51938252 chr3:51938239-51938250 chr3:51938244-51938253 chr3:51938240-51938251 chr3:51938239-51938254
22	MAFK	chr3:51938068-51938433	HepG2	liver:	n/a	chr3:51938239-51938255 chr3:51938239-51938250 chr3:51938240-51938251 chr3:51938238-51938252 chr3:51938239-51938250 chr3:51938244-51938253 chr3:51938240-51938251 chr3:51938239-51938254
23	MAFK	chr3:51938137-51938372	H1-hESC	embryonic stem cell:	n/a	chr3:51938239-51938255 chr3:51938239-51938250 chr3:51938240-51938251 chr3:51938238-51938252 chr3:51938239-51938250 chr3:51938244-51938253 chr3:51938240-51938251 chr3:51938239-51938254
24	MAFK	chr3:51938078-51938431	IMR90	lung:	n/a	chr3:51938239-51938255 chr3:51938239-51938250 chr3:51938240-51938251 chr3:51938238-51938252 chr3:51938239-51938250 chr3:51938244-51938253 chr3:51938240-51938251 chr3:51938239-51938254
25	MYC	chr3:51936437-51936610	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:51931044-51932219	HCT-116	colon:	n/a	n/a
27	POLR2A	chr3:51931413-51931995	HCT-116	colon:	n/a	n/a
28	POLR2A	chr3:51936402-51936695	HCT-116	colon:	n/a	n/a
29	POLR2A	chr3:51935944-51936010	H1-hESC	embryonic stem cell:	n/a	n/a
30	RUNX3	chr3:51936489-51936707	GM12878	blood:	n/a	n/a
31	SP1	chr3:51936293-51936749	HCT-116	colon:	n/a	n/a
32	SP1	chr3:51936349-51936733	HCT-116	colon:	n/a	n/a
33	STAT3	chr3:51936452-51936584	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr3:51936346-51936777	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr3:51936379-51936757	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr3:51936379-51936755	MCF10A-Er-Src	breast:	n/a	n/a
37	YY1	chr3:51936472-51936674	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
IQCF1	TF binding region

Extended variants
information (count: 212 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:212 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs561069611	chr3:51931927-51931928	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
2	rs185978138	chr3:51931945-51931946	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs191931938	chr3:51931951-51931952	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs561780651	chr3:51931952-51931953	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs549789283	chr3:51931957-51931958	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs571223401	chr3:51931958-51931959	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs537316923	chr3:51931989-51931990	Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs4687786	chr3:51932002-51932003	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs552068316	chr3:51932008-51932009	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs183570408	chr3:51932084-51932085	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs534432003	chr3:51932097-51932098	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs117887099	chr3:51932127-51932128	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs567785374	chr3:51932150-51932151	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs114011729	chr3:51932158-51932159	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs140469964	chr3:51932160-51932161	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs149721825	chr3:51932195-51932196	Enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs140091209	chr3:51932273-51932274	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs34717502	chr3:51932274-51932275	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555001552	chr3:51932275-51932276	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs398062325	chr3:51932292-51932293	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs538563872	chr3:51932299-51932300	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs553686018	chr3:51932314-51932315	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs370450673	chr3:51932328-51932329	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs7612847	chr3:51932364-51932365	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs543112354	chr3:51932382-51932383	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs553240275	chr3:51932383-51932384	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs560917312	chr3:51932433-51932434	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs565627750	chr3:51932434-51932435	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs117287034	chr3:51932467-51932468	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs374874105	chr3:51932476-51932477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs543497113	chr3:51932572-51932573	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs371476828	chr3:51932605-51932606	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs539782179	chr3:51932639-51932640	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs60334046	chr3:51932644-51932645	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs187273006	chr3:51932690-51932691	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs143440052	chr3:51932712-51932713	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs7619650	chr3:51932720-51932721	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs111568735	chr3:51932745-51932746	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs549560539	chr3:51932779-51932780	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs370568577	chr3:51932824-51932825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs373915430	chr3:51932847-51932848	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs567705590	chr3:51932861-51932862	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs111906671	chr3:51932873-51932874	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs140880980	chr3:51932958-51932959	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs77473652	chr3:51932976-51932977	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs80030246	chr3:51932988-51932989	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs78690603	chr3:51932989-51932990	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs571393829	chr3:51933090-51933091	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs570181246	chr3:51933127-51933128	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs1847677	chr3:51933178-51933179	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Bladder cancer	21909424	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51931600-51932000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr3:51931600-51932000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:51931600-51932200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:51931600-51932200	Bivalent Enhancer	Placenta	Placenta
5	chr3:51931600-51932600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:51931600-51932800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:51931800-51932000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:51932000-51932200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:51932200-51932800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:51932200-51933800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:51932800-51933000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:51932800-51934800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:51933000-51934600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:51934600-51935600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:51934800-51935400	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:51934800-51935400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:51935000-51935600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr3:51935800-51936400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr3:51935800-51937600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:51936000-51936400	Enhancers	Stomach Mucosa	stomach
21	chr3:51936000-51937400	Enhancers	HMEC	breast
22	chr3:51936200-51936400	Enhancers	NHEK	skin
23	chr3:51936200-51937200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:51936400-51936800	Weak transcription	NHEK	skin
25	chr3:51936800-51937600	ZNF genes & repeats	NHEK	skin
26	chr3:51937600-51941600	Weak transcription	HMEC	breast
27	chr3:51938200-51938600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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