Variant report

Variant	nsv1004457
Chromosome Location	chr3:28541307-28595311
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	CEBPB	chr3:28549962-28550155	H1-hESC	embryonic stem cell:	n/a	chr3:28550064-28550075
2	CEBPB	chr3:28549998-28550169	A549	lung:	n/a	chr3:28550064-28550075
3	CEBPB	chr3:28559971-28560291	IMR90	lung:	n/a	chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560135-28560148
4	CEBPB	chr3:28549987-28550096	HepG2	liver:	n/a	chr3:28550064-28550075
5	CEBPB	chr3:28559962-28560305	A549	lung:	n/a	chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560135-28560148
6	CEBPB	chr3:28589094-28589328	IMR90	lung:	n/a	n/a
7	CEBPB	chr3:28589061-28589349	A549	lung:	n/a	n/a
8	CEBPB	chr3:28589164-28589351	K562	blood:	n/a	n/a
9	CEBPB	chr3:28559953-28560294	HepG2	liver:	n/a	chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560137-28560146 chr3:28560135-28560148
10	CEBPB	chr3:28589143-28589381	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr3:28545603-28545702	H1-hESC	embryonic stem cell:	n/a	n/a
12	CHD2	chr3:28544001-28544116	GM12878	blood:	n/a	n/a
13	CTCF	chr3:28569941-28570043	GM20000	blood:	n/a	n/a
14	CTCF	chr3:28576705-28576729	GM20000	blood:	n/a	n/a
15	CTCF	chr3:28582550-28582607	GM10266	blood:	n/a	n/a
16	E2F4	chr3:28587403-28587448	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr3:28544021-28544142	GM12878	blood:	n/a	n/a
18	FOS	chr3:28587462-28587649	MCF10A-Er-Src	breast:	n/a	chr3:28587523-28587534
19	FOXA1	chr3:28563227-28563498	HepG2	liver:	n/a	n/a
20	GATA3	chr3:28548660-28548782	SH-SY5Y	brain:	n/a	n/a
21	GATA3	chr3:28556022-28556533	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr3:28544353-28544538	SH-SY5Y	brain:	n/a	n/a
23	JUND	chr3:28548007-28548251	HepG2	liver:	n/a	n/a
24	MAFK	chr3:28554089-28554289	HepG2	liver:	n/a	n/a
25	MAFK	chr3:28581757-28581905	HepG2	liver:	n/a	chr3:28581824-28581839
26	MAFK	chr3:28545153-28545165	HepG2	liver:	n/a	n/a
27	MAFK	chr3:28592862-28592865	HepG2	liver:	n/a	n/a
28	MAFK	chr3:28581753-28581907	HepG2	liver:	n/a	chr3:28581824-28581839
29	MAFK	chr3:28545642-28545770	HepG2	liver:	n/a	n/a
30	MAX	chr3:28561179-28561351	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYC	chr3:28553036-28553216	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:28564655-28564667	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:28548020-28548032	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr3:28546464-28546557	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:28561609-28561623	MCF-7	breast:	n/a	n/a
36	POLR2A	chr3:28594738-28595105	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr3:28594711-28595160	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr3:28553986-28554124	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:28561099-28561170	ProgFib	skin:	n/a	n/a
40	POLR2A	chr3:28561595-28561632	MCF-7	breast:	n/a	n/a
41	POLR2A	chr3:28545523-28545675	MCF-7	breast:	n/a	n/a
42	SETDB1	chr3:28582249-28582517	U2OS	brain:	n/a	n/a
43	SPI1	chr3:28576948-28577390	HL-60	blood:	n/a	n/a
44	STAT3	chr3:28592815-28592831	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr3:28578061-28578323	MCF10A-Er-Src	breast:	n/a	chr3:28578145-28578152
46	STAT3	chr3:28575728-28575785	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr3:28566525-28566700	MCF10A-Er-Src	breast:	n/a	n/a
48	TCF12	chr3:28556005-28556506	SK-N-SH	brain:	n/a	n/a
49	ZC3H11A	chr3:28557673-28557872	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28536026..28538572-chr3:28540874..28543752,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AZI2-5	chr3:28590350-28591764	ucscGeneNc_uc003cej_1
2	lnc-ZCWPW2-3	chr3:28592607-28592991	l_2335_chr3:28592606-28775292_brain

Variant related genes	Relation type
ZCWPW2	TF binding region

Extended variants
information (count: 1712 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:1712 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11712484	chr3:28541335-28541336	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs571401096	chr3:28541359-28541360	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs533879157	chr3:28541369-28541370	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs544231793	chr3:28541373-28541374	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs6799999	chr3:28541376-28541377	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs11712489	chr3:28541379-28541380	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs572740105	chr3:28541400-28541401	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs555908235	chr3:28541631-28541632	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs6800120	chr3:28541633-28541634	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs141182088	chr3:28541674-28541675	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs558102022	chr3:28541692-28541693	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs150731107	chr3:28541747-28541748	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs540614434	chr3:28541770-28541771	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs560365601	chr3:28541798-28541799	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs573309291	chr3:28541816-28541817	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs542183685	chr3:28541824-28541825	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs562265667	chr3:28541867-28541868	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs531335606	chr3:28541872-28541873	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs6764496	chr3:28541874-28541875	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs564976430	chr3:28541885-28541886	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs183730596	chr3:28541893-28541894	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs547719467	chr3:28541918-28541919	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs567529134	chr3:28541933-28541934	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs564649193	chr3:28541961-28541962	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs529325525	chr3:28541997-28541998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs549424597	chr3:28542050-28542051	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs188363646	chr3:28542056-28542057	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs55758484	chr3:28542075-28542076	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs533260433	chr3:28542080-28542081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs181129083	chr3:28542130-28542131	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs534361746	chr3:28542206-28542207	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs10460987	chr3:28542341-28542342	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs573969246	chr3:28542358-28542359	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs542892934	chr3:28542440-28542441	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs552524842	chr3:28542475-28542476	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs185729571	chr3:28542477-28542478	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs575981173	chr3:28542505-28542506	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs544826499	chr3:28542506-28542507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs189793116	chr3:28542558-28542559	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs527506146	chr3:28542562-28542563	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs73048811	chr3:28542611-28542612	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs149966550	chr3:28542650-28542651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs530048204	chr3:28542684-28542685	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs550087873	chr3:28542708-28542709	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs181863910	chr3:28542716-28542717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs528370144	chr3:28542739-28542740	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs531685024	chr3:28542770-28542771	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs551592004	chr3:28542807-28542808	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs551988443	chr3:28542848-28542849	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs571679152	chr3:28542864-28542865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	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
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	16618734	CNVD
Cancer	20164919	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28514800-28575800	Weak transcription	Ovary	ovary
2	chr3:28541200-28542400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:28541200-28543200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr3:28541400-28542600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr3:28541400-28543200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:28541600-28541800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr3:28541600-28541800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:28541600-28542600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr3:28541800-28543800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:28542000-28546600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:28542200-28542400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:28542400-28542600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:28542400-28543200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:28542400-28546000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:28542600-28543200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:28542600-28546200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:28542600-28546400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:28542800-28543000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:28542800-28544000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:28543000-28543600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:28543200-28543600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:28543200-28543600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:28543200-28543800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:28543200-28544400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:28543600-28544200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:28543600-28544400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:28543600-28544400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:28543800-28544000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:28543800-28544400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:28543800-28544400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:28543800-28545000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:28544000-28544400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:28544000-28544400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr3:28544000-28546400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:28544200-28544400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:28544200-28544400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:28544200-28546600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:28544400-28546000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:28544400-28546200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:28544400-28546200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:28544400-28546600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:28544400-28549400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:28545000-28546200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:28546000-28547200	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr3:28546000-28548000	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr3:28546200-28546800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:28546200-28547200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:28546200-28547200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:28546200-28547400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:28546200-28547400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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