Variant report

Variant	nsv589859
Chromosome Location	chr3:20414230-20436493
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr3:20416798-20417091	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:20416950-20417260	K562	blood:	n/a	n/a
3	CEBPB	chr3:20421949-20421971	HepG2	liver:	n/a	n/a
4	CEBPB	chr3:20417034-20417209	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:20421835-20421992	K562	blood:	n/a	n/a
6	CTCF	chr3:20413924-20414242	K562	blood:	n/a	n/a
7	CTCF	chr3:20423900-20424050	GM12866	blood:	n/a	n/a
8	CTCF	chr3:20425961-20426058	Spleen_OC	spleen:	n/a	n/a
9	CTCF	chr3:20421429-20421486	GM13976	blood:	n/a	n/a
10	CUX1	chr3:20419922-20420115	K562	blood:	n/a	n/a
11	E2F4	chr3:20419428-20419437	MCF10A-Er-Src	breast:	n/a	n/a
12	EBF1	chr3:20417008-20417208	GM12878	blood:	n/a	chr3:20417095-20417106
13	EP300	chr3:20424412-20424469	GM12878	blood:	n/a	n/a
14	EP300	chr3:20416888-20416962	GM12878	blood:	n/a	n/a
15	FOS	chr3:20427130-20427287	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXA1	chr3:20435940-20436185	ECC-1	luminal epithelium:	n/a	n/a
17	IRF1	chr3:20419784-20419918	K562	blood:	n/a	n/a
18	POLR2A	chr3:20419170-20419315	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:20435951-20435969	MCF-7	breast:	n/a	n/a
20	POLR2A	chr3:20424500-20424536	Gliobla	brain:	n/a	n/a
21	POLR2A	chr3:20435900-20435936	MCF-7	breast:	n/a	n/a
22	RCOR1	chr3:20419973-20420005	K562	blood:	n/a	n/a
23	RPC155	chr3:20424301-20424664	K562	blood:	n/a	n/a
24	SPI1	chr3:20435958-20436189	K562	blood:	n/a	n/a
25	SPI1	chr3:20435961-20436282	HL-60	blood:	n/a	n/a
26	STAT3	chr3:20432020-20432163	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr3:20414110-20414287	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr3:20415203-20415348	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr3:20433847-20434004	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr3:20432677-20432847	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr3:20430502-20430560	MCF10A-Er-Src	breast:	n/a	n/a
32	TAL1	chr3:20421861-20422098	K562	blood:	n/a	n/a
33	TBP	chr3:20424307-20424654	K562	blood:	n/a	n/a
34	ZNF143	chr3:20426088-20426093	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20418856-20418906	Caco-2	colon:	n/a
2	chr3:20418856-20418906	HRPEpiC	eye:	n/a
3	chr3:20418856-20418906	A549	lung:	n/a
4	chr3:20418856-20418906	HPAEpiC	pulmonary alveolar:	n/a
5	chr3:20418856-20418906	PrEC	prostate:	n/a
6	chr3:20418856-20418906	HEK293	kidney:	embryo
7	chr3:20418856-20418906	AG09319	gingival:	n/a
8	chr3:20418856-20418906	NB4	blood:	n/a
9	chr3:20418856-20418906	HCF	heart:	n/a
10	chr3:20418856-20418906	Hepatocyte	liver:	n/a
11	chr3:20418856-20418906	HCM	heart:	n/a
12	chr3:20418856-20418906	RPTEC	kidney:	n/a
13	chr3:20418856-20418906	HIPEpiC	eye:	n/a
14	chr3:20418856-20418906	HAEpiC	amniotic membrane:	n/a
15	chr3:20418856-20418906	HUVEC	blood vessel:	n/a
16	chr3:20418856-20418906	HMEC	breast:	n/a
17	chr3:20418856-20418906	HNPCEpiC	eye:	n/a
18	chr3:20418856-20418906	HEEpiC	esophagus:	n/a
19	chr3:20418856-20418906	HCPEpiC	choroid plexus:	n/a
20	chr3:20418856-20418906	SAEC	small airway:	n/a
21	chr3:20418856-20418906	T-47D	breast:	n/a
22	chr3:20418856-20418906	MCF-7	breast:	n/a
23	chr3:20418856-20418906	MCF10A-Er-Src	breast:	n/a
24	chr3:20418856-20418906	NHDF-neo	bronchial:	n/a
25	chr3:20418856-20418906	AG10803	skin:	n/a
26	chr3:20418856-20418906	BE2_C	brain:	n/a
27	chr3:20418856-20418906	ECC-1	luminal epithelium:	n/a
28	chr3:20418856-20418906	H1-hESC	embryonic stem cell:	embryo
29	chr3:20418856-20418906	AG04450	lung:	fetal
30	chr3:20418856-20418906	HCT-116	colon:	n/a
31	chr3:20418856-20418906	GM19239	blood:	n/a
32	chr3:20418856-20418906	SK-N-MC	brain:	n/a
33	chr3:20418856-20418906	K562	blood:	n/a
34	chr3:20418856-20418906	CMK	blood:	n/a
35	chr3:20418856-20418906	AG04449	skin:	fetal
36	chr3:20418856-20418906	ovcar-3	ovarian:	n/a
37	chr3:20418856-20418906	NT2-D1	testis:	n/a
38	chr3:20418856-20418906	GM12891	blood:	n/a
39	chr3:20418856-20418906	AoSMC	blood vessel:	n/a
40	chr3:20418856-20418906	U87	brain:	n/a
41	chr3:20418856-20418906	GM12892	blood:	n/a
42	chr3:20418856-20418906	SK-N-SH_RA	brain:	n/a
43	chr3:20418856-20418906	AG09309	skin:	n/a
44	chr3:20418856-20418906	IMR90	lung:	fetal
45	chr3:20418856-20418906	ProgFib	skin:	n/a
46	chr3:20418856-20418906	SK-N-SH	brain:	n/a
47	chr3:20418856-20418906	GM06990	blood:	n/a
48	chr3:20418856-20418906	HRCEpiC	kidney:	n/a
49	chr3:20418856-20418906	NH-A	brain:	n/a
50	chr3:20418856-20418906	Hela-S3	cervix:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:20413525..20416049-chr3:20420124..20421856,2	K562	blood:
2	chr3:20413525..20416049-chr3:20420124..20421856,2	K562	blood:
3	chr3:20436330..20438604-chr3:20439437..20442062,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KAT2B-3	chr3:20429741-20432054	ENSG00000261734.1

No data

Variant related genes	Relation type
ENSG00000261734	TF binding region
ENSG00000261734	CpG island

Extended variants
information (count: 833 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:833 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9854943	chr3:20414230-20414231	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs77427646	chr3:20414331-20414332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs571174509	chr3:20414351-20414352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs529099048	chr3:20414354-20414355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs550325622	chr3:20414364-20414365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs568696432	chr3:20414369-20414370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs146408905	chr3:20414372-20414373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs551459074	chr3:20414373-20414374	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs566794432	chr3:20414406-20414407	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs534158026	chr3:20414410-20414411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs188354733	chr3:20414416-20414417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs193191236	chr3:20414498-20414499	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs538521390	chr3:20414550-20414551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs185240538	chr3:20414566-20414567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140721530	chr3:20414596-20414597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs539579867	chr3:20414605-20414606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557792715	chr3:20414606-20414607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs143799448	chr3:20414617-20414618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs540197556	chr3:20414635-20414636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs561850425	chr3:20414653-20414654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188950023	chr3:20414656-20414657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs73187103	chr3:20414660-20414661	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs562390954	chr3:20414664-20414665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs532953442	chr3:20414687-20414688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs552201348	chr3:20414696-20414697	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs192531807	chr3:20414710-20414711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs115186514	chr3:20414739-20414740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs527709752	chr3:20414752-20414753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs148145416	chr3:20414783-20414784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs567527924	chr3:20414844-20414845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs141031115	chr3:20414863-20414864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs183644641	chr3:20414874-20414875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs571877763	chr3:20414883-20414884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs150227450	chr3:20414972-20414973	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs188443362	chr3:20414989-20414990	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs572861447	chr3:20414993-20414994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs533635148	chr3:20415014-20415015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs555369310	chr3:20415053-20415054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs115426695	chr3:20415054-20415055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs544141993	chr3:20415057-20415058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs562403097	chr3:20415124-20415125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs577421214	chr3:20415158-20415159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs368604572	chr3:20415240-20415241	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs138792568	chr3:20415248-20415249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs527823034	chr3:20415251-20415252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs143056993	chr3:20415260-20415261	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs535275942	chr3:20415363-20415364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs549482809	chr3:20415438-20415439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs6763225	chr3:20415512-20415513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs538301015	chr3:20415619-20415620	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
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
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
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20408200-20415600	Weak transcription	Fetal Intestine Small	intestine
2	chr3:20415600-20415800	Enhancers	Fetal Intestine Large	intestine
3	chr3:20415600-20417200	Enhancers	Fetal Intestine Small	intestine
4	chr3:20415800-20416000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:20415800-20417000	Weak transcription	Fetal Intestine Large	intestine
6	chr3:20416000-20418400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:20417000-20420000	Enhancers	Fetal Intestine Large	intestine
8	chr3:20417200-20418200	Weak transcription	Fetal Intestine Small	intestine
9	chr3:20418200-20419400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:20418200-20420200	Enhancers	Fetal Intestine Small	intestine
11	chr3:20418400-20419000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:20418400-20419200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:20418400-20419600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:20418400-20420000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:20418400-20420000	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr3:20418400-20420400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:20418600-20420200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:20418600-20420200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:20419000-20419800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:20419200-20419400	Enhancers	Small Intestine	intestine
21	chr3:20419200-20419800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:20419200-20420400	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:20419400-20420000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr3:20419800-20420000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:20419800-20420200	Enhancers	Fetal Stomach	stomach
26	chr3:20419800-20420600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr3:20420000-20420200	Enhancers	Small Intestine	intestine
28	chr3:20420000-20420400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:20420000-20421800	Weak transcription	Fetal Intestine Large	intestine
30	chr3:20420200-20421800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:20420400-20421800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:20421800-20422000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:20421800-20422200	Enhancers	Aorta	Aorta
34	chr3:20421800-20422200	Enhancers	Fetal Intestine Large	intestine
35	chr3:20421800-20422200	Enhancers	Fetal Intestine Small	intestine
36	chr3:20422000-20422200	Enhancers	Fetal Stomach	stomach
37	chr3:20422200-20423400	Weak transcription	Fetal Intestine Large	intestine
38	chr3:20422200-20423400	Weak transcription	Fetal Intestine Small	intestine
39	chr3:20423400-20424800	Enhancers	Fetal Intestine Large	intestine
40	chr3:20423400-20425000	Enhancers	Fetal Intestine Small	intestine
41	chr3:20426800-20427600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr3:20427600-20433200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:20433000-20433400	Enhancers	H1 Cell Line	embryonic stem cell
44	chr3:20433000-20433600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:20433200-20433400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:20433200-20433600	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:20433400-20435800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:20433600-20435800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:20435600-20436200	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr3:20435800-20436000	Enhancers	HUES6 Cell Line	embryonic stem cell

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