Variant report

Variant	rs540734119
Chromosome Location	chr12:48559251-48559252
allele	G/T
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	SMC3	chr12:48558898-48559272	K562	blood:	n/a	n/a
2	RAD21	chr12:48558786-48559312	H1-hESC	embryonic stem cell:	n/a	chr12:48558865-48558875
3	RFX5	chr12:48558939-48559262	GM12878	blood:	n/a	n/a
4	CTCF	chr12:48558855-48559280	A549	lung:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
5	CTCF	chr12:48558763-48559625	A549	lung:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
6	CTCF	chr12:48558791-48559336	SK-N-SH	brain:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
7	CTCF	chr12:48558629-48559470	HCT-116	colon:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
8	CTCF	chr12:48558854-48559301	IMR90	lung:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
9	RAD21	chr12:48558792-48559343	ECC-1	luminal epithelium:	n/a	chr12:48558865-48558875
10	CTCF	chr12:48558891-48559292	HepG2	liver:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
11	RAD21	chr12:48558792-48559262	H1-hESC	embryonic stem cell:	n/a	chr12:48558865-48558875
12	CUX1	chr12:48558915-48559322	K562	blood:	n/a	n/a
13	RAD21	chr12:48558777-48559582	SK-N-SH	brain:	n/a	chr12:48558865-48558875
14	CTCF	chr12:48558776-48559362	MCF-7	breast:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
15	CTCF	chr12:48558808-48559438	HCT-116	colon:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
16	CTCF	chr12:48558827-48559338	MCF-7	breast:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
17	RAD21	chr12:48558864-48559252	IMR90	lung:	n/a	chr12:48558865-48558875
18	RAD21	chr12:48558729-48559375	HCT-116	colon:	n/a	chr12:48558865-48558875
19	RAD21	chr12:48558888-48559261	HepG2	liver:	n/a	n/a
20	RAD21	chr12:48558825-48559293	SK-N-SH_RA	brain:	n/a	chr12:48558865-48558875
21	RAD21	chr12:48558762-48559374	ECC-1	luminal epithelium:	n/a	chr12:48558865-48558875
22	RAD21	chr12:48558894-48559252	A549	lung:	n/a	n/a
23	ZNF143	chr12:48558888-48559268	GM12878	blood:	n/a	n/a
24	CTCF	chr12:48558847-48559251	ECC-1	luminal epithelium:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
25	CTCF	chr12:48558846-48559261	K562	blood:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
26	CTCF	chr12:48558939-48559256	Spleen_OC	spleen:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
27	RAD21	chr12:48558720-48559349	HepG2	liver:	n/a	chr12:48558865-48558875
28	RAD21	chr12:48558764-48559393	HCT-116	colon:	n/a	chr12:48558865-48558875
29	CTCF	chr12:48558809-48559301	K562	blood:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
30	RAD21	chr12:48558873-48559286	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr12:48558882-48559368	HepG2	liver:	n/a	n/a
32	SMC3	chr12:48558842-48559461	SK-N-SH	brain:	n/a	n/a
33	RAD21	chr12:48558848-48559288	Hela-S3	cervix:	n/a	chr12:48558865-48558875
34	RAD21	chr12:48558840-48559302	GM12878	blood:	n/a	chr12:48558865-48558875
35	SMC3	chr12:48558840-48559299	Hela-S3	cervix:	n/a	n/a
36	RAD21	chr12:48558902-48559348	MCF-7	breast:	n/a	n/a
37	RAD21	chr12:48558805-48559316	A549	lung:	n/a	chr12:48558865-48558875
38	CTCF	chr12:48558806-48559296	T-47D	breast:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
39	RAD21	chr12:48558694-48559290	MCF-7	breast:	n/a	chr12:48558865-48558875
40	CTCF	chr12:48558797-48559288	A549	lung:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
41	RAD21	chr12:48558897-48559255	K562	blood:	n/a	n/a
42	SMC3	chr12:48558732-48559351	GM12878	blood:	n/a	n/a
43	CTCF	chr12:48558859-48559290	GM12878	blood:	n/a	chr12:48559078-48559087 chr12:48559072-48559090
44	ARID3A	chr12:48558889-48559348	K562	blood:	n/a	n/a
45	RAD21	chr12:48558728-48559374	A549	lung:	n/a	chr12:48558865-48558875

No.	Distal block	Cell Line	Cell type
1	chr12:48559108..48559625-chr12:48848164..48848665,2	MCF-7	breast:
2	chr12:48477561..48478652-chr12:48558658..48559651,7	MCF-7	breast:
3	chr12:48477632..48478212-chr12:48558666..48559592,2	MCF-7	breast:
4	chr12:48336001..48336747-chr12:48558620..48559352,3	K562	blood:
5	chr12:48559054..48559616-chr12:48570377..48571168,2	K562	blood:
6	chr12:48298747..48299610-chr12:48558705..48559281,2	MCF-7	breast:
7	chr12:48549808..48555740-chr12:48556420..48560606,6	K562	blood:
8	chr12:48239241..48242168-chr12:48557559..48560161,2	K562	blood:

Variant related genes	Relation type
ENSG00000258051	TF binding region
ENSG00000177981	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000258051	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv976608	chr12:48558446-48563571	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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