Variant report

Variant	rs2569524
Chromosome Location	chr19:51435281-51435282
allele	C/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	NR2F2	chr19:51435082-51436008	MCF-7	breast:	n/a	n/a
2	GATA3	chr19:51435085-51436059	MCF-7	breast:	n/a	chr19:51435699-51435707 chr19:51435698-51435710
3	SIN3AK20	chr19:51435148-51435961	MCF-7	breast:	n/a	n/a
4	CEBPB	chr19:51435192-51435718	MCF-7	breast:	n/a	n/a
5	FOS	chr19:51435152-51435544	MCF10A-Er-Src	breast:	n/a	n/a
6	HDAC2	chr19:51435086-51435948	MCF-7	breast:	n/a	chr19:51435699-51435708 chr19:51435905-51435919 chr19:51435910-51435924 chr19:51435911-51435925 chr19:51435376-51435385 chr19:51435908-51435922
7	EGR1	chr19:51435180-51435639	MCF-7	breast:	n/a	n/a
8	FOSL1	chr19:51435010-51436000	HCT-116	colon:	n/a	n/a
9	FOS	chr19:51435087-51435757	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:51435176-51435844	HCT-116	colon:	n/a	n/a
11	POLR2A	chr19:51435224-51435618	HCT-116	colon:	n/a	n/a
12	TEAD4	chr19:51435102-51435907	HCT-116	colon:	n/a	n/a
13	STAT3	chr19:51435237-51435569	MCF10A-Er-Src	breast:	n/a	n/a
14	SP1	chr19:51435015-51436398	HCT-116	colon:	n/a	chr19:51435724-51435736 chr19:51435724-51435736
15	JUND	chr19:51435085-51436352	HCT-116	colon:	n/a	n/a
16	MAX	chr19:51435196-51435800	MCF-7	breast:	n/a	n/a
17	EGR1	chr19:51435094-51435851	HCT-116	colon:	n/a	n/a
18	MAX	chr19:51435021-51435951	HCT-116	colon:	n/a	n/a
19	HDAC2	chr19:51435218-51435642	MCF-7	breast:	n/a	chr19:51435376-51435385
20	MYC	chr19:51435153-51435746	MCF10A-Er-Src	breast:	n/a	n/a
21	FOSL2	chr19:51435181-51435769	MCF-7	breast:	n/a	n/a
22	JUND	chr19:51435011-51435665	MCF-7	breast:	n/a	n/a
23	STAT3	chr19:51435272-51435674	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr19:51435150-51435743	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr19:51435152-51435744	MCF10A-Er-Src	breast:	n/a	n/a
26	EGR1	chr19:51435084-51436025	HCT-116	colon:	n/a	n/a
27	NR2F2	chr19:51435088-51435988	MCF-7	breast:	n/a	n/a
28	GATA3	chr19:51434901-51436165	MCF-7	breast:	n/a	chr19:51435699-51435707 chr19:51435698-51435710
29	CBX3	chr19:51435030-51436414	HCT-116	colon:	n/a	n/a
30	SP1	chr19:51434937-51436401	HCT-116	colon:	n/a	chr19:51435724-51435736 chr19:51435724-51435736
31	FOS	chr19:51435087-51435761	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr19:51435090-51435746	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51432732..51437222-chr19:51477627..51480793,4	MCF-7	breast:
2	chr19:51434633..51437276-chr19:51470056..51473720,4	MCF-7	breast:
3	chr19:51435279..51436842-chr19:51510358..51513256,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228674	TF binding region
ENSG00000213022	Chromatin interaction
ENSG00000167755	Chromatin interaction
ENSG00000267879	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10164366	1.00[ASN][1000 genomes]
rs12459790	1.00[ASN][1000 genomes]
rs12460497	1.00[ASN][1000 genomes]
rs12461743	0.88[ASN][1000 genomes]
rs1654546	0.94[ASN][1000 genomes]
rs1654548	0.94[ASN][1000 genomes]
rs1701905	0.94[ASN][1000 genomes]
rs1701910	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17727736	0.88[ASN][1000 genomes]
rs17800825	0.88[ASN][1000 genomes]
rs2472258	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2659081	0.91[ASN][1000 genomes]
rs2659092	0.85[ASN][1000 genomes]
rs268913	0.94[ASN][1000 genomes]
rs268914	0.94[ASN][1000 genomes]
rs2739401	0.88[ASN][1000 genomes]
rs2739402	0.88[ASN][1000 genomes]
rs2739409	0.85[ASN][1000 genomes]
rs4802761	0.85[ASN][1000 genomes]
rs73600813	0.88[ASN][1000 genomes]
rs73932685	0.94[ASN][1000 genomes]
rs9304706	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv961236	chr19:51429291-51435801	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51432800-51435400	Weak transcription	Esophagus	oesophagus
2	chr19:51432800-51437400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:51433200-51437600	Enhancers	HMEC	breast
4	chr19:51434000-51453200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:51434400-51435400	Enhancers	NHEK	skin
6	chr19:51434400-51435600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:51434600-51435600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:51435000-51436000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:51435200-51435600	Enhancers	Hela-S3	cervix
10	chr19:51435200-51436000	Enhancers	A549	lung

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