Variant report

Variant	rs17659543
Chromosome Location	chr2:113716306-113716307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113506982..113507826-chr2:113716083..113717303,4	MCF-7	breast:
2	chr2:113506786..113507995-chr2:113716136..113717026,4	K562	blood:
3	chr2:113506583..113509292-chr2:113716187..113718342,2	K562	blood:
4	chr2:113504578..113507107-chr2:113715041..113717876,2	MCF-7	breast:
5	chr2:113716265..113720193-chr2:113720770..113723429,3	MCF-7	breast:
6	chr2:113716174..113716685-chr2:113789552..113790103,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10173618	0.91[EUR][1000 genomes]
rs10196340	0.91[EUR][1000 genomes]
rs10496447	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs11676969	0.82[ASN][1000 genomes]
rs11677903	1.00[ASN][1000 genomes]
rs11680584	1.00[ASN][1000 genomes]
rs11680975	1.00[ASN][1000 genomes]
rs11683669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11685418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11689621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11692391	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11692429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11694258	0.82[ASN][1000 genomes]
rs11694657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11694863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11696002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13392494	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs13407838	0.91[EUR][1000 genomes]
rs13410389	0.92[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs13415097	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446516	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17042591	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17042691	0.91[EUR][1000 genomes]
rs17607787	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17660913	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs28938790	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs28947168	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28947170	0.91[ASN][1000 genomes]
rs28947203	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28954071	0.91[EUR][1000 genomes]
rs28954077	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28993969	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35229022	0.91[ASN][1000 genomes]
rs3768769	0.91[ASN][1000 genomes]
rs3923566	1.00[ASN][1000 genomes]
rs4592853	1.00[ASN][1000 genomes]
rs56198490	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59995729	0.82[ASN][1000 genomes]
rs6542107	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6714534	0.92[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs7597623	1.00[ASN][1000 genomes]
rs7600475	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7602576	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17659543	ZC3H8	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113714800-113716600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113715800-113716400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:113715800-113716600	Enhancers	Stomach Mucosa	stomach
4	chr2:113715800-113720600	Weak transcription	Fetal Intestine Small	intestine
5	chr2:113716000-113716600	Enhancers	HMEC	breast
6	chr2:113716200-113716400	Enhancers	NHEK	skin
7	chr2:113716200-113716400	Bivalent Enhancer	Osteobl	bone
8	chr2:113716200-113716600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:113716200-113716600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:113716200-113716600	Enhancers	NH-A	brain
11	chr2:113716200-113716800	Enhancers	Liver	Liver
12	chr2:113716200-113716800	Enhancers	K562	blood
13	chr2:113716200-113717000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:113716200-113717200	Enhancers	HUES6 Cell Line	embryonic stem cell

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