Variant report

Variant	rs17825773
Chromosome Location	chr6:56307237-56307238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56302272..56304298-chr6:56305503..56307408,2	K562	blood:
2	chr6:56302994..56305596-chr6:56305706..56307687,2	MCF-7	breast:
3	chr6:56305777..56307286-chr6:56406303..56408683,2	MCF-7	breast:
4	chr6:56300576..56302403-chr6:56306257..56307780,2	MCF-7	breast:
5	chr6:56305616..56308132-chr6:56311129..56313082,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11753813	0.89[MEX][hapmap]
rs11756977	0.84[MEX][hapmap]
rs11758339	0.89[MEX][hapmap]
rs11759493	0.89[MEX][hapmap]
rs1535612	0.89[MEX][hapmap]
rs1547625	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2273972	0.83[MEX][hapmap]
rs2273973	0.89[MEX][hapmap]
rs2894837	0.83[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4236140	0.84[MEX][hapmap]
rs4236145	0.84[MEX][hapmap]
rs4283892	0.89[MEX][hapmap]
rs4454141	0.84[MEX][hapmap]
rs4499917	0.84[MEX][hapmap]
rs4712132	0.84[MEX][hapmap]
rs4712133	0.84[MEX][hapmap]
rs4715626	0.84[MEX][hapmap]
rs4715627	0.83[MEX][hapmap]
rs4715629	0.84[MEX][hapmap]
rs4715631	0.84[MEX][hapmap]
rs58705220	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs594435	0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs606894	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs607271	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6459161	0.94[MEX][hapmap]
rs656550	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs656988	0.94[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs657057	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6904202	0.94[MEX][hapmap]
rs6911307	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6911502	0.89[CHB][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs6914325	0.84[ASN][1000 genomes]
rs6916287	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7749370	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7761281	0.84[MEX][hapmap]
rs9296848	0.89[MEX][hapmap]
rs9349822	0.83[ASN][1000 genomes]
rs9357918	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9396210	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9396211	0.85[ASN][1000 genomes]
rs9396213	0.89[MEX][hapmap]
rs9396214	0.89[MEX][hapmap]
rs9464388	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475713	0.84[MEX][hapmap]
rs9475714	0.83[MEX][hapmap]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56303200-56309600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:56304200-56314800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:56304800-56307400	Enhancers	Fetal Intestine Small	intestine
4	chr6:56304800-56309600	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:56305000-56307400	Enhancers	Liver	Liver
6	chr6:56305600-56313000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:56305600-56315800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:56305600-56318600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:56305600-56319600	Weak transcription	HMEC	breast
10	chr6:56305800-56309600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:56306000-56309000	Weak transcription	Pancreas	Pancrea
12	chr6:56306600-56319000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:56307000-56307400	Enhancers	Ovary	ovary
14	chr6:56307200-56309600	Weak transcription	Aorta	Aorta

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