Variant report

Variant	rs12208090
Chromosome Location	chr6:54565844-54565845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:54558970..54566519-chr6:54708534..54713743,16	MCF-7	breast:
2	chr6:54563782..54566701-chr6:54762502..54764565,2	MCF-7	breast:
3	chr6:54564442..54567295-chr6:54579442..54581907,3	MCF-7	breast:
4	chr6:54564646..54566812-chr6:54747166..54750251,3	MCF-7	breast:
5	chr6:54559522..54567174-chr6:54707552..54714330,37	MCF-7	breast:
6	chr6:54564726..54568882-chr6:54587061..54590275,4	MCF-7	breast:
7	chr6:54564170..54566593-chr6:54739128..54740974,2	MCF-7	breast:
8	chr6:54560120..54562700-chr6:54564068..54565878,2	MCF-7	breast:
9	chr6:54561293..54570100-chr6:54582505..54590247,14	MCF-7	breast:
10	chr6:54559803..54567776-chr6:54579525..54585377,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1018141	0.87[EUR][1000 genomes]
rs10447377	0.81[GIH][hapmap]
rs10948842	0.87[EUR][1000 genomes]
rs11757171	0.81[GIH][hapmap]
rs11967781	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11967833	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12198936	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12211545	0.82[EUR][1000 genomes]
rs12527497	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529276	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395632	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1395635	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1948954	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs1983140	0.91[CHB][hapmap]
rs2089411	0.88[EUR][1000 genomes]
rs34970714	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712070	0.86[JPT][hapmap]
rs4715469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540890	0.85[EUR][1000 genomes]
rs6903280	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6906715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7746312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753256	0.87[EUR][1000 genomes]
rs9296764	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54564200-54571000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:54564400-54570800	Weak transcription	Stomach Mucosa	stomach
3	chr6:54564400-54575200	Weak transcription	Fetal Lung	lung
4	chr6:54565200-54566200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:54565400-54575400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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