Variant report

Variant	rs6473676
Chromosome Location	chr8:52915941-52915942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52809196..52811979-chr8:52914393..52916351,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168300	Chromatin interaction
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12541693	0.88[JPT][hapmap]
rs12544872	0.81[JPT][hapmap]
rs12546159	0.88[JPT][hapmap]
rs12547615	0.90[ASN][1000 genomes]
rs1399857	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1399858	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1399859	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1399860	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017534	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2280179	0.83[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.94[YRI][hapmap];0.87[ASN][1000 genomes]
rs2554461	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs268924	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs268925	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6473673	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6473675	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6473677	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982212	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6991598	0.90[ASN][1000 genomes]
rs7005809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7838307	0.89[CHB][hapmap]
rs9298469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1031672	chr8:52872448-52917469	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1020673	chr8:52878946-52917469	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1017700	chr8:52886765-52917469	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv520947	chr8:52887541-52915994	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv611353	chr8:52887541-52915994	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1027822	chr8:52897278-52916486	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52913200-52918600	Weak transcription	Fetal Thymus	thymus
2	chr8:52913400-52918800	Weak transcription	Thymus	Thymus
3	chr8:52913800-52920400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:52913800-52920600	Weak transcription	Primary T cells from cord blood	blood
5	chr8:52914600-52920000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr8:52914800-52920400	Weak transcription	GM12878-XiMat	blood

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