Variant report

Variant	rs9820804
Chromosome Location	chr3:51878796-51878797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51878113..51880884-chr3:51974906..51977632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000041880	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13325762	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857801	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61011489	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61299098	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792143	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6806593	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6806812	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73838712	0.86[AFR][1000 genomes]
rs7632944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9822619	0.83[AMR][1000 genomes]
rs9822994	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823975	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9831594	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840747	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9858279	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9859820	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9863019	0.83[AMR][1000 genomes]
rs9867278	0.81[AFR][1000 genomes]
rs9877178	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878564	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880623	0.83[AMR][1000 genomes]
rs9880631	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv3416846	chr3:51781117-51888179	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
6	nsv1001350	chr3:51860817-51899966	Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51878600-51879600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:51878600-51879600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:51878600-51880200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr3:51878600-51880400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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