Variant report

Variant	rs9880623
Chromosome Location	chr3:51856126-51856127
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51851120..51852647-chr3:51853299..51856241,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229972	Chromatin interaction
ENSG00000224792	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12637540	1.00[CHB][hapmap]
rs12639503	1.00[CHB][hapmap]
rs13325762	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1394812	1.00[CHB][hapmap]
rs1468019	1.00[CHB][hapmap]
rs1857801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28776255	0.84[AFR][1000 genomes]
rs4522758	1.00[CHB][hapmap]
rs61011489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61048512	0.84[AFR][1000 genomes]
rs61299098	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6762083	1.00[CHB][hapmap]
rs6762371	1.00[CHB][hapmap]
rs6789601	0.80[AFR][1000 genomes]
rs6792143	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6802583	1.00[CHB][hapmap]
rs6805324	1.00[CHB][hapmap]
rs6806593	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6806812	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7623760	0.84[AFR][1000 genomes]
rs7632944	1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9815475	1.00[CHB][hapmap]
rs9820804	0.83[AMR][1000 genomes]
rs9822619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822994	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823975	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9826967	1.00[CHB][hapmap]
rs9831594	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839703	0.82[AFR][1000 genomes]
rs9840336	1.00[CHB][hapmap]
rs9840747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846102	0.84[AFR][1000 genomes]
rs9853511	1.00[CHB][hapmap]
rs9856180	0.84[AFR][1000 genomes]
rs9858279	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9859656	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs9859820	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9863019	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866552	1.00[CHB][hapmap]
rs9877178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9880631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51855200-51857000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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