Variant report

Variant	rs458197
Chromosome Location	chr3:161092764-161092765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161038392..161046344-chr3:161085640..161093564,25	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:161090533..161094064-chr8:101963094..101965869,3	MCF-7	breast:
5	chr21:41709121..41711584-chr3:161091853..161094106,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164924	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000240138	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12488318	0.84[ASN][1000 genomes]
rs12494261	0.85[ASN][1000 genomes]
rs1450519	0.85[ASN][1000 genomes]
rs1471440	0.89[ASN][1000 genomes]
rs1478567	0.85[ASN][1000 genomes]
rs163138	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336544	0.91[ASN][1000 genomes]
rs336545	0.91[ASN][1000 genomes]
rs336546	0.90[ASN][1000 genomes]
rs336564	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336565	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336566	0.97[ASN][1000 genomes]
rs336571	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs336573	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336574	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336576	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs336581	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336587	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336588	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs336592	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs419703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs455739	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs459067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs461616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs462081	0.99[ASN][1000 genomes]
rs57201455	0.89[ASN][1000 genomes]
rs73162530	0.89[ASN][1000 genomes]
rs9290075	0.84[ASN][1000 genomes]
rs978933	0.89[ASN][1000 genomes]
rs9811833	0.90[ASN][1000 genomes]
rs9812083	0.85[ASN][1000 genomes]
rs9827833	0.82[ASN][1000 genomes]
rs9828189	0.85[ASN][1000 genomes]
rs9828231	0.80[ASN][1000 genomes]
rs9839404	0.85[ASN][1000 genomes]
rs9859045	0.85[ASN][1000 genomes]
rs9876553	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 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	chr3:161091200-161092800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:161091200-161093200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:161091200-161096800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:161091400-161093000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:161091400-161102800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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