Variant report

Variant	rs1397439
Chromosome Location	chr4:28380212-28380213
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	chr4:28375818..28378318-chr4:28378628..28381458,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10011519	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1024120	0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10939211	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11722931	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726308	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11734656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735854	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737313	0.81[AMR][1000 genomes]
rs12507595	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512541	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111729	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13114507	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116091	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13126477	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13139194	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145217	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145453	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510696	0.82[EUR][1000 genomes]
rs1510700	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1705039	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17682996	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995910	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250259	0.84[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.83[AFR][1000 genomes]
rs2666119	0.83[AFR][1000 genomes]
rs292031	0.83[AFR][1000 genomes]
rs292069	0.83[AFR][1000 genomes]
rs35293178	0.83[AFR][1000 genomes]
rs36124654	0.83[AFR][1000 genomes]
rs4267724	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4429724	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs479514	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481450	0.83[AFR][1000 genomes]
rs57398190	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs602888	0.83[AFR][1000 genomes]
rs604244	0.83[AFR][1000 genomes]
rs6448577	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs664330	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986866	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[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	nsv1005382	chr4:28157180-28403800	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv878775	chr4:28163856-28473048	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1000514	chr4:28192982-28445194	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1012210	chr4:28246489-28419673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1013013	chr4:28323465-28419673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 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	chr4:28378200-28380400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:28378600-28381800	Weak transcription	HMEC	breast
3	chr4:28380000-28380400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:28380200-28380400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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