Variant report

Variant	rs12645652
Chromosome Location	chr4:28344410-28344411
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	chr4:28342479..28345187-chr4:28356107..28357849,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12641399	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12642302	0.85[ASN][1000 genomes]
rs12647447	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1497712	0.81[ASN][1000 genomes]
rs1497713	0.81[ASN][1000 genomes]
rs16880440	0.81[ASN][1000 genomes]
rs16880483	0.89[ASN][1000 genomes]
rs1846123	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4411974	0.81[ASN][1000 genomes]
rs55869481	0.80[EUR][1000 genomes]
rs57457365	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60551952	0.81[ASN][1000 genomes]
rs67152745	0.88[ASN][1000 genomes]
rs67357525	0.81[ASN][1000 genomes]
rs67568650	0.81[ASN][1000 genomes]
rs6830652	0.82[ASN][1000 genomes]
rs6839474	0.81[ASN][1000 genomes]
rs6852577	0.85[ASN][1000 genomes]
rs73221875	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73221879	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73221881	0.80[EUR][1000 genomes]
rs73221886	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73221887	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221888	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221889	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221892	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73221899	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73221900	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73224006	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv3366276	chr4:28344259-28344461	Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28342800-28356600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:28343000-28344800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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