Variant report

Variant	rs6097601
Chromosome Location	chr20:52436831-52436832
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	chr17:56707699..56709301-chr20:52435740..52437872,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10211708	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10211779	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211840	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211846	1.00[EUR][1000 genomes]
rs10211847	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10211852	1.00[EUR][1000 genomes]
rs16998448	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870289	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4597593	1.00[CEU][hapmap]
rs6091749	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6091750	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6091751	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6091752	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6091753	1.00[YRI][hapmap]
rs6097589	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097590	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097593	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097594	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097595	1.00[EUR][1000 genomes]
rs6097596	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097597	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097598	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6097602	1.00[AFR][1000 genomes]
rs6097603	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6097604	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6097605	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6097606	1.00[YRI][hapmap]
rs6097607	0.91[AFR][1000 genomes]
rs6097619	1.00[CEU][hapmap]
rs67891850	1.00[EUR][1000 genomes]
rs7273809	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272038	1.00[EUR][1000 genomes]
rs73272042	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272044	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272060	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs73272062	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8120680	0.89[EUR][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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52431600-52439400	Weak transcription	A549	lung
3	chr20:52435400-52442200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr20:52436000-52437200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:52436000-52439400	Weak transcription	Thymus	Thymus
6	chr20:52436200-52437000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:52436200-52437000	Enhancers	NHEK	skin
8	chr20:52436200-52437200	Enhancers	HMEC	breast
9	chr20:52436200-52437400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:52436400-52437000	Enhancers	Liver	Liver
11	chr20:52436400-52437600	Enhancers	Pancreas	Pancrea
12	chr20:52436600-52437000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr20:52436800-52437200	Enhancers	Esophagus	oesophagus
14	chr20:52436800-52441200	Weak transcription	HepG2	liver

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