Variant report

Variant	rs6097789
Chromosome Location	chr20:52756952-52756953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52756212..52758727-chr20:55838230..55840160,2	MCF-7	breast:
2	chr20:52749967..52752847-chr20:52755293..52758111,2	K562	blood:
3	chr17:58164161..58167016-chr20:52755740..52758316,2	MCF-7	breast:
4	chr17:56735164..56738216-chr20:52753477..52757342,3	MCF-7	breast:
5	chr17:57036101..57038729-chr20:52756859..52759059,2	MCF-7	breast:
6	chr1:185122925..185124653-chr20:52755101..52757157,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261040	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12624824	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045844	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022979	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6091821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6091822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097777	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6097779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6097795	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6097809	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6123360	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127114	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62214478	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62214479	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62214503	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8117026	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8120563	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8124440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv586280	chr20:52718555-52758416	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	84 gene(s)	inside rSNPs	diseases
3	nsv912945	chr20:52746724-52772741	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52751200-52758000	Weak transcription	Placenta	Placenta
2	chr20:52751400-52757000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr20:52751400-52757200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:52751400-52758200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr20:52754000-52758400	Enhancers	HepG2	liver
6	chr20:52755600-52757000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:52755600-52758400	Enhancers	NHEK	skin
8	chr20:52755600-52758600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52755600-52758600	Enhancers	NH-A	brain
10	chr20:52755600-52758800	Enhancers	HMEC	breast
11	chr20:52755600-52759000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr20:52755800-52758200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr20:52756000-52757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:52756000-52758600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:52756200-52757400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr20:52756200-52758000	Enhancers	A549	lung
17	chr20:52756200-52758200	Enhancers	HSMM	muscle
18	chr20:52756600-52757400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr20:52756600-52758000	Enhancers	Muscle Satellite Cultured Cells	--
20	chr20:52756600-52758400	Enhancers	Osteobl	bone
21	chr20:52756800-52757000	Enhancers	Fetal Muscle Trunk	muscle
22	chr20:52756800-52757400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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