Variant report

Variant	rs6091824
Chromosome Location	chr20:52773236-52773237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52772678..52774287-chr6:26204337..26206417,2	MCF-7	breast:
2	chr20:46413154..46416038-chr20:52772786..52775009,2	MCF-7	breast:
3	chr17:56734965..56736962-chr20:52770464..52773250,2	MCF-7	breast:
4	chr17:56707553..56710474-chr20:52772691..52776017,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000198518	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1570669	0.96[ASN][1000 genomes]
rs1570670	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1985565	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2274130	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2274132	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296237	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296238	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296239	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296240	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3787553	0.94[ASN][1000 genomes]
rs4809956	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4809957	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4811494	0.90[ASN][1000 genomes]
rs56808842	0.91[ASN][1000 genomes]
rs59895069	0.83[ASN][1000 genomes]
rs6091825	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6091826	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6097805	0.91[ASN][1000 genomes]
rs6097806	0.91[ASN][1000 genomes]
rs6097807	0.91[ASN][1000 genomes]
rs6097810	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs751087	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs751089	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs912505	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs927648	0.90[ASN][1000 genomes]
rs927651	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs927652	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv1063981	chr20:52765317-52776613	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2762085	chr20:52765329-52776625	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1058882	chr20:52765979-52794372	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52769800-52777600	Weak transcription	HepG2	liver
5	chr20:52771200-52779000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr20:52773000-52773600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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