Variant report

Variant	rs2616277
Chromosome Location	chr20:52745040-52745041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57913131..57926939-chr20:52735776..52751538,42	MCF-7	breast:
2	chr17:59487671..59489379-chr20:52744061..52747040,2	MCF-7	breast:
3	chr17:59475016..59476729-chr20:52744400..52746392,3	MCF-7	breast:
4	chr20:52743275..52747158-chr21:41755624..41758073,3	MCF-7	breast:
5	chr20:52743653..52745576-chr9:100745087..100747272,2	MCF-7	breast:
6	chr20:52743807..52746345-chr20:53641652..53644045,2	MCF-7	breast:
7	chr20:47480812..47483099-chr20:52743435..52745311,2	MCF-7	breast:
8	chr17:57927352..57929835-chr20:52743297..52745268,3	MCF-7	breast:
9	chr17:56704127..56711907-chr20:52729106..52752952,70	MCF-7	breast:
10	chr20:46412052..46416965-chr20:52743612..52746150,4	MCF-7	breast:
11	chr17:56706370..56714481-chr20:52725604..52746501,43	MCF-7	breast:
12	chr17:56735007..56738214-chr20:52743410..52746208,4	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000201524	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2585412	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2585447	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2585448	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585449	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2585451	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2616278	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616279	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2762918	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2762919	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762920	0.82[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762921	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762928	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2762932	0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2762933	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2762934	0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2762935	0.88[ASN][1000 genomes]
rs6022987	0.88[ASN][1000 genomes]
rs751088	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52740200-52748600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:52740600-52748200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:52740600-52748200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr20:52741200-52748200	Weak transcription	Placenta	Placenta
5	chr20:52742000-52748200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr20:52743400-52745400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:52743400-52745400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:52743400-52745400	Enhancers	HMEC	breast
9	chr20:52743400-52745400	Enhancers	NHEK	skin
10	chr20:52743600-52745400	Enhancers	HepG2	liver
11	chr20:52743800-52748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr20:52744400-52745400	Genic enhancers	A549	lung
13	chr20:52744400-52745400	Enhancers	Hela-S3	cervix
14	chr20:52744600-52745400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:52744600-52749800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr20:52745000-52748400	Weak transcription	NH-A	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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