Variant report

Variant	rs953927
Chromosome Location	chr2:20609954-20609955
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20541478..20544272-chr2:20609802..20611413,2	K562	blood:
2	chr16:69290869..69293281-chr2:20609230..20610894,2	MCF-7	breast:
3	chr2:20607895..20612833-chr2:20645228..20650823,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10209568	0.83[ASN][1000 genomes]
rs11901184	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464277	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476941	0.87[ASN][1000 genomes]
rs1985318	0.95[ASN][1000 genomes]
rs1985319	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348705	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343138	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs343140	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs343142	0.81[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs343143	0.96[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs343144	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs343147	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343151	0.81[CHB][hapmap]
rs343152	0.93[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4666306	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4666386	0.87[ASN][1000 genomes]
rs4666387	0.87[ASN][1000 genomes]
rs4666389	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4666390	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6531236	0.87[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6705947	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6734065	0.89[ASN][1000 genomes]
rs67511352	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563890	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564799	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564810	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7576439	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576806	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7603518	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604195	0.81[AMR][1000 genomes];0.97[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	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv581165	chr2:20581058-20616990	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20601400-20614800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:20609800-20610200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
3	chr2:20609800-20610200	ZNF genes & repeats	HSMMtube	muscle

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