Variant report

Variant	rs56342040
Chromosome Location	chr2:64027450-64027451
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	chr2:64024404..64027865-chr2:64066481..64068926,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS54-1	chr2:64027396-64027505	XLOC_002120
2	lnc-VPS54-1	chr2:64027410-64027505	NONHSAT071073

Variant related genes	Relation type
ENSG00000169764	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13431437	1.00[ASN][1000 genomes]
rs17028099	1.00[ASN][1000 genomes]
rs17554748	1.00[ASN][1000 genomes]
rs28838707	1.00[ASN][1000 genomes]
rs3924029	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55748575	1.00[ASN][1000 genomes]
rs57120200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57184962	1.00[ASN][1000 genomes]
rs57329063	1.00[ASN][1000 genomes]
rs57413391	1.00[ASN][1000 genomes]
rs57844293	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57877849	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58208651	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58422338	1.00[ASN][1000 genomes]
rs58472560	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58495096	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540641	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136361	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136362	0.95[EUR][1000 genomes]
rs62136364	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136366	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136367	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136369	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136391	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136393	0.81[EUR][1000 genomes]
rs62136397	0.81[EUR][1000 genomes]
rs62136400	0.81[EUR][1000 genomes]
rs62136402	0.81[EUR][1000 genomes]
rs62137457	0.90[AMR][1000 genomes]
rs62138760	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138819	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138822	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138823	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62138824	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745518	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751397	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937260	1.00[ASN][1000 genomes]
rs73937264	1.00[ASN][1000 genomes]
rs73937268	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582457	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601187	1.00[ASN][1000 genomes]
rs7606341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013375	chr2:63969820-64231550	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63976400-64028600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:64019000-64029000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:64020400-64032000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:64023600-64032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:64024000-64028800	Weak transcription	Liver	Liver
6	chr2:64024600-64028800	Weak transcription	Adipose Nuclei	Adipose

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