Variant report

Variant	rs62297620
Chromosome Location	chr4:80563160-80563161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:80562829..80565369-chr4:80570389..80573368,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10022663	0.84[EUR][1000 genomes]
rs1031005	0.85[EUR][1000 genomes]
rs11098770	0.85[EUR][1000 genomes]
rs11728755	0.80[EUR][1000 genomes]
rs11941782	0.84[EUR][1000 genomes]
rs12643491	0.85[EUR][1000 genomes]
rs13104009	0.85[EUR][1000 genomes]
rs13112067	0.84[EUR][1000 genomes]
rs13112577	0.84[EUR][1000 genomes]
rs1371989	0.85[EUR][1000 genomes]
rs1371993	0.85[EUR][1000 genomes]
rs1440853	0.85[EUR][1000 genomes]
rs1837645	0.82[EUR][1000 genomes]
rs1837646	0.82[EUR][1000 genomes]
rs1866835	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2165386	0.85[EUR][1000 genomes]
rs2582681	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2709847	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3109166	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3111790	0.94[ASN][1000 genomes]
rs3943669	0.85[EUR][1000 genomes]
rs4389603	0.85[EUR][1000 genomes]
rs4975056	0.85[EUR][1000 genomes]
rs60613746	1.00[ASN][1000 genomes]
rs62297619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62297622	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6812760	0.85[EUR][1000 genomes]
rs6850999	0.85[EUR][1000 genomes]
rs7665378	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7687586	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7688923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894054	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs894055	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9307545	0.85[EUR][1000 genomes]
rs9307551	0.85[EUR][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	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62297620	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs62297620	LINC00989	cis	Whole Blood	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80555600-80566600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:80555600-80566800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr4:80559600-80566600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:80562600-80563200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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