Variant report

Variant	rs62338677
Chromosome Location	chr5:2000922-2000923
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	chr5:1996033..1997672-chr5:2000548..2003493,3	MCF-7	breast:
2	chr10:61465368..61467475-chr5:2000083..2002351,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11739768	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11741348	0.88[EUR][1000 genomes]
rs11742050	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11742124	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11742732	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11743335	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11743444	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11743517	0.95[EUR][1000 genomes]
rs11743549	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11746472	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11747860	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17539841	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2035612	0.95[EUR][1000 genomes]
rs28608609	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3950476	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56144523	0.95[EUR][1000 genomes]
rs62337139	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62338660	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62338665	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62338679	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6860447	0.95[EUR][1000 genomes]
rs6860916	0.94[EUR][1000 genomes]
rs7725117	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7726401	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7726409	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv4681	chr5:1967628-2010091	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1992000-2007000	Weak transcription	Right Ventricle	heart
2	chr5:1997600-2002800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:1998800-2001400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:1998800-2003600	Weak transcription	Pancreas	Pancrea
5	chr5:2000800-2002000	Enhancers	Dnd41	blood

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