Variant report

Variant	rs3902820
Chromosome Location	chr5:2000330-2000331
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:61465368..61467475-chr5:2000083..2002351,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10035144	0.93[ASN][1000 genomes]
rs10043083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045683	0.92[ASN][1000 genomes]
rs1017924	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10462750	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10474733	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10474734	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11133918	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1123381	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1123390	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1123391	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11749073	0.92[ASN][1000 genomes]
rs11952205	0.86[ASN][1000 genomes]
rs12188545	0.91[ASN][1000 genomes]
rs12716127	0.93[ASN][1000 genomes]
rs13166888	0.92[ASN][1000 genomes]
rs1486937	1.00[ASN][1000 genomes]
rs1552435	0.80[EUR][1000 genomes]
rs1601641	1.00[ASN][1000 genomes]
rs16902318	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16902321	0.80[EUR][1000 genomes]
rs2129471	0.80[EUR][1000 genomes]
rs2129472	0.80[EUR][1000 genomes]
rs28392808	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4246752	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4246753	0.80[EUR][1000 genomes]
rs4246754	0.85[EUR][1000 genomes]
rs4254943	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4314451	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4371796	0.92[ASN][1000 genomes]
rs4398675	0.80[EUR][1000 genomes]
rs4398680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4407661	0.91[ASN][1000 genomes]
rs4413568	0.80[EUR][1000 genomes]
rs4463207	0.80[EUR][1000 genomes]
rs4505990	0.80[EUR][1000 genomes]
rs4526149	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975719	0.81[EUR][1000 genomes]
rs4975777	0.91[ASN][1000 genomes]
rs4975779	0.97[ASN][1000 genomes]
rs4975786	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4975795	0.80[EUR][1000 genomes]
rs4975796	0.80[EUR][1000 genomes]
rs4975797	0.80[EUR][1000 genomes]
rs4975798	0.80[EUR][1000 genomes]
rs55860207	0.81[ASN][1000 genomes]
rs57434783	0.93[ASN][1000 genomes]
rs61177713	0.80[EUR][1000 genomes]
rs61656301	0.87[ASN][1000 genomes]
rs62337135	0.87[ASN][1000 genomes]
rs67659713	0.90[ASN][1000 genomes]
rs6867032	0.80[EUR][1000 genomes]
rs7729761	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs9312970	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs965276	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	esv3324262	chr5:1996152-2000850	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3347968	chr5:1997052-2000350	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 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	chr5:1999400-2000800	Weak transcription	Dnd41	blood

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