Variant report

Variant	rs7868562
Chromosome Location	chr9:97243607-97243608
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	chr9:97242816..97244907-chr9:97253508..97257110,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs2006685	0.85[ASN][1000 genomes]
rs2049008	0.92[ASN][1000 genomes]
rs2277182	0.84[ASN][1000 genomes]
rs2479601	1.00[CEU][hapmap]
rs2479602	1.00[CEU][hapmap]
rs3118756	0.84[CEU][hapmap]
rs3131910	0.88[CEU][hapmap]
rs4434674	0.84[ASN][1000 genomes]
rs4477096	0.84[ASN][1000 genomes]
rs4497033	0.85[ASN][1000 genomes]
rs4509403	0.93[ASN][1000 genomes]
rs4743953	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743954	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743955	0.94[ASN][1000 genomes]
rs4744340	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4744346	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688165	1.00[CEU][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7020879	0.95[ASN][1000 genomes]
rs7023744	0.84[ASN][1000 genomes]
rs7023915	0.83[ASN][1000 genomes]
rs7024159	0.93[ASN][1000 genomes]
rs7025755	0.84[ASN][1000 genomes]
rs7027465	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7027489	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7031088	0.98[ASN][1000 genomes]
rs7031496	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7031949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7037198	0.95[ASN][1000 genomes]
rs7038593	0.83[ASN][1000 genomes]
rs7040577	0.84[ASN][1000 genomes]
rs7040710	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041112	0.91[AFR][1000 genomes]
rs7041503	0.83[ASN][1000 genomes]
rs7047279	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7047295	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7047930	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7048688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848221	0.85[ASN][1000 genomes]
rs7848227	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7863310	0.85[ASN][1000 genomes]
rs7863312	0.85[ASN][1000 genomes]
rs7873525	0.92[ASN][1000 genomes]
rs9299421	0.90[ASN][1000 genomes]
rs9299422	0.92[ASN][1000 genomes]
rs9409512	0.92[CEU][hapmap]
rs9409513	0.89[CEU][hapmap]
rs9409552	0.85[ASN][1000 genomes]
rs9409575	0.91[AFR][1000 genomes]
rs9409759	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409763	0.84[ASN][1000 genomes]
rs9409765	0.84[ASN][1000 genomes]
rs9409777	0.95[ASN][1000 genomes]
rs9409779	0.95[ASN][1000 genomes]
rs9409792	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9409793	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9777207	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7868562	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97241200-97243800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:97241800-97262800	Weak transcription	Liver	Liver
3	chr9:97243000-97243800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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