Variant report

Variant	rs12339355
Chromosome Location	chr9:13019965-13019966
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:13008470..13010567-chr9:13018005..13020586,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10738310	0.88[ASN][1000 genomes]
rs10738311	0.88[ASN][1000 genomes]
rs10738312	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10738313	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10738315	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756439	0.88[ASN][1000 genomes]
rs10756440	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10809873	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10960879	0.89[ASN][1000 genomes]
rs11789175	0.86[ASN][1000 genomes]
rs12339335	0.98[ASN][1000 genomes]
rs12341917	0.93[ASN][1000 genomes]
rs12345688	0.96[ASN][1000 genomes]
rs12345742	0.96[ASN][1000 genomes]
rs12351740	1.00[ASN][1000 genomes]
rs12351821	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328909	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1332072	0.83[ASN][1000 genomes]
rs1360517	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1410777	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1412303	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1412304	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1887884	0.83[ASN][1000 genomes]
rs2183136	0.89[ASN][1000 genomes]
rs28569788	0.87[ASN][1000 genomes]
rs4741267	0.87[ASN][1000 genomes]
rs7018902	0.95[ASN][1000 genomes]
rs7018967	0.95[ASN][1000 genomes]
rs7022183	0.91[ASN][1000 genomes]
rs7028022	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv892576	chr9:12925921-13093345	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv917331	chr9:12941193-13146852	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv892578	chr9:12942956-13485035	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892579	chr9:12954161-13120380	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1033313	chr9:12985981-13037413	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1023816	chr9:13008542-13064793	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13014800-13020200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr9:13015200-13020000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:13019800-13020000	Enhancers	Rectal Smooth Muscle	rectum
4	chr9:13019800-13020800	Flanking Active TSS	Fetal Lung	lung

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