Variant report

Variant	rs12236455
Chromosome Location	chr9:86453245-86453246
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	chr9:86320718..86323719-chr9:86450162..86455199,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11140179	0.92[EUR][1000 genomes]
rs11140182	0.92[EUR][1000 genomes]
rs11140183	0.92[EUR][1000 genomes]
rs11140191	0.92[EUR][1000 genomes]
rs11140192	0.92[EUR][1000 genomes]
rs11140199	0.92[EUR][1000 genomes]
rs11140203	0.92[EUR][1000 genomes]
rs11140215	0.92[EUR][1000 genomes]
rs11140217	0.92[EUR][1000 genomes]
rs11140219	0.92[EUR][1000 genomes]
rs11140225	0.92[EUR][1000 genomes]
rs11140228	0.92[EUR][1000 genomes]
rs11140229	0.92[EUR][1000 genomes]
rs11140230	0.84[EUR][1000 genomes]
rs11140235	0.92[EUR][1000 genomes]
rs11140248	0.92[EUR][1000 genomes]
rs11140250	0.92[EUR][1000 genomes]
rs11140252	0.92[EUR][1000 genomes]
rs11140254	0.92[EUR][1000 genomes]
rs11140257	0.92[EUR][1000 genomes]
rs11140258	0.92[EUR][1000 genomes]
rs11140266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140269	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140270	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11559387	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11560627	0.92[EUR][1000 genomes]
rs12235151	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236743	0.92[EUR][1000 genomes]
rs12237262	0.92[EUR][1000 genomes]
rs12237555	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12238365	0.92[EUR][1000 genomes]
rs12238575	0.92[EUR][1000 genomes]
rs2282221	0.92[EUR][1000 genomes]
rs2282222	0.92[EUR][1000 genomes]
rs28627139	0.92[EUR][1000 genomes]
rs28655802	0.87[ASN][1000 genomes]
rs3763626	0.92[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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv6590	chr9:86435603-86480442	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 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	chr9:86447800-86461200	Weak transcription	Fetal Brain Female	brain
2	chr9:86447800-86470800	Weak transcription	Brain Germinal Matrix	brain
3	chr9:86448600-86458800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr9:86452000-86467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:86452200-86464000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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