Variant report

Variant	rs2417652
Chromosome Location	chr9:108641179-108641180
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	chr9:108637117..108641470-chr9:108642736..108644815,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10816351	0.88[ASN][1000 genomes]
rs10978318	0.93[ASN][1000 genomes]
rs10978319	0.93[ASN][1000 genomes]
rs10978320	0.91[ASN][1000 genomes]
rs10978321	0.92[ASN][1000 genomes]
rs10978327	0.93[ASN][1000 genomes]
rs10978329	0.89[ASN][1000 genomes]
rs10978334	0.88[ASN][1000 genomes]
rs13297669	0.92[ASN][1000 genomes]
rs13299235	0.93[ASN][1000 genomes]
rs13301197	0.92[ASN][1000 genomes]
rs13301463	0.87[ASN][1000 genomes]
rs16925004	0.92[ASN][1000 genomes]
rs2417645	0.88[ASN][1000 genomes]
rs2417653	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35315267	0.87[ASN][1000 genomes]
rs35457712	0.95[ASN][1000 genomes]
rs4742963	0.90[ASN][1000 genomes]
rs4742964	0.88[ASN][1000 genomes]
rs4742971	0.87[ASN][1000 genomes]
rs6477477	0.88[ASN][1000 genomes]
rs7872318	0.88[ASN][1000 genomes]
rs9969729	0.88[ASN][1000 genomes]
rs9969730	0.88[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	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv893694	chr9:108486533-108854018	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1041073	chr9:108535813-108731343	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1036849	chr9:108582944-108651205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1052684	chr9:108582944-108730280	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv615140	chr9:108592589-108725567	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv831679	chr9:108603112-108785347	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108636800-108643000	Weak transcription	Fetal Brain Female	brain
2	chr9:108640600-108643000	Weak transcription	Brain Anterior Caudate	brain
3	chr9:108640600-108643000	Weak transcription	Fetal Brain Male	brain
4	chr9:108640800-108641200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:108640800-108650000	Weak transcription	Fetal Heart	heart
6	chr9:108641000-108642000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr9:108641000-108642200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:108641000-108649800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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