Variant report

Variant	rs2417650
Chromosome Location	chr9:108640222-108640223
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	chr9:108637117..108641470-chr9:108642736..108644815,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10115085	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10117602	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10120538	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10739215	0.94[ASN][1000 genomes]
rs10759148	0.95[ASN][1000 genomes]
rs10816352	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10978330	0.98[ASN][1000 genomes]
rs10978331	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10978332	0.94[ASN][1000 genomes]
rs13296649	0.98[ASN][1000 genomes]
rs16925032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2417643	0.94[ASN][1000 genomes]
rs2417644	0.94[ASN][1000 genomes]
rs2417656	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900404	0.94[ASN][1000 genomes]
rs4598317	0.94[ASN][1000 genomes]
rs4742967	0.93[ASN][1000 genomes]
rs4742969	0.97[ASN][1000 genomes]
rs6477482	0.95[ASN][1000 genomes]
rs7025973	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7040788	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7040794	0.94[ASN][1000 genomes]
rs7044156	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	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:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108636800-108643000	Weak transcription	Fetal Brain Female	brain
2	chr9:108639000-108640600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr9:108639200-108640600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:108639200-108640800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr9:108639800-108640600	Enhancers	Fetal Brain Male	brain
6	chr9:108640000-108640400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr9:108640000-108640400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:108640000-108640400	Enhancers	Primary B cells from peripheral blood	blood
9	chr9:108640000-108640600	Enhancers	Brain Germinal Matrix	brain
10	chr9:108640000-108640600	Enhancers	Fetal Muscle Leg	muscle
11	chr9:108640000-108640800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:108640000-108640800	Enhancers	Fetal Heart	heart
13	chr9:108640000-108641000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:108640200-108640400	Enhancers	Brain Substantia Nigra	brain
15	chr9:108640200-108640600	Enhancers	Brain Anterior Caudate	brain

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