Variant report

Variant	rs2417656
Chromosome Location	chr9:108644107-108644108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108604240..108604942-chr9:108643640..108644635,3	K562	blood:
2	chr9:108371329..108372110-chr9:108643764..108644603,2	MCF-7	breast:
3	chr9:108604011..108605118-chr9:108643716..108644609,5	MCF-7	breast:
4	chr9:108637117..108641470-chr9:108642736..108644815,3	MCF-7	breast:
5	chr9:108643116..108645667-chr9:108673078..108675664,2	MCF-7	breast:
6	chr9:108371010..108371969-chr9:108643719..108644744,6	K562	blood:

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

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

rs_ID	r²[population]
rs10115085	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10117602	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10120538	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10739215	0.96[ASN][1000 genomes]
rs10759148	0.97[ASN][1000 genomes]
rs10816352	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978330	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10978331	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978332	0.96[ASN][1000 genomes]
rs13296649	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16925032	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2417643	0.96[ASN][1000 genomes]
rs2417644	0.96[ASN][1000 genomes]
rs2417650	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2900404	0.96[ASN][1000 genomes]
rs4598317	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4742967	0.95[ASN][1000 genomes]
rs4742969	0.99[ASN][1000 genomes]
rs6477482	0.97[ASN][1000 genomes]
rs7025973	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7040788	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7040794	0.96[ASN][1000 genomes]
rs7044156	0.96[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108640800-108650000	Weak transcription	Fetal Heart	heart
2	chr9:108641000-108649800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:108641800-108645400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:108642000-108645400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:108642200-108645200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:108642600-108648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:108643000-108644200	Enhancers	Brain Hippocampus Middle	brain
8	chr9:108643000-108644200	Enhancers	Fetal Brain Male	brain
9	chr9:108643800-108644200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:108643800-108644200	Active TSS	Brain Angular Gyrus	brain
11	chr9:108643800-108644200	Active TSS	Brain Cingulate Gyrus	brain
12	chr9:108643800-108644200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr9:108643800-108647800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:108643800-108648400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:108644000-108644200	Enhancers	Psoas Muscle	Psoas
16	chr9:108644000-108644200	Enhancers	K562	blood
17	chr9:108644000-108647600	Weak transcription	Brain Substantia Nigra	brain

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