Variant report

Variant	rs13297669
Chromosome Location	chr9:108647398-108647399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108641786..108643784-chr9:108646838..108648345,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10816351	0.92[ASN][1000 genomes]
rs10978318	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978319	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10978320	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978321	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978327	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10978329	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10978334	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13299235	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13301197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16925004	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2417645	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2417652	0.92[ASN][1000 genomes]
rs2417653	0.97[ASN][1000 genomes]
rs35315267	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35457712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742963	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742964	0.92[ASN][1000 genomes]
rs4742971	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6477477	0.92[ASN][1000 genomes]
rs7872318	0.93[ASN][1000 genomes]
rs9299115	0.88[EUR][1000 genomes]
rs9969729	0.93[ASN][1000 genomes]
rs9969730	0.93[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:20 , 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	chr9:108642600-108648000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:108643800-108647800	Weak transcription	Brain Anterior Caudate	brain
5	chr9:108643800-108648400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:108644000-108647600	Weak transcription	Brain Substantia Nigra	brain
7	chr9:108644200-108647800	Weak transcription	Brain Angular Gyrus	brain
8	chr9:108644200-108647800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:108644200-108647800	Weak transcription	Brain Hippocampus Middle	brain
10	chr9:108644400-108647600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:108645400-108647600	Enhancers	Primary hematopoietic stem cells	blood
12	chr9:108645400-108653600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:108645800-108647600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:108646200-108650800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:108646200-108651800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:108646600-108648800	Enhancers	Fetal Muscle Leg	muscle
17	chr9:108646600-108649600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr9:108646800-108647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:108646800-108649600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:108647200-108648000	Weak transcription	Psoas Muscle	Psoas

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