Variant report

Variant	rs9470890
Chromosome Location	chr6:38463000-38463001
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	chr6:38461115..38463494-chr6:38466391..38469115,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11964058	0.88[ASN][1000 genomes]
rs12524209	0.88[ASN][1000 genomes]
rs12526608	0.82[ASN][1000 genomes]
rs12528414	0.82[ASN][1000 genomes]
rs12528646	0.88[ASN][1000 genomes]
rs12528840	0.88[ASN][1000 genomes]
rs16890715	0.88[ASN][1000 genomes]
rs28587676	0.82[ASN][1000 genomes]
rs28889620	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35978718	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4236059	0.90[EUR][1000 genomes]
rs4454130	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58163486	0.88[ASN][1000 genomes]
rs61088409	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6912811	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6914430	0.84[ASN][1000 genomes]
rs6941817	0.87[ASN][1000 genomes]
rs7764900	0.83[ASN][1000 genomes]
rs9470889	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38444600-38496200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr6:38450600-38469800	Weak transcription	HSMMtube	muscle
3	chr6:38451600-38471000	Weak transcription	Psoas Muscle	Psoas
4	chr6:38452400-38496600	Weak transcription	Primary B cells from cord blood	blood
5	chr6:38454400-38486400	Weak transcription	Primary T cells from cord blood	blood
6	chr6:38460000-38464600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:38460800-38473000	Enhancers	Brain Germinal Matrix	brain
8	chr6:38461000-38467800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:38461200-38467000	Enhancers	Brain Angular Gyrus	brain
10	chr6:38461200-38467400	Enhancers	Brain Substantia Nigra	brain
11	chr6:38461400-38463200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:38461800-38463000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:38461800-38463000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:38461800-38463200	Weak transcription	GM12878-XiMat	blood
15	chr6:38461800-38464000	Weak transcription	Brain Anterior Caudate	brain
16	chr6:38461800-38464600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:38462200-38463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:38462200-38464200	Weak transcription	Fetal Brain Male	brain
19	chr6:38462200-38471200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:38462400-38463800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:38462800-38463600	Enhancers	Brain Hippocampus Middle	brain
22	chr6:38462800-38467600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:38462800-38468000	Enhancers	Brain Cingulate Gyrus	brain
24	chr6:38463000-38463600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:38463000-38463600	Enhancers	Brain Inferior Temporal Lobe	brain

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