Variant report

Variant	rs6479304
Chromosome Location	chr9:108010210-108010211
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	chr9:108005558..108008995-chr9:108010064..108014248,9	MCF-7	breast:
2	chr9:107904194..107906765-chr9:108007305..108010272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12341869	0.84[ASW][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688962	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57877883	1.00[AMR][1000 genomes]
rs59290851	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6479300	1.00[AFR][1000 genomes]
rs6479301	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479302	1.00[ASW][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6479303	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7024012	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7026389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7031663	0.83[MKK][hapmap]
rs7033929	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7039638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7046185	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7048497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72744219	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72744225	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs73510211	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510289	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73510295	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666624	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73666625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7847744	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7847952	0.94[AFR][1000 genomes]
rs7853038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7853709	0.83[AMR][1000 genomes]
rs7854064	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7854282	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7857088	0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7860356	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7869261	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7873924	0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs7874307	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9777083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv893691	chr9:107994629-108020284	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108006200-108010400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr9:108006200-108011800	Active TSS	Brain Hippocampus Middle	brain
3	chr9:108006400-108011800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr9:108006400-108012000	Active TSS	Brain Substantia Nigra	brain
5	chr9:108006600-108011200	Active TSS	Brain Angular Gyrus	brain
6	chr9:108008200-108011400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:108008200-108015800	Weak transcription	Gastric	stomach
8	chr9:108008200-108015800	Weak transcription	Pancreas	Pancrea
9	chr9:108008200-108033600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:108008400-108019400	Weak transcription	Left Ventricle	heart
11	chr9:108008400-108020000	Weak transcription	Primary T cells from cord blood	blood
12	chr9:108008600-108010400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:108008600-108010400	Enhancers	Small Intestine	intestine
14	chr9:108008600-108010800	Enhancers	Colon Smooth Muscle	Colon
15	chr9:108008600-108011800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:108008600-108015800	Weak transcription	Colonic Mucosa	Colon
17	chr9:108008600-108020000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr9:108008800-108010600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr9:108008800-108022400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr9:108009000-108010400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:108009000-108037200	Weak transcription	Aorta	Aorta
22	chr9:108009200-108010400	Enhancers	Fetal Intestine Large	intestine
23	chr9:108009200-108010400	Enhancers	Fetal Intestine Small	intestine
24	chr9:108009200-108010400	Enhancers	Hela-S3	cervix
25	chr9:108009200-108010600	Enhancers	Stomach Mucosa	stomach
26	chr9:108009200-108011600	Enhancers	Liver	Liver
27	chr9:108009200-108017800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:108009200-108019400	Weak transcription	Ovary	ovary
29	chr9:108009400-108010400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:108009400-108010400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr9:108009400-108010400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:108009400-108010600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr9:108009400-108010600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr9:108009400-108011400	Weak transcription	Adipose Nuclei	Adipose
35	chr9:108009400-108011600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr9:108009400-108011600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:108009400-108011600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:108009400-108011800	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr9:108009400-108011800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:108009400-108012800	Enhancers	Fetal Brain Male	brain
41	chr9:108009400-108013200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:108009400-108013400	Enhancers	HepG2	liver
43	chr9:108009400-108013600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:108009400-108013800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr9:108009400-108016600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:108009400-108017600	Weak transcription	NHDF-Ad	bronchial
47	chr9:108009400-108022200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:108009600-108011800	Enhancers	Fetal Lung	lung
49	chr9:108009600-108015800	Weak transcription	NHEK	skin
50	chr9:108009800-108010400	Flanking Active TSS	Brain Anterior Caudate	brain

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