Variant report

Variant	rs9474308
Chromosome Location	chr6:13480395-13480396
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	chr6:13479967..13483779-chr6:13484008..13490030,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2115062	1.00[EUR][1000 genomes]
rs2195307	1.00[EUR][1000 genomes]
rs34295856	1.00[EUR][1000 genomes]
rs542978	1.00[TSI][hapmap]
rs559205	1.00[EUR][1000 genomes]
rs73725828	1.00[EUR][1000 genomes]
rs73725829	1.00[EUR][1000 genomes]
rs73725830	1.00[EUR][1000 genomes]
rs7763818	1.00[EUR][1000 genomes]
rs7766813	1.00[EUR][1000 genomes]
rs9474154	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9474175	1.00[EUR][1000 genomes]
rs9474177	1.00[EUR][1000 genomes]
rs9474197	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3354997	chr6:13478773-13482371	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13452200-13483400	Weak transcription	Gastric	stomach
2	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
3	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
4	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
6	chr6:13462800-13484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:13463200-13481000	Weak transcription	A549	lung
8	chr6:13463600-13484400	Weak transcription	Primary T cells from cord blood	blood
9	chr6:13463800-13484600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:13465200-13485000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:13469400-13485800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:13470800-13483600	Weak transcription	Fetal Stomach	stomach
13	chr6:13471000-13485400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:13471000-13485600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:13471200-13483400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:13471200-13483400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:13471400-13480400	Weak transcription	Fetal Lung	lung
18	chr6:13471400-13484200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:13471600-13481600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:13471600-13483600	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:13471600-13485000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:13471800-13485600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:13472000-13481800	Weak transcription	Brain Germinal Matrix	brain
24	chr6:13472200-13484400	Weak transcription	Brain Substantia Nigra	brain
25	chr6:13472400-13481800	Weak transcription	Brain Anterior Caudate	brain
26	chr6:13472800-13481000	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:13473200-13480600	Weak transcription	Brain Angular Gyrus	brain
28	chr6:13474800-13484800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:13475200-13483600	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:13475400-13484400	Weak transcription	Hela-S3	cervix
31	chr6:13476400-13481200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:13476600-13481200	Weak transcription	K562	blood
33	chr6:13477200-13482000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr6:13477400-13481200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:13477600-13485800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:13477800-13481600	Weak transcription	Pancreas	Pancrea
37	chr6:13478200-13480400	Enhancers	Fetal Thymus	thymus
38	chr6:13478200-13480800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr6:13478200-13482000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:13478400-13480400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:13478600-13480600	Strong transcription	Adipose Nuclei	Adipose
42	chr6:13478600-13480600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
43	chr6:13478800-13480800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr6:13478800-13482200	Enhancers	Liver	Liver
45	chr6:13478800-13484600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:13479000-13481800	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:13479000-13482000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr6:13479000-13482000	Enhancers	HMEC	breast
49	chr6:13479000-13482200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:13479200-13480800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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