Variant report

Variant	rs6489253
Chromosome Location	chr12:123601686-123601687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123582057..123584351-chr12:123601284..123603250,2	MCF-7	breast:
2	chr12:123594098..123598804-chr12:123600213..123604964,5	K562	blood:
3	chr12:123597462..123600001-chr12:123600120..123602268,2	MCF-7	breast:
4	chr12:123600130..123602126-chr12:123634112..123635880,2	MCF-7	breast:
5	chr12:123574271..123575945-chr12:123599295..123601794,2	MCF-7	breast:
6	chr12:123601284..123602809-chr12:123617657..123619807,2	K562	blood:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11061612	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11834598	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310205	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313619	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12317784	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6650207	0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7307833	0.81[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7953918	0.93[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
5	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv870326	chr12:123585990-123719323	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123561600-123604000	Genic enhancers	Fetal Thymus	thymus
2	chr12:123590000-123603800	Enhancers	Left Ventricle	heart
3	chr12:123592800-123611200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:123594000-123602200	Enhancers	Brain Cingulate Gyrus	brain
5	chr12:123594600-123607200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr12:123594600-123634000	Weak transcription	Brain Germinal Matrix	brain
7	chr12:123595200-123610800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:123596600-123604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:123597400-123608200	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:123597800-123602000	Enhancers	Brain Angular Gyrus	brain
11	chr12:123597800-123602600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr12:123597800-123610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:123598000-123603400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:123598000-123608400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:123598200-123604800	Enhancers	Primary T cells from cord blood	blood
16	chr12:123598600-123602000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr12:123598600-123602000	Enhancers	Right Atrium	heart
18	chr12:123598600-123606400	Weak transcription	HepG2	liver
19	chr12:123598800-123601800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:123598800-123602800	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:123598800-123603600	Enhancers	Right Ventricle	heart
22	chr12:123598800-123603800	Enhancers	Ovary	ovary
23	chr12:123598800-123605000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr12:123599000-123601800	Enhancers	Spleen	Spleen
25	chr12:123599000-123602000	Enhancers	Liver	Liver
26	chr12:123599000-123603800	Enhancers	Lung	lung
27	chr12:123599000-123604000	Enhancers	Placenta	Placenta
28	chr12:123599200-123624600	Weak transcription	Fetal Brain Female	brain
29	chr12:123599600-123603200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:123599800-123601800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:123599800-123603400	Weak transcription	Gastric	stomach
32	chr12:123600000-123601800	Enhancers	Primary B cells from cord blood	blood
33	chr12:123600000-123601800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:123600000-123604800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr12:123600000-123605000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:123600000-123605200	Weak transcription	Fetal Intestine Large	intestine
37	chr12:123600000-123611200	Weak transcription	Aorta	Aorta
38	chr12:123600200-123605200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:123600600-123603400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:123600600-123604400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:123600600-123604400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr12:123600600-123610600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:123600600-123610800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:123600600-123610800	Weak transcription	Fetal Intestine Small	intestine
45	chr12:123600600-123610800	Weak transcription	Stomach Mucosa	stomach
46	chr12:123600600-123611000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:123600600-123611000	Weak transcription	Small Intestine	intestine
48	chr12:123600800-123601800	Weak transcription	A549	lung
49	chr12:123600800-123602800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:123600800-123602800	Enhancers	Fetal Heart	heart

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