Variant report

Variant	rs6715620
Chromosome Location	chr2:47144532-47144533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:
2	chr2:47140335..47142832-chr2:47143395..47145229,2	K562	blood:
3	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
4	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
5	chr2:47143555..47145098-chr2:47147081..47148697,2	K562	blood:
6	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180398	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10190862	0.94[EUR][1000 genomes]
rs10190882	0.94[EUR][1000 genomes]
rs10197474	0.94[EUR][1000 genomes]
rs10199965	0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.96[ASN][1000 genomes]
rs13388612	1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13394007	0.94[EUR][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs13410702	0.94[EUR][1000 genomes]
rs13415655	0.94[EUR][1000 genomes]
rs13415771	0.94[EUR][1000 genomes]
rs13419072	0.94[EUR][1000 genomes]
rs1446499	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1446500	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17035859	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17035867	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17035884	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17035887	0.94[ASN][1000 genomes]
rs2084192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs3087857	1.00[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56213467	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58589709	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60194846	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136788	0.94[EUR][1000 genomes]
rs62136818	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136819	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62136820	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62136822	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62140556	0.85[AMR][1000 genomes]
rs6544938	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.96[ASN][1000 genomes]
rs6715391	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6716381	1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729120	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729604	1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	0.94[ASN][1000 genomes]
rs6743994	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6745578	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6755303	0.98[ASN][1000 genomes]
rs6758093	1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs71423929	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720827	0.94[EUR][1000 genomes]
rs7340475	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73926966	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754411	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.85[ASN][1000 genomes]
rs7574833	0.83[ASN][1000 genomes]
rs7575172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586004	0.94[ASN][1000 genomes]
rs7596198	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601491	1.00[ASN][1000 genomes]
rs8861	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9973504	0.90[ASN][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47142000-47144600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:47142200-47144600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr2:47142200-47144800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:47142400-47144600	Active TSS	Osteobl	bone
5	chr2:47143400-47145400	Flanking Active TSS	Dnd41	blood
6	chr2:47143600-47144600	Enhancers	Spleen	Spleen
7	chr2:47143800-47145200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:47143800-47146000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:47143800-47146000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:47143800-47146000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:47143800-47146000	Weak transcription	Stomach Mucosa	stomach
12	chr2:47143800-47146200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:47143800-47146200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:47143800-47146200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:47143800-47146400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:47143800-47147200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:47143800-47147200	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:47143800-47148800	Weak transcription	NH-A	brain
19	chr2:47143800-47149000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:47143800-47151800	Weak transcription	Lung	lung
21	chr2:47144000-47144600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:47144000-47144600	Enhancers	Fetal Heart	heart
23	chr2:47144000-47144600	Enhancers	Fetal Intestine Small	intestine
24	chr2:47144000-47144600	Enhancers	Thymus	Thymus
25	chr2:47144000-47144800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:47144000-47144800	Enhancers	Small Intestine	intestine
27	chr2:47144000-47145000	Enhancers	Adipose Nuclei	Adipose
28	chr2:47144000-47145000	Enhancers	Liver	Liver
29	chr2:47144000-47145000	Flanking Active TSS	K562	blood
30	chr2:47144000-47146000	Flanking Active TSS	GM12878-XiMat	blood
31	chr2:47144000-47146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:47144000-47146200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr2:47144000-47146200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr2:47144000-47148800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:47144000-47150800	Weak transcription	Placenta	Placenta
36	chr2:47144200-47144600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:47144200-47144600	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:47144200-47144600	Enhancers	Fetal Intestine Large	intestine
39	chr2:47144200-47144600	Enhancers	Fetal Thymus	thymus
40	chr2:47144200-47144600	Enhancers	HMEC	breast
41	chr2:47144200-47144800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:47144200-47144800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:47144200-47144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:47144200-47144800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:47144200-47144800	Enhancers	Brain Angular Gyrus	brain
46	chr2:47144200-47144800	Enhancers	Fetal Lung	lung
47	chr2:47144200-47144800	Enhancers	NHEK	skin
48	chr2:47144200-47145000	Enhancers	Colon Smooth Muscle	Colon
49	chr2:47144200-47145000	Enhancers	Fetal Brain Female	brain
50	chr2:47144200-47145200	Enhancers	Brain Anterior Caudate	brain

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