Variant report

Variant	rs6064013
Chromosome Location	chr20:52488471-52488472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52487126..52489050-chr20:55848338..55851293,2	MCF-7	breast:
2	chr20:52488392..52489116-chr20:52532178..52532689,2	MCF-7	breast:
3	chr20:52425734..52426665-chr20:52488330..52488904,2	MCF-7	breast:
4	chr17:59491669..59494227-chr20:52486642..52489549,2	MCF-7	breast:
5	chr17:57922823..57924749-chr20:52487976..52490735,3	MCF-7	breast:
6	chr17:57169567..57172179-chr20:52487064..52489132,2	MCF-7	breast:
7	chr14:71787305..71788925-chr20:52486960..52489477,2	MCF-7	breast:
8	chr20:52478179..52488683-chr20:55835744..55846940,26	MCF-7	breast:
9	chr20:52471901..52491673-chr20:55835708..55845674,34	MCF-7	breast:
10	chr20:52488130..52488636-chr20:52532185..52533145,2	MCF-7	breast:
11	chr17:56707630..56709159-chr20:52486995..52489742,2	MCF-7	breast:
12	chr17:56736331..56737963-chr20:52488201..52489902,2	MCF-7	breast:
13	chr20:52486286..52488897-chr20:55826084..55828899,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11086444	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697016	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11699573	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11906676	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13037872	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13038143	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859902	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35507231	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6064016	0.82[EUR][1000 genomes]
rs6068699	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6068702	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7352529	0.87[EUR][1000 genomes]
rs8114312	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
6	nsv586222	chr20:52473679-52506380	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	74 gene(s)	inside rSNPs	diseases
7	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52481800-52489200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:52482800-52489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr20:52482800-52489400	Weak transcription	Aorta	Aorta
4	chr20:52482800-52489800	Weak transcription	Esophagus	oesophagus
5	chr20:52482800-52492000	Weak transcription	Gastric	stomach
6	chr20:52483400-52489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:52483400-52495000	Weak transcription	Spleen	Spleen
8	chr20:52483600-52490600	Weak transcription	Right Atrium	heart
9	chr20:52483800-52488600	Weak transcription	NHLF	lung
10	chr20:52484000-52488800	Weak transcription	HSMMtube	muscle
11	chr20:52484200-52488800	Weak transcription	Fetal Stomach	stomach
12	chr20:52484400-52488800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr20:52484400-52488800	Weak transcription	Brain Hippocampus Middle	brain
14	chr20:52484800-52489400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr20:52485000-52489200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr20:52485000-52489800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:52485000-52493000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr20:52485600-52489000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr20:52485600-52490400	Enhancers	Fetal Thymus	thymus
20	chr20:52485800-52488600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr20:52485800-52489000	Enhancers	Liver	Liver
22	chr20:52485800-52489600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr20:52485800-52490200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:52485800-52490400	Enhancers	Fetal Intestine Small	intestine
25	chr20:52485800-52491000	Enhancers	Fetal Intestine Large	intestine
26	chr20:52486000-52488800	Enhancers	Primary T cells from cord blood	blood
27	chr20:52486000-52488800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr20:52486000-52489000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr20:52486000-52489000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr20:52486000-52489000	Enhancers	Fetal Brain Male	brain
31	chr20:52486000-52489200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr20:52486000-52489400	Enhancers	Duodenum Mucosa	Duodenum
33	chr20:52486000-52489800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr20:52486000-52490000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr20:52486000-52490200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr20:52486000-52490200	Enhancers	NHEK	skin
37	chr20:52486000-52490400	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr20:52486000-52490400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr20:52486200-52489200	Enhancers	Fetal Kidney	kidney
40	chr20:52486200-52490000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:52486200-52490200	Enhancers	Primary hematopoietic stem cells	blood
42	chr20:52486200-52490200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr20:52486200-52490400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr20:52486200-52490400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr20:52486400-52488800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:52486400-52488800	Weak transcription	Brain Anterior Caudate	brain
47	chr20:52486400-52489400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr20:52486600-52488600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr20:52486600-52488600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr20:52486600-52488600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links