Variant report

Variant	rs6063997
Chromosome Location	chr20:52403556-52403557
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:38)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:38 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52403226..52403958-chr20:52555890..52557064,3	MCF-7	breast:
2	chr20:52402271..52403940-chr20:52480276..52481396,7	MCF-7	breast:
3	chr20:52401119..52404039-chr21:41758413..41760335,2	MCF-7	breast:
4	chr13:115044907..115047274-chr20:52401538..52403946,2	MCF-7	breast:
5	chr20:52401248..52403796-chr3:62303588..62306557,2	MCF-7	breast:
6	chr17:56734940..56737605-chr20:52402876..52404399,2	MCF-7	breast:
7	chr17:56703908..56706201-chr20:52403227..52406128,2	MCF-7	breast:
8	chr20:52403315..52403970-chr20:52482550..52483200,2	MCF-7	breast:
9	chr1:190317641..190318618-chr20:52402718..52403693,2	MCF-7	breast:
10	chr20:52401777..52404273-chr3:63855314..63857223,2	MCF-7	breast:
11	chr20:52403400..52404343-chr20:52480514..52481175,2	MCF-7	breast:
12	chr17:57920570..57925578-chr20:52400635..52405206,5	MCF-7	breast:
13	chr17:57920138..57922959-chr20:52400823..52403888,3	MCF-7	breast:
14	chr20:52401773..52405148-chr20:55839891..55841915,4	MCF-7	breast:
15	chr20:45986288..45987789-chr20:52401390..52404325,2	MCF-7	breast:
16	chr20:52402173..52404345-chr7:25164232..25165772,2	MCF-7	breast:
17	chr20:52355379..52357254-chr20:52402772..52404323,2	K562	blood:
18	chr20:52402743..52403941-chr20:52531991..52532944,5	MCF-7	breast:
19	chr1:14624861..14627152-chr20:52402945..52404528,2	MCF-7	breast:
20	chr20:52401244..52403957-chr21:44494158..44496334,2	MCF-7	breast:
21	chr20:52401336..52404306-chr8:103874838..103877830,2	MCF-7	breast:
22	chr20:52401623..52403995-chr20:52486040..52487259,28	MCF-7	breast:
23	chr2:117073210..117074730-chr20:52401599..52404302,2	MCF-7	breast:
24	chr20:52403342..52404336-chr20:52481470..52481988,2	MCF-7	breast:
25	chr20:52237480..52238145-chr20:52403251..52403766,2	MCF-7	breast:
26	chr20:52403022..52404783-chr20:55842284..55845031,2	MCF-7	breast:
27	chr17:59474142..59479097-chr20:52403146..52407414,5	MCF-7	breast:
28	chr20:52402471..52404272-chr20:55917874..55920084,2	MCF-7	breast:
29	chr20:52401639..52403990-chr20:52486019..52487230,15	MCF-7	breast:
30	chr20:52401075..52404235-chr20:55838784..55842042,3	MCF-7	breast:
31	chr20:52402990..52404228-chr20:52531584..52532958,14	MCF-7	breast:
32	chr19:1247945..1249666-chr20:52401472..52404362,3	MCF-7	breast:
33	chr20:50384014..50386808-chr20:52401448..52405357,3	MCF-7	breast:
34	chr17:57915941..57918627-chr20:52402974..52405387,3	MCF-7	breast:
35	chr20:52278055..52279007-chr20:52402723..52403658,3	MCF-7	breast:
36	chr20:52194980..52196290-chr20:52401631..52404661,16	MCF-7	breast:
37	chr20:52401511..52403835-chr20:55849653..55852433,2	MCF-7	breast:
38	chr20:52401888..52404343-chr20:52481570..52483956,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000160200	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000114405	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000169062	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000241472	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000054793	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000172115	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2870285	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2870286	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4811464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4811465	0.91[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6013794	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6013795	0.93[ASN][1000 genomes]
rs6013796	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6022734	0.84[ASN][1000 genomes]
rs6022739	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs6022740	0.89[ASN][1000 genomes]
rs6022742	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6022747	0.84[EUR][1000 genomes]
rs6022750	0.80[EUR][1000 genomes]
rs6063994	0.92[ASN][1000 genomes]
rs6063995	0.92[ASN][1000 genomes]
rs6063996	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6068659	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6068661	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6068664	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6068667	0.86[EUR][1000 genomes]
rs740778	0.80[ASN][1000 genomes]
rs740779	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
6	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv965888	chr20:52394959-52410541	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	33 gene(s)	inside rSNPs	diseases
8	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
9	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52401800-52403800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52401800-52403800	Enhancers	Primary B cells from peripheral blood	blood
3	chr20:52401800-52404000	Enhancers	Liver	Liver
4	chr20:52401800-52404200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:52401800-52404200	Enhancers	NHEK	skin
6	chr20:52402000-52403600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr20:52402000-52403800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr20:52402000-52403800	Enhancers	Stomach Mucosa	stomach
9	chr20:52402000-52403800	Enhancers	GM12878-XiMat	blood
10	chr20:52402000-52404000	Flanking Active TSS	A549	lung
11	chr20:52402000-52404000	Enhancers	HMEC	breast
12	chr20:52402000-52404200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:52402000-52404400	Enhancers	Duodenum Mucosa	Duodenum
14	chr20:52402000-52407600	Enhancers	Placenta	Placenta
15	chr20:52402200-52403800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr20:52402200-52403800	Enhancers	Fetal Lung	lung
17	chr20:52402200-52404000	Enhancers	Primary B cells from cord blood	blood
18	chr20:52402200-52404200	Enhancers	Fetal Intestine Large	intestine
19	chr20:52402200-52405000	Enhancers	Fetal Intestine Small	intestine
20	chr20:52402200-52409400	Weak transcription	Esophagus	oesophagus
21	chr20:52402400-52403600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr20:52402400-52403600	Enhancers	Primary hematopoietic stem cells	blood
23	chr20:52402400-52403800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr20:52402600-52403600	Enhancers	Fetal Kidney	kidney
25	chr20:52402600-52403800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr20:52402600-52403800	Enhancers	Small Intestine	intestine
27	chr20:52402600-52404000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr20:52402800-52403600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr20:52402800-52403600	Enhancers	Primary T cells from cord blood	blood
30	chr20:52402800-52403600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr20:52402800-52403800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr20:52402800-52403800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr20:52402800-52403800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:52402800-52403800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr20:52402800-52403800	Enhancers	K562	blood
36	chr20:52402800-52404000	Flanking Active TSS	HepG2	liver
37	chr20:52403000-52403800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr20:52403000-52403800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr20:52403000-52403800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr20:52403000-52406200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr20:52403200-52403600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr20:52403200-52403800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr20:52403200-52403800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr20:52403200-52403800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
45	chr20:52403200-52403800	Enhancers	Hela-S3	cervix
46	chr20:52403200-52404400	Enhancers	HUVEC	blood vessel
47	chr20:52403400-52403600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr20:52403400-52403600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr20:52403400-52403800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr20:52403400-52403800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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