Variant report

Variant	rs6064045
Chromosome Location	chr20:52701293-52701294
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52686610..52687511-chr20:52701157..52702126,3	MCF-7	breast:
2	chr20:52699786..52702321-chr7:44193459..44196461,3	MCF-7	breast:
3	chr20:46612981..46615231-chr20:52699973..52702715,2	MCF-7	breast:
4	chr20:46419051..46422145-chr20:52700320..52703232,3	MCF-7	breast:
5	chr20:52701214..52702166-chr20:52739951..52740819,4	MCF-7	breast:
6	chr17:56734545..56738013-chr20:52696672..52702961,12	MCF-7	breast:
7	chr20:52700468..52702286-chr20:52872421..52874639,2	MCF-7	breast:
8	chr17:57920620..57923516-chr20:52699929..52701690,2	MCF-7	breast:
9	chr20:46475461..46477684-chr20:52701066..52703629,2	MCF-7	breast:
10	chr12:16502598..16504840-chr20:52700346..52703261,2	MCF-7	breast:
11	chr17:57913465..57916226-chr20:52700387..52703244,3	MCF-7	breast:
12	chr20:52701238..52702114-chr20:52811547..52812555,3	MCF-7	breast:
13	chr20:52686969..52687485-chr20:52701292..52702100,2	MCF-7	breast:
14	chr20:52701238..52701958-chr20:52719706..52720239,2	MCF-7	breast:
15	chr20:52684089..52684879-chr20:52701289..52702251,3	MCF-7	breast:
16	chr20:46412955..46417498-chr20:52699874..52705785,9	MCF-7	breast:
17	chr20:52701223..52702039-chr20:52815896..52817066,3	MCF-7	breast:
18	chr20:52686259..52688022-chr20:52700895..52702301,5	MCF-7	breast:
19	chr17:56707745..56710309-chr20:52697502..52703858,9	MCF-7	breast:
20	chr17:56735122..56737701-chr20:52700294..52703497,3	MCF-7	breast:
21	chr20:41014614..41017340-chr20:52700025..52702300,3	MCF-7	breast:
22	chr17:56716754..56717639-chr20:52701243..52701770,2	MCF-7	breast:
23	chr20:46412091..46416534-chr20:52700009..52706788,8	MCF-7	breast:
24	chr20:52686917..52687488-chr20:52701281..52702008,3	MCF-7	breast:
25	chr20:52701149..52702080-chr20:52811523..52812597,5	MCF-7	breast:
26	chr20:52698958..52701623-chr20:55839587..55843056,3	MCF-7	breast:
27	chr17:56703018..56712407-chr20:52697460..52725685,93	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064787	Chromatin interaction
ENSG00000008394	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11699339	0.83[MEX][hapmap]
rs13041834	0.89[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543703	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6064043	0.83[MEX][hapmap]
rs6068773	0.83[AMR][1000 genomes]
rs6068774	0.82[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs6068776	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6512935	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

Variant related diseases (count:1)

Disease	PMID	Source
IgG glycosylation	23382691	GWAS catalog

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52699200-52707000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr20:52700800-52702800	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr20:52700800-52703800	Enhancers	Stomach Mucosa	stomach
4	chr20:52701000-52706600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr20:52701200-52701600	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr20:52701200-52702000	Flanking Active TSS	A549	lung
7	chr20:52701200-52702400	Weak transcription	Gastric	stomach
8	chr20:52701200-52702600	Enhancers	HepG2	liver
9	chr20:52701200-52703000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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