Variant report

Variant	rs6013944
Chromosome Location	chr20:52885852-52885853
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52885360..52886093-chr20:52967759..52968496,2	MCF-7	breast:
2	chr20:52884699..52888516-chr20:52964644..52967204,3	MCF-7	breast:
3	chr20:49347658..49349686-chr20:52884532..52886332,2	MCF-7	breast:
4	chr20:52836483..52840611-chr20:52882316..52886295,8	MCF-7	breast:
5	chr20:52885262..52886034-chr20:53264976..53265669,2	MCF-7	breast:
6	chr20:52823148..52829420-chr20:52882441..52888238,13	MCF-7	breast:
7	chr20:52864263..52865094-chr20:52885677..52886537,2	MCF-7	breast:
8	chr20:52883328..52886194-chr20:52903780..52906080,2	MCF-7	breast:
9	chr20:52739968..52740956-chr20:52885332..52886103,2	MCF-7	breast:
10	chr20:52765381..52766270-chr20:52885301..52885922,2	MCF-7	breast:
11	chr20:52884175..52887299-chr20:52959985..52962637,4	MCF-7	breast:
12	chr20:52885191..52887868-chr20:55839667..55841629,2	MCF-7	breast:
13	chr20:52739897..52740786-chr20:52885429..52886265,2	MCF-7	breast:
14	chr20:52843780..52845745-chr20:52884098..52886121,2	MCF-7	breast:
15	chr20:52883714..52887393-chr20:53262850..53265125,5	MCF-7	breast:
16	chr20:52832813..52835165-chr20:52884473..52886237,2	MCF-7	breast:
17	chr20:52885127..52886115-chr7:8008156..8008786,2	MCF-7	breast:
18	chr15:65596894..65598661-chr20:52883990..52886001,2	MCF-7	breast:
19	chr20:52885163..52887679-chr20:53176549..53178400,2	MCF-7	breast:
20	chr20:52835744..52843522-chr20:52881395..52889377,15	MCF-7	breast:
21	chr20:52823141..52827110-chr20:52881540..52888271,10	MCF-7	breast:
22	chr20:52740380..52740956-chr20:52885457..52886103,2	MCF-7	breast:
23	chr20:52885398..52886107-chr20:53073038..53073570,3	MCF-7	breast:
24	chr20:52884195..52887005-chr20:53073312..53075000,2	MCF-7	breast:
25	chr20:52881899..52886453-chr20:53260602..53265051,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1293132	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs1293137	0.81[EUR][1000 genomes]
rs1293144	0.85[CEU][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs1298513	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1382015	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1477730	0.89[ASN][1000 genomes]
rs1542523	0.84[EUR][1000 genomes]
rs2061721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2153964	0.83[EUR][1000 genomes]
rs2153965	0.83[EUR][1000 genomes]
rs2185849	0.85[EUR][1000 genomes]
rs2585418	0.81[CEU][hapmap]
rs2616330	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2616335	0.83[EUR][1000 genomes]
rs292120	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs292123	0.89[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs292125	0.89[CEU][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs292126	0.89[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs292132	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs292139	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs292141	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs292143	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs292144	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs292146	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs368933	0.87[CEU][hapmap]
rs6013925	0.81[CEU][hapmap]
rs6013960	0.81[EUR][1000 genomes]
rs6023082	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6127152	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv178887	chr20:52885413-52894836	Enhancers Weak transcription	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6013944	AURKA	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52883400-52886600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr20:52883600-52886000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:52883600-52886000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:52883600-52886200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr20:52883600-52886200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr20:52883800-52886000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr20:52883800-52886000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:52884000-52886000	Enhancers	Fetal Lung	lung
9	chr20:52884000-52889400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr20:52884600-52889200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr20:52885000-52889600	Weak transcription	Pancreas	Pancrea
12	chr20:52885200-52889600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr20:52885200-52889600	Weak transcription	Ovary	ovary
14	chr20:52885600-52886000	Enhancers	HepG2	liver
15	chr20:52885600-52889000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr20:52885800-52889200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr20:52885800-52889600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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