Variant report

Variant	rs60065065
Chromosome Location	chr15:53087427-53087428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr15:53086521-53088992	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:53087400-53087550	GM12875	blood:	n/a	chr15:53087414-53087427
3	SUZ12	chr15:53086684-53088933	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-11	chr15:53086548-53087549	XLOC_011257

Variant related genes	Relation type
ONECUT1	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10518694	0.92[EUR][1000 genomes]
rs2120450	0.88[EUR][1000 genomes]
rs2243790	0.96[EUR][1000 genomes]
rs2440315	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2440316	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2440322	0.92[EUR][1000 genomes]
rs2440376	0.93[EUR][1000 genomes]
rs2456506	0.98[ASN][1000 genomes]
rs2456507	0.95[EUR][1000 genomes]
rs2456522	0.97[EUR][1000 genomes]
rs2456523	0.87[ASN][1000 genomes]
rs2456524	0.97[EUR][1000 genomes]
rs2456525	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456526	0.97[EUR][1000 genomes]
rs2456529	0.91[EUR][1000 genomes]
rs2456530	0.85[EUR][1000 genomes]
rs2456532	0.93[EUR][1000 genomes]
rs2460	0.98[ASN][1000 genomes]
rs28475375	0.87[EUR][1000 genomes]
rs7180600	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53083600-53088400	Weak transcription	Pancreas	Pancrea
2	chr15:53083600-53088600	Weak transcription	Liver	Liver
3	chr15:53086600-53087800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr15:53086800-53087800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr15:53086800-53087800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
6	chr15:53086800-53088000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
7	chr15:53087000-53088200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr15:53087000-53088600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:53087200-53087600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:53087200-53088000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
11	chr15:53087400-53087600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:53087400-53087600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:53087400-53087600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr15:53087400-53087600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
15	chr15:53087400-53087800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
16	chr15:53087400-53087800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr15:53087400-53088000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr15:53087400-53088000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:53087400-53088400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr15:53087400-53090200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links