Variant report

Variant	rs3943621
Chromosome Location	chr15:53092610-53092611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:53091716..53093481-chr15:53093879..53095531,2	MCF-7	breast:
2	chr15:53078999..53085478-chr15:53088216..53096885,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ONECUT1-1	chr15:53092221-53093114	XLOC_011481
2	lnc-ONECUT1-1	chr15:53092407-53093114	XLOC_011481

Variant related genes	Relation type
ENSG00000169856	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12440218	1.00[EUR][1000 genomes]
rs17652361	1.00[EUR][1000 genomes]
rs17708832	1.00[EUR][1000 genomes]
rs1899753	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075613	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34850380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3858909	0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3858910	0.86[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53090800-53092800	Bivalent Enhancer	HepG2	liver
2	chr15:53091400-53094200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:53091400-53095400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr15:53091400-53095600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:53091600-53095400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr15:53091800-53092800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
7	chr15:53091800-53092800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
8	chr15:53092000-53094200	Enhancers	Liver	Liver
9	chr15:53092200-53094200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr15:53092400-53092800	Bivalent Enhancer	Primary T cells from cord blood	blood
11	chr15:53092400-53094200	Enhancers	Pancreas	Pancrea
12	chr15:53092600-53092800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
13	chr15:53092600-53092800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:53092600-53092800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
15	chr15:53092600-53092800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:53092600-53092800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:53092600-53092800	Bivalent Enhancer	Lung	lung
18	chr15:53092600-53093400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr15:53092600-53093400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr15:53092600-53093600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr15:53092600-53093800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood

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