Variant report

Variant	rs1899752
Chromosome Location	chr15:53092937-53092938
allele	A/G
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: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2165991	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2243790	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2440315	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2440316	0.97[EUR][1000 genomes]
rs2440352	0.80[CEU][hapmap]
rs2440374	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2456506	0.94[EUR][1000 genomes]
rs2456523	0.91[EUR][1000 genomes]
rs2456531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs28687152	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[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:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53091400-53094200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:53091400-53095400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr15:53091400-53095600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:53091600-53095400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
5	chr15:53092000-53094200	Enhancers	Liver	Liver
6	chr15:53092200-53094200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr15:53092400-53094200	Enhancers	Pancreas	Pancrea
8	chr15:53092600-53093400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr15:53092600-53093400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
10	chr15:53092600-53093600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
11	chr15:53092600-53093800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
12	chr15:53092800-53093000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:53092800-53093000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
14	chr15:53092800-53093000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:53092800-53093000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:53092800-53093000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:53092800-53093000	Bivalent Enhancer	Fetal Brain Male	brain
18	chr15:53092800-53093000	Bivalent Enhancer	Fetal Heart	heart
19	chr15:53092800-53093000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
20	chr15:53092800-53093200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr15:53092800-53093200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:53092800-53093400	Bivalent Enhancer	Brain Germinal Matrix	brain
23	chr15:53092800-53093600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr15:53092800-53093600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr15:53092800-53093800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
26	chr15:53092800-53094000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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