Variant report

Variant	rs2870337
Chromosome Location	chr20:53276305-53276306
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	chr20:53272210..53276849-chr3:64512036..64515886,4	MCF-7	breast:
2	chr20:53275192..53277053-chr8:102504518..102506807,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083307	Chromatin interaction
ENSG00000254024	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1012643	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13040265	1.00[CHD][hapmap]
rs1474763	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1569985	1.00[CHD][hapmap]
rs1983702	1.00[CHD][hapmap]
rs1997834	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs2870333	1.00[CHD][hapmap]
rs2870340	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2904389	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4334548	1.00[CHD][hapmap]
rs4362623	0.82[EUR][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6014111	0.81[EUR][1000 genomes]
rs6014112	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023367	1.00[CHD][hapmap]
rs6023406	1.00[CHD][hapmap]
rs6023423	1.00[CHD][hapmap]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap]
rs6023474	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023475	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6064093	1.00[CHD][hapmap]
rs6064102	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6068924	1.00[CHD][hapmap]
rs6068935	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098108	1.00[CHD][hapmap]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
rs6127251	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7263678	1.00[CHD][hapmap]
rs7270451	1.00[CHD][hapmap]
rs7270971	1.00[CHD][hapmap]
rs8115071	1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][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	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53267000-53277200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr20:53275800-53276400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:53275800-53277600	Weak transcription	Fetal Brain Female	brain
4	chr20:53276000-53276400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr20:53276000-53276400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr20:53276000-53276400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:53276000-53276400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr20:53276000-53280600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:53276200-53276400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr20:53276200-53276400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr20:53276200-53276400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr20:53276200-53277000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:53276200-53277600	Weak transcription	Fetal Brain Male	brain
14	chr20:53276200-53278400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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