Variant report

Variant	rs2870333
Chromosome Location	chr20:53249180-53249181
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:53249127..53250955-chr20:53263341..53265497,2	MCF-7	breast:
2	chr20:53239460..53242242-chr20:53249088..53250613,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs1569985	1.00[CHD][hapmap]
rs1983702	1.00[CHD][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2224269	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2904387	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3918505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4334548	1.00[CHD][hapmap]
rs4809969	1.00[CHD][hapmap]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
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];0.94[GIH][hapmap]
rs6023474	1.00[CHD][hapmap]
rs6064093	1.00[CHD][hapmap]
rs6064102	1.00[CHD][hapmap]
rs6068924	0.85[CEU][hapmap];1.00[CHD][hapmap];0.85[EUR][1000 genomes]
rs6098108	1.00[CHD][hapmap]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
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:6 , 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	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
2	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:53241400-53249800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:53242400-53249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:53243000-53249600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:53243000-53249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr20:53244600-53249600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr20:53244600-53249800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr20:53246400-53249800	Weak transcription	Brain Germinal Matrix	brain
11	chr20:53246600-53251000	Enhancers	Fetal Brain Male	brain
12	chr20:53246800-53250000	Weak transcription	Fetal Muscle Leg	muscle
13	chr20:53248200-53249800	Weak transcription	Fetal Brain Female	brain
14	chr20:53248800-53249200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr20:53248800-53250400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr20:53249000-53249200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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