Variant report

Variant	rs2180462
Chromosome Location	chr20:53256245-53256246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52834718..52835643-chr20:53256141..53256960,2	MCF-7	breast:
2	chr20:53250383..53253224-chr20:53254055..53257121,4	MCF-7	breast:
3	chr20:52824537..52826295-chr20:53254798..53257293,2	MCF-7	breast:
4	chr20:53235605..53237909-chr20:53254058..53257053,2	MCF-7	breast:
5	chr20:52981982..52984941-chr20:53255246..53257720,2	MCF-7	breast:
6	chr20:53254267..53257182-chr20:53259848..53265627,6	MCF-7	breast:
7	chr20:52821463..52842130-chr20:53255769..53272087,93	MCF-7	breast:
8	chr20:53242261..53247525-chr20:53253994..53258088,8	MCF-7	breast:
9	chr20:53255269..53257076-chr20:53258321..53260016,2	K562	blood:
10	chr20:53073165..53075653-chr20:53254316..53256773,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs1569982	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1569983	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1569984	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1569985	0.84[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs1983702	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2904388	0.91[GIH][hapmap]
rs4302265	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4334548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs4811514	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6014081	1.00[CHD][hapmap]
rs6014103	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6014105	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6014106	1.00[CHD][hapmap];0.91[GIH][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]
rs6023441	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6023474	1.00[CHD][hapmap]
rs6064093	1.00[CHD][hapmap]
rs6064100	0.93[AMR][1000 genomes]
rs6064102	1.00[CHD][hapmap]
rs6068924	1.00[CHD][hapmap]
rs6068929	0.91[CEU][hapmap];0.97[AMR][1000 genomes];0.95[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	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
6	esv2760673	chr20:53254815-53258810	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2180462	SALL4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:53249600-53259800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:53250600-53259800	Weak transcription	Fetal Brain Female	brain
4	chr20:53250800-53256800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr20:53250800-53256800	Weak transcription	Brain Germinal Matrix	brain
6	chr20:53250800-53260000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:53251000-53256400	Weak transcription	Fetal Brain Male	brain
8	chr20:53254000-53259800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:53255600-53256400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr20:53255600-53256400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr20:53255600-53256800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr20:53255600-53256800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr20:53256000-53256400	Weak transcription	H9 Cell Line	embryonic stem cell

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