Variant report

Variant	rs838525
Chromosome Location	chr1:119882235-119882236
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	chr1:119874569..119876262-chr1:119880980..119883218,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10802089	0.82[EUR][1000 genomes]
rs1409056	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1891224	0.82[EUR][1000 genomes]
rs2153738	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2226102	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2243981	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2253988	0.82[EUR][1000 genomes]
rs2254528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2254664	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2257016	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2265628	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2265629	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2265630	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477889	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477890	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672571	0.82[EUR][1000 genomes]
rs6694847	1.00[MEX][hapmap]
rs699771	0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs838512	0.94[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs838513	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs838514	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838515	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs838516	0.87[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838517	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838519	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838520	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs838523	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838524	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs838526	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs838527	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs838537	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs838538	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs866788	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs947422	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs947423	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs947424	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs947425	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv2761649	chr1:119840645-119925936	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr1:119870800-119883400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:119875000-119886600	Weak transcription	GM12878-XiMat	blood
3	chr1:119875200-119883600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:119876000-119884000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:119878600-119891200	Enhancers	Liver	Liver
6	chr1:119879000-119883400	Enhancers	HepG2	liver
7	chr1:119879800-119885800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:119880200-119882600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:119881000-119884000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:119881400-119882600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:119881600-119882600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr1:119881600-119886400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:119882000-119883800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:119882000-119883800	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:119882200-119882400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:119882200-119882400	Enhancers	Placenta	Placenta

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