Variant report

Variant	rs12404544
Chromosome Location	chr1:119993357-119993358
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	chr1:119915031..119915964-chr1:119992237..119993475,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10802096	0.87[EUR][1000 genomes]
rs10923830	1.00[EUR][1000 genomes]
rs10923833	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11804864	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12406375	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12406401	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12407939	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818928	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60945833	0.91[EUR][1000 genomes]
rs6673366	1.00[EUR][1000 genomes]
rs6677283	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693235	0.87[EUR][1000 genomes]
rs6693243	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6701346	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6701556	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74113567	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74113568	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74113578	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524361	1.00[EUR][1000 genomes]
rs7531186	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	esv3431786	chr1:119977797-120005821	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	38 gene(s)	inside rSNPs	diseases
10	nsv470733	chr1:119991429-120018155	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv946177	chr1:119991531-120004718	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119986200-119995800	Weak transcription	Right Atrium	heart
2	chr1:119989800-119993800	Weak transcription	Fetal Intestine Small	intestine
3	chr1:119992800-119993400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr1:119992800-119993600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:119992800-119995600	Enhancers	Liver	Liver
6	chr1:119993000-119993400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:119993000-119994400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:119993000-119995000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:119993000-119995200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:119993200-119994000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr1:119993200-119994400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:119993200-119996600	Enhancers	Fetal Intestine Large	intestine

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