Variant report

Variant	rs12417601
Chromosome Location	chr11:119981205-119981206
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	chr11:119598394..119601999-chr11:119977722..119981899,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction
ENSG00000254854	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1073634	0.98[ASN][1000 genomes]
rs1073636	0.98[ASN][1000 genomes]
rs10892536	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10892538	0.96[ASN][1000 genomes]
rs10892542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110704	0.91[ASN][1000 genomes]
rs11217678	0.86[ASN][1000 genomes]
rs11217679	0.82[ASN][1000 genomes]
rs11217683	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11217684	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11217685	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11217690	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11217691	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11217692	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11217693	0.91[ASN][1000 genomes]
rs11217694	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11217696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217697	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11217699	0.81[AMR][1000 genomes]
rs11604169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12418174	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12418635	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12419706	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12421654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276159	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2368961	0.95[ASN][1000 genomes]
rs3781667	0.86[AMR][1000 genomes]
rs3781668	0.86[AMR][1000 genomes]
rs3781669	0.86[AMR][1000 genomes]
rs3895896	0.86[ASN][1000 genomes]
rs3896312	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3915646	0.88[ASN][1000 genomes]
rs4938776	0.88[ASN][1000 genomes]
rs4938778	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57144901	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58043425	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6589795	0.93[ASN][1000 genomes]
rs6589798	0.93[ASN][1000 genomes]
rs6589800	0.98[ASN][1000 genomes]
rs6589801	0.98[ASN][1000 genomes]
rs7109733	0.88[ASN][1000 genomes]
rs7118773	0.91[ASN][1000 genomes]
rs7131339	0.95[ASN][1000 genomes]
rs7938843	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119978800-119982600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:119979600-119981400	Weak transcription	Esophagus	oesophagus
3	chr11:119979600-119984600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:119979600-119988800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:119979800-119981400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:119980000-119981800	Weak transcription	HMEC	breast
7	chr11:119980000-119981800	Weak transcription	NHEK	skin
8	chr11:119980000-119983000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:119980000-119983800	Weak transcription	Hela-S3	cervix
10	chr11:119980400-119981600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:119980800-119981800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:119980800-119982000	Weak transcription	Placenta	Placenta

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