Variant report

Variant	rs7972407
Chromosome Location	chr12:84896663-84896664
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	chr12:82752258..82753057-chr12:84896534..84897103,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133773	Chromatin interaction
ENSG00000127720	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10862876	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10862877	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116361	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11116366	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11116367	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11116413	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11116428	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11116429	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116431	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116434	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116435	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116436	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11116487	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs1380406	0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1380407	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011948	0.81[ASN][1000 genomes]
rs4469935	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60610518	0.80[AFR][1000 genomes]
rs7954812	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955870	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7957168	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970336	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970452	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv899363	chr12:84450824-84940345	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv899365	chr12:84511125-84940345	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899369	chr12:84536107-85067814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1035863	chr12:84710250-85331290	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1035236	chr12:84790507-85350433	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv430521	chr12:84886467-84926332	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv899373	chr12:84891803-84999922	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	4 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	chr12:84895400-84896800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:84895600-84897000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:84895600-84897600	Enhancers	HMEC	breast
4	chr12:84895800-84897000	Enhancers	Hela-S3	cervix
5	chr12:84895800-84897000	Enhancers	NHEK	skin
6	chr12:84896000-84897000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:84896000-84897200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:84896200-84897000	Enhancers	HUVEC	blood vessel
9	chr12:84896200-84897400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:84896400-84897000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:84896400-84897000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:84896400-84897000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:84896400-84897000	Enhancers	Colon Smooth Muscle	Colon
14	chr12:84896600-84897000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:84896600-84897000	Enhancers	NHDF-Ad	bronchial
16	chr12:84896600-84897200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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