Variant report

Variant	rs787196
Chromosome Location	chr3:120026928-120026929
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	chr3:120025111..120027109-chr3:120067982..120069603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163428	Chromatin interaction
ENSG00000240661	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10048964	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1085614	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085616	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1085617	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147681	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147688	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147689	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1147690	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11914405	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11928731	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13318758	0.84[AMR][1000 genomes]
rs13318838	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327125	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1625178	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716855	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1716856	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1733326	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1733328	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2638597	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28535957	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28826066	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6764516	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6767308	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6777979	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6799005	0.81[AMR][1000 genomes]
rs6808913	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs787186	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787187	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787189	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787190	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787192	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787193	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787200	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787205	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs787206	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787207	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs787208	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs809792	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923729	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs951658	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9810784	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9822636	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9822759	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9851711	0.84[AMR][1000 genomes]
rs9856670	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9876547	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120022800-120028600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:120024400-120029400	Weak transcription	NHEK	skin
3	chr3:120024400-120032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:120024600-120032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
7	chr3:120026600-120030600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:120026800-120030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:120026800-120032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:120026800-120032600	Weak transcription	Pancreas	Pancrea
13	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:120026800-120067200	Weak transcription	Aorta	Aorta

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