Variant report

Variant	rs3212656
Chromosome Location	chr5:52283027-52283028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52278874..52281430-chr5:52281937..52284347,4	MCF-7	breast:
2	chr5:52277482..52279538-chr5:52282210..52284601,2	K562	blood:
3	chr5:52243208..52246085-chr5:52282017..52284486,2	MCF-7	breast:
4	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:
5	chr5:52282372..52286768-chr5:52384365..52386788,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247796	Chromatin interaction
ENSG00000164172	Chromatin interaction
ENSG00000272123	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10513004	0.84[EUR][1000 genomes]
rs10940280	0.84[EUR][1000 genomes]
rs11738606	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739571	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742694	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11742813	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11748504	0.84[EUR][1000 genomes]
rs11749081	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12186544	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13156420	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13165509	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13179969	0.83[EUR][1000 genomes]
rs13180488	0.85[EUR][1000 genomes]
rs1421943	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1592795	0.81[EUR][1000 genomes]
rs3212383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212414	0.81[EUR][1000 genomes]
rs34288275	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34352729	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34512129	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34865297	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35597318	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657730	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35862618	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35926366	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4865755	0.92[EUR][1000 genomes]
rs6859171	0.83[EUR][1000 genomes]
rs7702766	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7713782	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9791046	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52273600-52283800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:52279000-52283400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:52279000-52283400	Enhancers	HUVEC	blood vessel
4	chr5:52279200-52283400	Enhancers	HMEC	breast
5	chr5:52279200-52284000	Enhancers	NHEK	skin
6	chr5:52279200-52284200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:52279400-52283200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:52279400-52283200	Enhancers	Hela-S3	cervix
9	chr5:52279400-52283400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:52280200-52283200	Weak transcription	NH-A	brain
11	chr5:52280800-52283200	Weak transcription	A549	lung
12	chr5:52280800-52283200	Weak transcription	NHLF	lung
13	chr5:52281000-52283400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:52281200-52283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:52281200-52283200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:52281200-52283800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:52281600-52283200	Weak transcription	Osteobl	bone
18	chr5:52281600-52283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:52281600-52283600	Weak transcription	NHDF-Ad	bronchial
20	chr5:52282200-52283200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:52282400-52283400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:52282400-52283600	Enhancers	HepG2	liver
23	chr5:52282600-52284400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:52282800-52284600	Weak transcription	Lung	lung
25	chr5:52283000-52283400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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