Variant report

Variant	rs4656122
Chromosome Location	chr1:86619342-86619343
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86617696..86619956-chr1:86620495..86622655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171502	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11161736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161738	0.81[ASN][1000 genomes]
rs11161741	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11161742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023254	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12024954	0.80[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12048065	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12057841	0.81[ASN][1000 genomes]
rs12057874	0.81[ASN][1000 genomes]
rs12057993	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12075854	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12117437	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12117849	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12118936	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs12120396	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507266	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1507284	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2039602	0.81[ASN][1000 genomes]
rs2039603	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2039604	0.81[ASN][1000 genomes]
rs2390014	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2892909	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs55713534	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55740735	0.85[EUR][1000 genomes]
rs55912038	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57251624	0.81[ASN][1000 genomes]
rs61802232	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802233	0.81[ASN][1000 genomes]
rs61802236	0.81[ASN][1000 genomes]
rs61802237	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802238	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61802243	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6576806	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663055	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6663057	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6675364	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6675562	0.81[ASN][1000 genomes]
rs6678131	0.81[ASN][1000 genomes]
rs6686446	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6690591	0.92[CEU][hapmap]
rs6690902	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67222626	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72716178	0.88[EUR][1000 genomes]
rs7550559	1.00[JPT][hapmap]
rs7550571	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9660356	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9660357	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2763578	chr1:86584695-86622285	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 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	chr1:86616400-86620000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:86617400-86620600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:86617800-86620000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:86617800-86620000	Weak transcription	NH-A	brain
5	chr1:86617800-86620000	Weak transcription	NHEK	skin
6	chr1:86617800-86621600	Weak transcription	HSMM	muscle
7	chr1:86618000-86620200	Weak transcription	NHDF-Ad	bronchial
8	chr1:86618200-86620000	Enhancers	Rectal Smooth Muscle	rectum
9	chr1:86618200-86620400	Enhancers	Colon Smooth Muscle	Colon
10	chr1:86618400-86620000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:86618600-86620400	Enhancers	Fetal Lung	lung
12	chr1:86619000-86619800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:86619200-86619600	Weak transcription	Osteobl	bone
14	chr1:86619200-86620400	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links