Variant report

Variant	rs1425053
Chromosome Location	chr8:120212990-120212991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:120211698..120216543-chr8:120218864..120221677,6	MCF-7	breast:
2	chr8:120210402..120213161-chr8:120216090..120218568,2	MCF-7	breast:
3	chr8:120210122..120216646-chr8:120218897..120222949,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147676	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10096921	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113336	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13252588	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1364706	0.87[CHB][hapmap]
rs1364708	0.86[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs1385491	0.82[JPT][hapmap]
rs1425052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1485291	0.82[JPT][hapmap]
rs1485292	0.82[JPT][hapmap]
rs1541726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1549415	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17182246	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs1905774	0.82[JPT][hapmap]
rs2326222	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450060	0.88[JPT][hapmap]
rs2450063	0.82[JPT][hapmap]
rs2450073	0.82[JPT][hapmap]
rs2450079	0.82[JPT][hapmap]
rs2465370	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2465373	0.92[ASN][1000 genomes]
rs2465377	0.92[ASN][1000 genomes]
rs2465379	0.92[ASN][1000 genomes]
rs2465389	0.82[JPT][hapmap]
rs2468171	0.80[CHB][hapmap]
rs2468173	0.84[ASN][1000 genomes]
rs2468184	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2468186	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4279627	0.82[JPT][hapmap]
rs4870897	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4871362	0.87[CHB][hapmap]
rs6994957	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs7000127	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7000278	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7386676	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7825089	0.87[CHB][hapmap]
rs9656931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2758169	chr8:119943309-120275750	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2759639	chr8:119943309-120275750	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Osteoprotegerin levels	25080503	GWAS catalog

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120211800-120213000	Enhancers	Hela-S3	cervix
2	chr8:120212000-120213000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:120212600-120213400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:120212600-120213400	Enhancers	Placenta	Placenta
5	chr8:120212600-120213600	Enhancers	NHEK	skin
6	chr8:120212600-120213800	Enhancers	Adipose Nuclei	Adipose
7	chr8:120212800-120213000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:120212800-120213400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr8:120212800-120213400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:120212800-120213600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:120212800-120213600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:120212800-120213600	Enhancers	HMEC	breast
13	chr8:120212800-120218600	Weak transcription	Esophagus	oesophagus

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