Variant report

Variant	rs1459247
Chromosome Location	chr3:48387709-48387710
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	chr3:48341909..48344364-chr3:48387381..48390289,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172113	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11130161	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12630599	0.85[EUR][1000 genomes]
rs12633518	0.82[JPT][hapmap]
rs13062576	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13094578	0.82[JPT][hapmap]
rs1380053	1.00[JPT][hapmap]
rs1380260	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1459243	0.95[EUR][1000 genomes]
rs1459244	0.95[EUR][1000 genomes]
rs1459245	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17080119	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1870441	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34138269	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34146962	0.84[AFR][1000 genomes]
rs34537842	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34857497	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs35703936	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3731532	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3731539	1.00[YRI][hapmap]
rs3731547	1.00[YRI][hapmap]
rs3969942	0.82[JPT][hapmap]
rs4858813	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4858814	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4858818	1.00[YRI][hapmap]
rs7434077	1.00[JPT][hapmap]
rs876597	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835902	1.00[JPT][hapmap]
rs9851771	1.00[JPT][hapmap]
rs9852211	1.00[YRI][hapmap]
rs986739	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs986740	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs986741	0.90[EUR][1000 genomes]
rs986742	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48377600-48387800	Weak transcription	Placenta	Placenta
2	chr3:48386200-48387800	Enhancers	HSMM	muscle
3	chr3:48386800-48388000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:48387200-48387800	Enhancers	HSMMtube	muscle
5	chr3:48387400-48388200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:48387600-48387800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:48387600-48387800	Enhancers	NHEK	skin
8	chr3:48387600-48388000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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