Variant report

Variant	rs1540949
Chromosome Location	chr6:164049551-164049552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:164046203..164050114-chr6:164051224..164053273,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1234977	1.00[CHB][hapmap]
rs1744929	1.00[CHB][hapmap]
rs2757573	1.00[CHB][hapmap]
rs2757585	1.00[CHB][hapmap]
rs2759396	1.00[CHB][hapmap]
rs4709000	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709730	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4709731	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902395	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744302	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749197	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751246	1.00[ASN][1000 genomes]
rs7754222	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs783139	1.00[CHB][hapmap]
rs803612	1.00[CHB][hapmap]
rs912028	1.00[ASN][1000 genomes]
rs9347765	1.00[CHB][hapmap]
rs9365575	1.00[CHB][hapmap]
rs9458843	1.00[CHB][hapmap]
rs9458860	1.00[CHB][hapmap]

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	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2758092	chr6:163992064-164161903	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2759490	chr6:163992064-164161903	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3379217	chr6:164048812-164050810	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:164048000-164061600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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