Variant report

Variant	rs2408509
Chromosome Location	chr12:46735303-46735304
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	chr12:46660537..46663877-chr12:46734524..46736795,3	MCF-7	breast:
2	chr12:46661464..46663971-chr12:46734593..46736197,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10506267	0.89[CHB][hapmap];1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	0.94[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183467	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11183482	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs1125908	0.94[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11834905	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12299499	0.84[CHB][hapmap]
rs12317255	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs12321512	0.89[CHB][hapmap]
rs13377959	0.83[CHB][hapmap]
rs17096884	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17096896	0.89[CHB][hapmap]
rs17096922	0.82[CHB][hapmap]
rs1948425	0.84[JPT][hapmap]
rs2125646	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2307059	0.84[JPT][hapmap]
rs2307062	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2307063	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742061	0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56222195	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57067899	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57149475	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57425661	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60977966	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61232019	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61406609	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73282561	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73282591	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7954314	0.83[CHB][hapmap]
rs7967889	0.83[CHB][hapmap]
rs923788	1.00[EUR][1000 genomes];0.84[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3423694	chr12:46733685-46745567	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46708800-46736200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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