Variant report

Variant	rs12039915
Chromosome Location	chr1:211587401-211587402
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	chr1:211581760..211583766-chr1:211585922..211587874,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10458470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10494935	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs10863885	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs11119717	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs11119720	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs11119725	1.00[CEU][hapmap];0.86[AMR][1000 genomes]
rs11119727	0.82[ASN][1000 genomes]
rs11119731	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119734	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11577764	0.82[ASN][1000 genomes]
rs12027277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12028306	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12030854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032988	0.92[EUR][1000 genomes]
rs12033418	0.96[AMR][1000 genomes]
rs12035966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12039683	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12065190	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12080561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12085730	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12097572	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17017360	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs17017401	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes]
rs2175633	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2289758	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920907	0.81[ASN][1000 genomes]
rs3738201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3738202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4443952	0.82[ASN][1000 genomes]
rs4951521	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4951743	0.82[ASN][1000 genomes]
rs57093875	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58164259	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58510761	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60169087	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61624054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663729	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6684356	0.81[ASN][1000 genomes]
rs6698113	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6698191	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs7540368	0.82[ASN][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	esv2762141	chr1:211538685-211603843	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
2	esv1824154	chr1:211565640-211614280	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211556800-211589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:211573800-211589600	Weak transcription	Ovary	ovary
3	chr1:211574000-211589600	Weak transcription	Liver	Liver
4	chr1:211575400-211588800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:211580400-211589600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:211581400-211608200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:211581800-211589600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:211581800-211589600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:211581800-211589600	Weak transcription	Gastric	stomach
10	chr1:211581800-211590600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:211585000-211589400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:211585400-211593200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:211587000-211589400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:211587400-211589400	Weak transcription	Brain Hippocampus Middle	brain

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