Variant report

Variant	rs12488127
Chromosome Location	chr3:161123526-161123527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:161003253..161016100-chr3:161121496..161137189,33	MCF-7	breast:
2	chr3:160939797..160942710-chr3:161123467..161125153,2	MCF-7	breast:
3	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
4	chr3:161057222..161057922-chr3:161123207..161123785,2	MCF-7	breast:
5	chr3:160816959..160819020-chr3:161122102..161124044,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1017799	0.89[JPT][hapmap]
rs12486111	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12486998	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12487002	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490149	1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs12491623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12494520	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13319558	0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs13319771	0.88[JPT][hapmap]
rs1450518	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2035499	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2306209	1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes]
rs4352387	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs4468992	0.89[JPT][hapmap]
rs56839556	0.94[ASN][1000 genomes]
rs58851337	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58892449	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59193340	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59368066	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6441375	1.00[GIH][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs6762064	1.00[GIH][hapmap]
rs6774919	1.00[GIH][hapmap]
rs6775446	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs6775931	0.89[JPT][hapmap]
rs6781086	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6782415	0.89[JPT][hapmap]
rs6782518	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs6785714	0.82[JPT][hapmap]
rs6787697	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6793980	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6795310	0.84[YRI][hapmap]
rs73878309	0.85[AMR][1000 genomes]
rs73878323	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878329	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7614130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	0.89[JPT][hapmap]
rs7629841	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7634299	0.89[JPT][hapmap]
rs7651924	0.89[JPT][hapmap];0.82[AMR][1000 genomes]
rs9819793	0.86[JPT][hapmap]
rs9822705	0.85[AMR][1000 genomes]
rs9822916	0.88[JPT][hapmap]
rs9824805	0.89[JPT][hapmap]
rs9833270	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs9835530	0.89[JPT][hapmap]
rs9847842	1.00[GIH][hapmap];0.89[JPT][hapmap]
rs9851699	0.82[AMR][1000 genomes]
rs9855572	0.82[AMR][1000 genomes]
rs9859641	0.88[JPT][hapmap]
rs9860980	0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs9862867	0.89[JPT][hapmap]
rs9871753	1.00[GIH][hapmap]
rs9877309	0.84[JPT][hapmap]
rs9880536	0.89[JPT][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases
5	nsv524747	chr3:161120483-161123526	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161113600-161127600	Weak transcription	NHEK	skin
2	chr3:161119000-161124400	Weak transcription	Liver	Liver
3	chr3:161121200-161124800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:161121200-161125000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:161121200-161126600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:161121400-161126800	Weak transcription	Hela-S3	cervix
7	chr3:161121600-161124400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:161123000-161124000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:161123000-161127400	Enhancers	HepG2	liver
10	chr3:161123200-161125000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:161123200-161125200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:161123200-161125600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:161123200-161126000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:161123200-161132000	Enhancers	Stomach Mucosa	stomach
15	chr3:161123400-161124800	Enhancers	Fetal Thymus	thymus
16	chr3:161123400-161125200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:161123400-161125200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:161123400-161125400	Enhancers	Primary T cells from cord blood	blood

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