Variant report

Variant	rs1395489
Chromosome Location	chr12:62048478-62048479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62048195..62048935-chr12:62399595..62401023,3	MCF-7	breast:
2	chr12:62048211..62049119-chr12:62586208..62587064,4	MCF-7	breast:
3	chr12:62048165..62049231-chr12:62387283..62388132,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10747941	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747942	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784252	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10784264	0.83[CEU][hapmap]
rs10877716	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1354787	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395492	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395494	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1506847	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1506848	0.93[EUR][1000 genomes]
rs1605325	0.93[EUR][1000 genomes]
rs1876278	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1911247	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983133	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2168452	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs2360681	0.92[CEU][hapmap]
rs2360682	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310677	0.91[EUR][1000 genomes]
rs4495952	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6581408	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581415	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581416	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581418	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581419	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581426	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs6581430	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs6581432	1.00[CEU][hapmap]
rs7135492	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136512	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137928	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297180	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7301397	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303770	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306730	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314715	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7398155	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7487386	0.92[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]
rs7488724	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954202	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7957259	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959668	0.92[CEU][hapmap]
rs7960162	0.84[CEU][hapmap]
rs7964077	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974958	0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[EUR][1000 genomes]
rs7977950	0.92[CEU][hapmap];0.92[CHB][hapmap]
rs9783426	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv1042044	chr12:61256015-62196885	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1039741	chr12:62046850-62491052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62047800-62048600	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr12:62047800-62049000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr12:62047800-62049200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr12:62047800-62049400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr12:62047800-62049400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:62048000-62048800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:62048200-62048600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:62048200-62049200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr12:62048200-62049400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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