Variant report

Variant	rs1421970
Chromosome Location	chr5:107769095-107769096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107717097..107719488-chr5:107767902..107770636,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10477892	0.92[JPT][hapmap]
rs11742777	0.90[JPT][hapmap]
rs12655232	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs13153782	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs13161833	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs13173916	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1544741	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs1588496	0.92[JPT][hapmap]
rs17161232	1.00[ASW][hapmap];0.83[CEU][hapmap];0.92[JPT][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs17452232	0.92[JPT][hapmap]
rs1828457	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs1849012	0.83[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1862196	0.92[JPT][hapmap]
rs2052464	0.92[JPT][hapmap]
rs2900122	1.00[YRI][hapmap]
rs2941693	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2941694	0.83[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2941697	1.00[ASW][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2966830	0.92[JPT][hapmap]
rs2966832	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2966834	0.92[JPT][hapmap]
rs4957755	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs4957756	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6594298	0.92[JPT][hapmap]
rs6594299	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6896653	0.92[JPT][hapmap];0.86[MEX][hapmap]
rs7711964	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs7724056	0.83[JPT][hapmap]
rs7726485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9326726	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs981755	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs988436	1.00[ASW][hapmap];0.90[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs988437	0.92[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	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv2587611	chr5:107769092-107769095	Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv2386566	chr5:107769092-107769096	Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1421970	NCRNA00219	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107767600-107769200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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