Variant report

Variant	rs12438264
Chromosome Location	chr15:56063653-56063654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56061686..56064215-chr15:56064871..56066642,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1011061	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10152116	0.83[AFR][1000 genomes]
rs11639086	0.83[AFR][1000 genomes]
rs11852746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11857254	1.00[CHB][hapmap]
rs12439011	0.83[AFR][1000 genomes]
rs12440103	0.83[AFR][1000 genomes]
rs12899976	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12907557	0.83[AFR][1000 genomes]
rs12908232	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12909497	1.00[CHB][hapmap]
rs12915092	0.83[AFR][1000 genomes]
rs12915888	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12916744	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550326	1.00[CHB][hapmap]
rs3985768	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4774222	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs491014	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs530798	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8028880	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8036481	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934886	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9920546	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12438264	MYO5C	cis	parietal	SCAN
rs12438264	CCPG1	cis	parietal	SCAN
rs12438264	PRTG	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56057400-56069400	Weak transcription	Right Atrium	heart
2	chr15:56057400-56078800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:56061200-56066200	Weak transcription	Hela-S3	cervix
4	chr15:56061400-56066600	Weak transcription	Placenta	Placenta
5	chr15:56061600-56065600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:56062600-56063800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:56063400-56065600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:56063400-56065600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:56063400-56065800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:56063400-56067200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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