Variant report

Variant	rs3812059
Chromosome Location	chr5:126625259-126625260
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:126625240-126625390	HVMF	connective:	n/a	n/a
2	RAD21	chr5:126625061-126626744	SK-N-SH	brain:	n/a	chr5:126625793-126625812 chr5:126625773-126625786 chr5:126626401-126626415
3	CTCF	chr5:126625075-126626720	SK-N-SH	brain:	n/a	chr5:126626266-126626279 chr5:126626266-126626275
4	SMC3	chr5:126624919-126627050	SK-N-SH	brain:	n/a	chr5:126626775-126626785

Variant related genes	Relation type
MEGF10	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10519949	1.00[CEU][hapmap]
rs12652963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12652982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12653273	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12654455	1.00[CEU][hapmap]
rs12655913	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12658126	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12659381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12659424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17684438	1.00[CEU][hapmap]
rs17684525	1.00[CEU][hapmap]
rs17762857	1.00[CEU][hapmap]
rs17762863	1.00[CEU][hapmap]
rs17839701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55638823	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57164852	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58011598	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58047377	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58727001	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59871357	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60138783	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6862045	1.00[CEU][hapmap]
rs73785546	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73785547	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73785555	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73785556	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73785558	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7723558	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7728190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs960927	0.93[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	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126623200-126625400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:126625200-126625600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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