Variant report

Variant	rs4679856
Chromosome Location	chr3:159109216-159109217
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	chr3:159025201..159027938-chr3:159107782..159110251,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1011374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12487721	0.84[CHD][hapmap]
rs12495863	0.87[CHD][hapmap]
rs13434321	0.86[CEU][hapmap]
rs1375409	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1448999	0.86[CEU][hapmap]
rs1449004	0.95[CEU][hapmap];0.82[MEX][hapmap]
rs1449006	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1449013	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1489922	0.82[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs1515627	0.91[CEU][hapmap]
rs16830350	0.84[CHD][hapmap]
rs2220521	0.82[CEU][hapmap]
rs2365835	0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2621302	0.86[CEU][hapmap]
rs4086062	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4440163	0.83[YRI][hapmap]
rs4680509	0.87[CHD][hapmap]
rs6441256	0.80[EUR][1000 genomes]
rs6441260	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6441261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6782775	0.95[CEU][hapmap]
rs7621541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7629746	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs7632141	0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7643870	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs878382	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs895876	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9290039	0.83[YRI][hapmap]
rs9290040	0.91[CEU][hapmap]
rs9834663	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1004990	chr3:159090974-159174954	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4679856	C3orf57	cis	cerebellum	SCAN
rs4679856	SCARNA7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159108400-159109400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr3:159108600-159109600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links