Variant report

Variant	rs6759275
Chromosome Location	chr2:113231682-113231683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113230273..113231905-chr2:113335611..113338554,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000207383	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11679929	1.00[ASN][1000 genomes]
rs11682795	0.85[CEU][hapmap]
rs11685514	0.85[CEU][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap]
rs11688511	0.85[CEU][hapmap]
rs12987434	1.00[ASN][1000 genomes]
rs12988536	1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13021601	0.84[AMR][1000 genomes]
rs13025468	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465817	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs1561266	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs34047777	1.00[ASN][1000 genomes]
rs34263686	1.00[ASN][1000 genomes]
rs34364366	1.00[ASN][1000 genomes]
rs34892661	1.00[ASN][1000 genomes]
rs36086865	1.00[ASN][1000 genomes]
rs3961916	0.92[CEU][hapmap];1.00[ASN][1000 genomes]
rs4516428	0.85[CEU][hapmap]
rs62158651	1.00[ASN][1000 genomes]
rs6542056	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs6707618	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.92[AMR][1000 genomes]
rs6708841	1.00[ASN][1000 genomes]
rs6708927	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs67178025	1.00[ASN][1000 genomes]
rs6726169	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs6729910	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6757757	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71414672	1.00[ASN][1000 genomes]
rs71414673	1.00[ASN][1000 genomes]
rs7570679	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs7573493	1.00[ASN][1000 genomes]
rs7586685	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6759275	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx
rs6759275	ZC3H8	cis	Artery Tibial	GTEx
rs6759275	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6759275	RGPD8	cis	Artery Tibial	GTEx
rs6759275	RGPD8	cis	Esophagus Mucosa	GTEx
rs6759275	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6759275	RGPD8	cis	Nerve Tibial	GTEx
rs6759275	RGPD8	cis	Whole Blood	GTEx
rs6759275	RGPD8	cis	lung	GTEx
rs6759275	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6759275	RGPD8	cis	Muscle Skeletal	GTEx
rs6759275	TTL	cis	parietal	SCAN
rs6759275	RGPD8	cis	Heart Left Ventricle	GTEx
rs6759275	RGPD8	cis	Esophagus Muscularis	GTEx
rs6759275	RGPD8	cis	Thyroid	GTEx
rs6759275	RGPD8	cis	Artery Aorta	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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