Variant report

Variant	rs7679303
Chromosome Location	chr4:110786517-110786518
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	chr4:110623136..110625842-chr4:110784972..110787630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138794	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11724973	0.87[CEU][hapmap]
rs11733397	0.82[CEU][hapmap]
rs12642452	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13107617	0.80[AMR][1000 genomes]
rs13115969	0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs1990250	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2190908	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347129	0.81[EUR][1000 genomes]
rs3188897	0.82[MEX][hapmap]
rs4035486	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698797	1.00[CEU][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6533469	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533470	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814789	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6827802	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7438763	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs764205	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7654140	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7654660	0.96[CEU][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7679048	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];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	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7679303	RRH	cis	parietal	SCAN
rs7679303	LRIT3	cis	cerebellum	SCAN
rs7679303	RRH	cis	cerebellum	SCAN
rs7679303	CYP2U1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110780400-110795000	Weak transcription	Esophagus	oesophagus
2	chr4:110786000-110791000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:110786200-110796600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:110786400-110790600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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