Variant report

Variant	rs9395500
Chromosome Location	chr6:49479930-49479931
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	chr6:49477846..49480791-chr6:49486673..49489629,2	MCF-7	breast:
2	chr6:49477015..49478603-chr6:49479650..49481514,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10755760	0.82[AFR][1000 genomes]
rs12190131	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12214753	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1480611	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1480612	0.88[ASN][1000 genomes]
rs1480613	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1480614	0.84[AFR][1000 genomes]
rs1480615	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947861	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2061972	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2061973	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2127754	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2127755	0.82[AFR][1000 genomes]
rs2396911	0.82[AFR][1000 genomes]
rs2498470	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2498471	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2498472	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2501969	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2501970	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2501971	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4367370	0.82[AFR][1000 genomes]
rs4715134	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6942364	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7453050	0.82[AFR][1000 genomes]
rs7740682	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7757014	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9296618	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9357618	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367357	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369904	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381791	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9381792	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395499	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463489	0.81[AFR][1000 genomes]
rs9463491	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463492	0.83[AFR][1000 genomes]
rs9463493	0.84[AFR][1000 genomes]
rs9473567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9473568	0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap]
rs9473582	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv3398270	chr6:49468042-49488082	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9395500	MUT	cis	multi-tissue	Pritchard
rs9395500	CENPQ	cis	lymphoblastoid	seeQTL
rs9395500	FBXO9	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49475200-49481000	Weak transcription	Stomach Mucosa	stomach
2	chr6:49478200-49480200	Weak transcription	HepG2	liver
3	chr6:49479200-49481000	Enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links