Variant report

Variant	rs6517474
Chromosome Location	chr21:40023133-40023134
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	chr21:40021665..40023567-chr21:40158455..40160815,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ETS2-6	chr21:40022929-40023481	NONHSAT082115

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1041780	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836604	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836616	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836618	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2836622	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836625	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836627	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836636	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28379071	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28446127	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718905	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs458465	0.96[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs464519	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4817954	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55742466	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55819392	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56154327	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62217558	0.87[ASN][1000 genomes]
rs733540	0.84[EUR][1000 genomes]
rs743447	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8126719	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8126858	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8134675	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9976018	0.87[CEU][hapmap];0.81[CHD][hapmap];0.94[LWK][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap]
rs9976546	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9979396	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9979424	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9979888	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9981408	0.87[CEU][hapmap]
rs9982483	0.88[EUR][1000 genomes]
rs9983626	0.90[EUR][1000 genomes];0.83[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	nsv1065541	chr21:40009959-40024976	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1057719	chr21:40009959-40025433	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1058663	chr21:40009959-40031681	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1055287	chr21:40013735-40031681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6517474	ATP5O	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40016000-40027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:40016200-40024000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40021400-40023800	Weak transcription	Aorta	Aorta
4	chr21:40022400-40024000	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links