Variant report

Variant	rs2822777
Chromosome Location	chr21:15948989-15948990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15942194..15946580-chr21:15946989..15950349,5	K562	blood:
2	chr21:15938738..15940240-chr21:15946079..15949018,2	K562	blood:
3	chr17:57923233..57923880-chr21:15948142..15949029,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1040341	0.86[ASN][1000 genomes]
rs10854319	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11909106	0.87[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12329657	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[TSI][hapmap]
rs1882916	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882917	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1974155	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980955	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2064024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064025	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2205365	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2205366	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223092	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2822761	0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs2822765	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2822767	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs2822776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810580	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs3930263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6516880	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7275507	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs7280293	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs7282042	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9980395	0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap]
rs9980490	0.87[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs9981275	0.81[ASN][1000 genomes]
rs9983245	0.86[CHB][hapmap];0.89[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059591	chr21:15835325-15969195	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1057934	chr21:15863224-15969195	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv834045	chr21:15900678-16112850	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv834046	chr21:15903792-16077369	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470879	chr21:15946828-15964278	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2822777	SAMSN1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15948600-15949000	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links