Variant report

Variant	rs1974155
Chromosome Location	chr21:15942216-15942217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:15942072..15943675-chr21:15953537..15956336,2	K562	blood:
2	chr21:15940693..15943113-chr21:15945415..15947276,2	K562	blood:
3	chr21:15920124..15923209-chr21:15941679..15944846,3	K562	blood:
4	chr21:15942194..15946580-chr21:15946989..15950349,5	K562	blood:

Variant related genes	Relation type
ENSG00000155307	Chromatin interaction
ENSG00000223662	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1040341	0.90[ASN][1000 genomes]
rs10854319	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11909106	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12329657	0.82[CHB][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs1882916	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882917	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1980955	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2064024	0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2064025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205365	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2205366	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2223092	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2822761	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap]
rs2822765	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2822767	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs2822776	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2822777	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]
rs3810580	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs3930263	0.87[CHB][hapmap];0.94[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6516880	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7275507	0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7280293	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7282042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9980395	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs9980490	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9981275	0.85[ASN][1000 genomes]
rs9983245	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1056423	chr21:15838309-15948474	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv544376	chr21:15855470-15948474	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1065823	chr21:15863224-15948474	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	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
6	nsv1058533	chr21:15896056-15948474	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv544377	chr21:15896056-15948474	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1974155	SAMSN1	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15938800-15943400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr21:15940200-15944000	Weak transcription	K562	blood
3	chr21:15940200-15946000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr21:15942000-15942600	Weak transcription	GM12878-XiMat	blood
5	chr21:15942200-15943400	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links