Variant report

Variant	rs2553218
Chromosome Location	chr15:54868668-54868669
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:54867084..54868948-chr15:54872476..54874542,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10152437	0.95[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10152907	0.85[CHB][hapmap]
rs10468009	0.81[AFR][1000 genomes]
rs11639005	0.84[MEX][hapmap]
rs12438101	0.83[EUR][1000 genomes]
rs12908706	0.80[EUR][1000 genomes]
rs12909682	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs12914472	0.88[CEU][hapmap]
rs1402111	0.84[JPT][hapmap]
rs16974861	0.85[CEU][hapmap]
rs1818705	0.81[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1850998	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2056342	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs2414326	0.85[CHB][hapmap]
rs2553222	0.85[CEU][hapmap]
rs2553223	0.85[CEU][hapmap]
rs2553227	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs2681954	0.92[CEU][hapmap]
rs2681956	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2681969	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2899546	0.95[CHB][hapmap]
rs35584128	0.84[EUR][1000 genomes]
rs4109295	0.90[CHB][hapmap]
rs605869	0.91[ASW][hapmap];0.95[CHB][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs6493687	0.95[CHB][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap]
rs7163424	0.85[CEU][hapmap]
rs7164826	0.84[JPT][hapmap]
rs7180226	0.84[JPT][hapmap]
rs746321	0.92[CEU][hapmap]
rs8023595	0.81[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8023918	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs8028630	0.92[CEU][hapmap]
rs8032415	0.95[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8039515	1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8040048	0.83[EUR][1000 genomes]
rs8040060	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs8040619	0.82[EUR][1000 genomes]
rs8040774	0.89[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs8041576	0.82[EUR][1000 genomes]
rs8042341	0.85[CEU][hapmap]
rs9920919	0.85[CHB][hapmap]

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	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immune response to smallpox vaccine (IL-6)	22542470	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2553218	AP4E1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54811000-54869600	Weak transcription	Aorta	Aorta
2	chr15:54867600-54871200	Enhancers	Fetal Lung	lung
3	chr15:54868600-54869600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links