Variant report

Variant	rs16909520
Chromosome Location	chr11:5085254-5085255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:5084774-5085447	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr11:5085099-5085320	HepG2	liver:	n/a	n/a
3	MAFK	chr11:5085178-5085298	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:5085239..5087074-chr11:5090783..5092387,2	K562	blood:
2	chr11:5078947..5082286-chr11:5082776..5087870,5	K562	blood:
3	11:5083896-5087036..11:5525863-5527719	GM12878	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR52E2-1	chr11:5085244-5085336	NONHSAT017660

No data

Variant related genes	Relation type
OR52E2	TF binding region
ENSG00000273085	Chromatin interaction
ENSG00000167355	Chromatin interaction
ENSG00000213931	Chromatin interaction
ENSG00000196565	Chromatin interaction
ENSG00000176787	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10500619	0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10500620	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12577596	0.86[ASN][1000 genomes]
rs12577999	0.83[ASN][1000 genomes]
rs16909513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267239	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs17267785	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs17268128	0.83[ASN][1000 genomes]
rs17342397	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs17342537	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs17350764	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17351915	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs17352264	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17352781	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2500055	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55657818	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58664826	0.86[ASN][1000 genomes]
rs61880477	0.83[ASN][1000 genomes]
rs61880508	1.00[ASN][1000 genomes]
rs61880509	0.86[ASN][1000 genomes]
rs61880510	0.86[ASN][1000 genomes]
rs7109263	0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv553219	chr11:5026200-5214413	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
8	nsv896919	chr11:5060941-5095774	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv896920	chr11:5068137-5221825	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv896921	chr11:5074301-5097802	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv975827	chr11:5080931-5104221	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16909520	OR51F1	cis	parietal	SCAN
rs16909520	TH	cis	parietal	SCAN
rs16909520	OR52N4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5084800-5085600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links