Variant report

Variant	rs11958808
Chromosome Location	chr5:44945090-44945091
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:44940944..44943906-chr5:44945067..44947395,2	K562	blood:
2	chr5:44943887..44946643-chr5:44948508..44950374,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10040082	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10040488	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10041518	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10044096	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10045264	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10054773	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10057521	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10059086	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060878	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10063172	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10064434	0.87[EUR][1000 genomes]
rs10065638	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10069220	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10070037	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10462081	0.81[ASN][1000 genomes]
rs10473376	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10473377	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1048758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10512865	0.88[EUR][1000 genomes]
rs1061310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11741772	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11746506	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11746980	0.87[EUR][1000 genomes]
rs11948387	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11948636	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11949847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11951760	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11957920	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11958451	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12109710	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12188871	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12517690	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12651949	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs13155698	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs13157608	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13159598	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13160259	0.88[EUR][1000 genomes]
rs13168400	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13174122	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs13177711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13183209	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs13187933	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13189120	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs1371023	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1371025	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1438819	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1438820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1438822	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438827	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1821934	0.88[EUR][1000 genomes]
rs1866406	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs2118764	0.88[EUR][1000 genomes]
rs2330572	0.82[EUR][1000 genomes]
rs2877172	0.85[EUR][1000 genomes]
rs34501299	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3761648	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3761650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4129642	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4329028	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4395640	0.85[EUR][1000 genomes]
rs4412123	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4457088	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4457089	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4518409	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4642377	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866783	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4866784	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866920	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57300972	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6451781	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6867533	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes]
rs6868232	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6868779	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870136	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6871820	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6872254	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6875287	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6881563	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6894324	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6896350	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6896417	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs727304	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs727305	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7380559	0.88[EUR][1000 genomes]
rs7703059	0.81[ASN][1000 genomes]
rs7703618	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7705343	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7708506	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7711136	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7711697	0.88[EUR][1000 genomes]
rs7716571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7717459	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs7720787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7728431	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7730841	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9292913	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9292914	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9292915	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs930394	0.81[ASN][1000 genomes]
rs9637783	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9790879	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9790896	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9791056	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791059	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9791164	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987394	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv880483	chr5:44827292-45038026	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11958808	RP11-53O19.3	cis	Nerve Tibial	GTEx
rs11958808	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:44942200-44946000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:44943000-44946400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:44943400-44945600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr5:44943400-44945600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr5:44943400-44946000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:44943400-44946400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:44943400-44946400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:44944800-44945200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:44944800-44946000	Weak transcription	H1 Cell Line	embryonic stem cell

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