Variant report

Variant	rs55822707
Chromosome Location	chr4:57762210-57762211
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-REST-2	chr4:57762056-57762743	refGeneNc_4399_NR_034081

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10008356	0.93[ASN][1000 genomes]
rs10030913	0.96[ASN][1000 genomes]
rs10866440	0.96[ASN][1000 genomes]
rs10866441	0.85[ASN][1000 genomes]
rs1105434	0.88[ASN][1000 genomes]
rs11727329	0.83[EUR][1000 genomes]
rs11730321	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11730476	0.88[ASN][1000 genomes]
rs11730525	0.98[ASN][1000 genomes]
rs11734953	0.94[ASN][1000 genomes]
rs11736192	0.86[ASN][1000 genomes]
rs11736869	0.88[ASN][1000 genomes]
rs11736965	0.87[ASN][1000 genomes]
rs11737689	0.83[ASN][1000 genomes]
rs11933908	0.98[ASN][1000 genomes]
rs12500454	0.88[ASN][1000 genomes]
rs12501224	0.85[ASN][1000 genomes]
rs12501990	0.88[ASN][1000 genomes]
rs12502076	0.84[ASN][1000 genomes]
rs13108245	0.94[ASN][1000 genomes]
rs13113802	0.95[ASN][1000 genomes]
rs13116564	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13125082	0.81[EUR][1000 genomes]
rs13130600	0.83[EUR][1000 genomes]
rs13131605	0.83[ASN][1000 genomes]
rs13136432	0.85[ASN][1000 genomes]
rs13146960	0.95[ASN][1000 genomes]
rs13149162	0.99[ASN][1000 genomes]
rs13150593	0.85[ASN][1000 genomes]
rs13152476	0.86[ASN][1000 genomes]
rs13353552	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1877669	0.98[ASN][1000 genomes]
rs1963666	0.82[ASN][1000 genomes]
rs2002153	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014870	0.85[ASN][1000 genomes]
rs2090962	0.95[ASN][1000 genomes]
rs3000	0.98[ASN][1000 genomes]
rs34124552	0.85[ASN][1000 genomes]
rs34448457	0.85[ASN][1000 genomes]
rs35267092	0.85[ASN][1000 genomes]
rs3806745	0.88[ASN][1000 genomes]
rs4276341	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4864606	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4864607	0.99[ASN][1000 genomes]
rs4864608	0.88[ASN][1000 genomes]
rs4865156	0.88[ASN][1000 genomes]
rs4865157	0.91[ASN][1000 genomes]
rs4865158	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4865159	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4865160	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56122758	0.89[ASN][1000 genomes]
rs62308110	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62308111	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62308135	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62308136	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62308137	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62308155	0.86[ASN][1000 genomes]
rs6554393	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6554394	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6554397	0.98[ASN][1000 genomes]
rs6554398	0.96[ASN][1000 genomes]
rs6816950	0.88[ASN][1000 genomes]
rs6835102	0.88[ASN][1000 genomes]
rs6835108	0.88[ASN][1000 genomes]
rs6838948	0.98[ASN][1000 genomes]
rs6839845	0.86[ASN][1000 genomes]
rs6840805	0.88[ASN][1000 genomes]
rs6852110	0.88[ASN][1000 genomes]
rs6854420	0.98[ASN][1000 genomes]
rs6855212	0.95[ASN][1000 genomes]
rs6857005	0.88[ASN][1000 genomes]
rs6857226	0.88[ASN][1000 genomes]
rs6858216	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs71601656	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs729844	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73242609	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7666804	0.95[ASN][1000 genomes]
rs7667302	0.95[ASN][1000 genomes]
rs7680734	0.88[ASN][1000 genomes]
rs7695970	0.98[ASN][1000 genomes]
rs899632	0.95[ASN][1000 genomes]
rs9684742	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55822707	RP11-738E22.3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57761600-57773000	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links