Variant report

Variant	rs2884808
Chromosome Location	chr3:54641568-54641569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRTM1-5	chr3:54641193-54641874	ucscGeneNc_uc003dhj_2

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10510769	0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510770	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510771	1.00[JPT][hapmap]
rs10510772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1130197	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914640	1.00[ASN][1000 genomes]
rs11914780	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914973	1.00[JPT][hapmap]
rs11920788	1.00[JPT][hapmap]
rs11924275	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11925949	1.00[JPT][hapmap]
rs12185982	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1427774	1.00[ASN][1000 genomes]
rs17054227	1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054246	0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17054250	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17054291	1.00[JPT][hapmap]
rs17054293	1.00[JPT][hapmap]
rs17054340	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17815617	1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816548	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17816566	1.00[ASN][1000 genomes]
rs1863858	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2359857	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs28455661	1.00[ASN][1000 genomes]
rs34478567	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41381544	1.00[ASN][1000 genomes]
rs4345041	1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4358270	0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs4386460	1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675480	1.00[ASN][1000 genomes]
rs55772258	1.00[ASN][1000 genomes]
rs55779022	0.88[EUR][1000 genomes]
rs56008232	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56091855	0.88[EUR][1000 genomes]
rs56112781	1.00[ASN][1000 genomes]
rs56209938	1.00[ASN][1000 genomes]
rs56260111	0.87[EUR][1000 genomes]
rs56356828	0.86[EUR][1000 genomes]
rs56976748	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57924227	1.00[ASN][1000 genomes]
rs58295654	1.00[ASN][1000 genomes]
rs59004379	1.00[ASN][1000 genomes]
rs62255527	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255532	0.88[EUR][1000 genomes]
rs62255533	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255534	1.00[ASN][1000 genomes]
rs62255535	1.00[ASN][1000 genomes]
rs62255536	1.00[ASN][1000 genomes]
rs62255538	1.00[ASN][1000 genomes]
rs6803005	0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs72870661	1.00[ASN][1000 genomes]
rs72870676	1.00[ASN][1000 genomes]
rs72870688	1.00[ASN][1000 genomes]
rs72872218	1.00[ASN][1000 genomes]
rs72872226	1.00[ASN][1000 genomes]
rs72872229	1.00[ASN][1000 genomes]
rs72872244	1.00[ASN][1000 genomes]
rs72872259	1.00[ASN][1000 genomes]
rs72872285	1.00[ASN][1000 genomes]
rs72874203	1.00[ASN][1000 genomes]
rs72874204	1.00[ASN][1000 genomes]
rs73068445	1.00[ASN][1000 genomes]
rs737517	1.00[JPT][hapmap]
rs7624695	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking 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
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv818141	chr3:54639209-54641568	Inactive region	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2884808	IQCF1	cis	cerebellum	SCAN
rs2884808	ESRG	cis	Whole Blood	GTEx
rs2884808	DNAH12	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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