Variant report

Variant	rs894054
Chromosome Location	chr4:80542408-80542409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10022663	0.91[EUR][1000 genomes]
rs1031005	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs11098770	0.84[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs11098788	0.94[ASN][1000 genomes]
rs11098789	0.93[ASN][1000 genomes]
rs11728755	0.87[EUR][1000 genomes]
rs11941782	0.91[EUR][1000 genomes]
rs12643491	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs13104009	0.93[EUR][1000 genomes]
rs13112067	0.91[EUR][1000 genomes]
rs13112577	0.91[EUR][1000 genomes]
rs1371989	0.93[EUR][1000 genomes]
rs1371993	0.92[EUR][1000 genomes]
rs1440853	0.93[EUR][1000 genomes]
rs1837645	0.89[EUR][1000 genomes]
rs1837646	0.90[EUR][1000 genomes]
rs1866835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2165386	0.93[EUR][1000 genomes]
rs2582681	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2709847	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109166	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3943669	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs4389603	0.93[EUR][1000 genomes]
rs4975056	0.93[EUR][1000 genomes]
rs62297619	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62297620	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62297622	0.86[AMR][1000 genomes]
rs6812760	0.93[EUR][1000 genomes]
rs6850999	0.93[EUR][1000 genomes]
rs7688923	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs894055	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9307545	0.84[CEU][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs9307551	0.92[EUR][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	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879507	chr4:80365765-80552199	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv879508	chr4:80398708-80552199	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs894054	PPEF2	cis	parietal	SCAN
rs894054	LINC00989	cis	Skin Sun Exposed Lower leg	GTEx
rs894054	LINC00989	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80541600-80543200	Enhancers	K562	blood
2	chr4:80541800-80548600	Enhancers	Rectal Smooth Muscle	rectum
3	chr4:80542200-80543600	Weak transcription	Colon Smooth Muscle	Colon

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