Variant report

Variant	rs2389880
Chromosome Location	chr4:120559870-120559871
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10009566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012252	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022185	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10050092	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098534	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737395	0.82[EUR][1000 genomes]
rs12499377	0.88[EUR][1000 genomes]
rs12504773	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505735	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12512646	0.87[EUR][1000 genomes]
rs12642411	0.89[ASN][1000 genomes]
rs13101722	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13122709	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13136462	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13140391	0.80[EUR][1000 genomes]
rs13140409	0.80[EUR][1000 genomes]
rs17051352	0.87[ASN][1000 genomes]
rs2389874	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389879	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2389882	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2389885	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2389886	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2389887	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28394116	0.86[EUR][1000 genomes]
rs28535956	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28578366	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28787668	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28850368	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34278750	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34835603	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756156	0.86[EUR][1000 genomes]
rs3806808	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4504231	0.88[EUR][1000 genomes]
rs4833624	0.86[EUR][1000 genomes]
rs58583086	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59867181	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6534149	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6829903	0.82[EUR][1000 genomes]
rs6832740	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6833334	0.80[EUR][1000 genomes]
rs6855918	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7664440	0.89[ASN][1000 genomes]
rs7669520	0.82[EUR][1000 genomes]
rs7671096	0.87[ASN][1000 genomes]
rs7676296	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680914	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7693919	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7695292	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1802546	chr4:120558608-120675026	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv3343433	chr4:120559454-120562352	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2389880	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_chr	lymphoblastoid	RTeQTL
rs2389880	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs2389880	RP11-33B1.1	cis	lung	GTEx
rs2389880	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2389880	RP11-33B1.1	cis	Whole Blood	GTEx
rs2389880	RP11-33B1.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120558600-120560000	Enhancers	Fetal Stomach	stomach
2	chr4:120559000-120560000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:120559400-120560000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:120559400-120560000	Enhancers	NHDF-Ad	bronchial
5	chr4:120559400-120560000	Enhancers	NHLF	lung
6	chr4:120559400-120561000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:120559600-120560000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:120559800-120567800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links