Variant report

Variant	rs2869461
Chromosome Location	chr4:76920893-76920894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76918050..76921353-chr4:76922033..76925702,4	K562	blood:
2	chr4:76918050..76921353-chr4:76922033..76925702,3	K562	blood:
3	chr4:76919294..76923061-chr4:76987395..76990335,3	MCF-7	breast:
4	chr4:76912055..76913763-chr4:76918600..76921053,2	K562	blood:

Variant related genes	Relation type
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10019066	1.00[JPT][hapmap]
rs10222911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1050176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856871	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11097192	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12499668	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12500200	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504915	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12509996	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12511352	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12511357	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs12511359	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12511861	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13106039	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1554015	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17001275	0.83[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17001284	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1910907	0.97[ASN][1000 genomes]
rs28703679	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733236	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4621456	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4859412	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55964684	0.88[ASN][1000 genomes]
rs56039229	0.88[ASN][1000 genomes]
rs56316945	0.88[ASN][1000 genomes]
rs58909712	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59559903	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61279846	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6532084	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6532167	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6532168	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6532169	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6532170	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs66477189	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs67210456	0.97[ASN][1000 genomes]
rs67297326	0.97[ASN][1000 genomes]
rs67413521	0.88[ASN][1000 genomes]
rs67687266	0.91[ASN][1000 genomes]
rs6828744	0.97[ASN][1000 genomes]
rs6834291	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6847716	0.97[ASN][1000 genomes]
rs6857358	1.00[ASN][1000 genomes]
rs72651387	0.97[ASN][1000 genomes]
rs7349626	0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7666094	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7670156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671125	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7679689	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7684879	0.82[ASN][1000 genomes]
rs7685390	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7692605	0.82[CHB][hapmap]
rs7693606	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7696286	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.97[ASN][1000 genomes]
rs9998233	0.85[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]

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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2869461	NAAA	cis	lymphoblastoid	seeQTL
rs2869461	ASAHL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76912400-76932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76920400-76924200	Enhancers	Fetal Intestine Small	intestine
3	chr4:76920600-76921600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:76920600-76922000	Enhancers	Pancreas	Pancrea
5	chr4:76920600-76924200	Enhancers	Fetal Intestine Large	intestine

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