Variant report

Variant	rs6793958
Chromosome Location	chr3:17853056-17853057
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17784350..17786060-chr3:17852299..17855085,2	K562	blood:
2	chr3:17850838..17853208-chr3:17856384..17858538,2	MCF-7	breast:

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10510478	0.87[CHD][hapmap]
rs10510481	0.89[EUR][1000 genomes]
rs11128836	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs11128838	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs11128849	0.85[CHB][hapmap]
rs11128850	0.85[CHB][hapmap]
rs11128860	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128862	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128863	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128864	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128865	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11128866	0.93[ASN][1000 genomes]
rs11128867	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128868	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128869	0.94[EUR][1000 genomes]
rs11128870	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121174	0.94[EUR][1000 genomes]
rs1121175	0.94[EUR][1000 genomes]
rs11914537	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs11915560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs11916141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916424	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs11923589	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs11923635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs11924147	0.85[AMR][1000 genomes]
rs11925066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925145	0.94[EUR][1000 genomes]
rs11925226	0.85[AMR][1000 genomes]
rs11926087	0.83[YRI][hapmap]
rs11927436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927611	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11927654	0.85[CHB][hapmap]
rs11927769	0.95[YRI][hapmap]
rs11927967	0.83[YRI][hapmap]
rs11929046	0.85[AMR][1000 genomes]
rs12106899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs12106900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12107061	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12107652	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374023	1.00[CEU][hapmap]
rs13076724	0.85[CHB][hapmap]
rs1430897	0.89[EUR][1000 genomes]
rs1430898	0.89[EUR][1000 genomes]
rs17044038	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044041	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044050	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044054	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044072	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17044097	0.89[EUR][1000 genomes]
rs17044102	0.89[EUR][1000 genomes]
rs17200923	0.94[EUR][1000 genomes]
rs17200930	0.94[EUR][1000 genomes]
rs17200937	0.94[EUR][1000 genomes]
rs17200944	0.94[EUR][1000 genomes]
rs17273076	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs17273083	0.94[EUR][1000 genomes]
rs17273090	0.94[EUR][1000 genomes]
rs17273097	0.94[EUR][1000 genomes]
rs17273139	0.89[EUR][1000 genomes]
rs2033378	0.85[CHB][hapmap]
rs28456004	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4260468	0.85[CHB][hapmap]
rs4377510	0.85[CHB][hapmap]
rs4611850	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs4637311	1.00[JPT][hapmap]
rs4908965	0.85[CHB][hapmap]
rs4908967	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs56726310	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56777792	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57816103	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58042633	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58280814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58921548	0.85[AMR][1000 genomes]
rs60245392	0.85[AMR][1000 genomes]
rs60744506	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60838916	0.85[AMR][1000 genomes]
rs61601581	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61650046	0.85[AMR][1000 genomes]
rs6577595	0.85[AMR][1000 genomes]
rs6577629	0.87[ASW][hapmap];0.83[YRI][hapmap]
rs6763348	0.85[AMR][1000 genomes]
rs6772619	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777064	0.85[AMR][1000 genomes]
rs6780341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786472	1.00[AMR][1000 genomes]
rs6794148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807020	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs73168749	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168750	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168752	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73168756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168763	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73168777	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73172909	0.85[AMR][1000 genomes]
rs73172914	0.85[AMR][1000 genomes]
rs73172924	0.85[AMR][1000 genomes]
rs7619879	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7620585	0.95[YRI][hapmap]
rs7627732	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs7648122	0.83[YRI][hapmap]
rs7651998	0.85[CHB][hapmap]
rs8179891	0.85[CHB][hapmap]
rs930147	0.89[EUR][1000 genomes]
rs9310528	0.85[CHB][hapmap]
rs9839588	0.82[CHB][hapmap]
rs9849948	1.00[ASN][1000 genomes]
rs992521	0.94[EUR][1000 genomes]
rs992522	0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6793958	ARAP3	trans	brain	seeQTL
rs6793958	CD247	trans	brain	seeQTL
rs6793958	DCAF7	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17850200-17853200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:17850400-17853200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:17850400-17853200	Enhancers	NHDF-Ad	bronchial
4	chr3:17850400-17853200	Enhancers	Osteobl	bone
5	chr3:17850400-17853600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:17851400-17861000	Weak transcription	Right Atrium	heart
7	chr3:17851800-17853200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:17852400-17853200	Enhancers	NHLF	lung

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