Variant report

Variant	rs17044102
Chromosome Location	chr3:17889839-17889840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:17888547..17890733-chr3:17892478..17895359,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10510481	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128860	0.89[EUR][1000 genomes]
rs11128861	0.89[EUR][1000 genomes]
rs11128862	0.89[EUR][1000 genomes]
rs11128863	0.89[EUR][1000 genomes]
rs11128864	0.89[EUR][1000 genomes]
rs11128867	0.89[EUR][1000 genomes]
rs11128868	0.89[EUR][1000 genomes]
rs11128869	0.94[EUR][1000 genomes]
rs11128870	0.89[EUR][1000 genomes]
rs1121174	0.94[EUR][1000 genomes]
rs1121175	0.94[EUR][1000 genomes]
rs11916141	0.89[EUR][1000 genomes]
rs11925066	0.89[EUR][1000 genomes]
rs11925145	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11927436	1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs11927611	0.89[EUR][1000 genomes]
rs12107652	0.89[EUR][1000 genomes]
rs1430897	1.00[EUR][1000 genomes]
rs1430898	1.00[EUR][1000 genomes]
rs17044038	0.89[EUR][1000 genomes]
rs17044041	0.89[EUR][1000 genomes]
rs17044050	0.89[EUR][1000 genomes]
rs17044053	1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs17044054	0.89[EUR][1000 genomes]
rs17044072	0.95[EUR][1000 genomes]
rs17044097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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[TSI][hapmap]
rs17273083	0.94[EUR][1000 genomes]
rs17273090	0.94[EUR][1000 genomes]
rs17273097	0.94[EUR][1000 genomes]
rs17273139	1.00[EUR][1000 genomes]
rs56726310	0.89[EUR][1000 genomes]
rs56777792	0.89[EUR][1000 genomes]
rs58042633	0.89[EUR][1000 genomes]
rs58280814	0.89[EUR][1000 genomes]
rs60744506	0.89[EUR][1000 genomes]
rs61601581	0.89[EUR][1000 genomes]
rs6772619	0.89[EUR][1000 genomes]
rs6780341	0.89[EUR][1000 genomes]
rs6785982	0.89[EUR][1000 genomes]
rs6793958	0.89[EUR][1000 genomes]
rs6794148	0.89[EUR][1000 genomes]
rs73168749	0.89[EUR][1000 genomes]
rs73168750	0.89[EUR][1000 genomes]
rs73168756	0.89[EUR][1000 genomes]
rs73168763	0.89[EUR][1000 genomes]
rs73168777	0.89[EUR][1000 genomes]
rs930147	1.00[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17044102	DDX6	trans	brain	seeQTL
rs17044102	COCH	trans	brain	seeQTL
rs17044102	CD247	trans	brain	seeQTL
rs17044102	ADORA2A	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17888000-17891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:17888400-17892200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:17888600-17892000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:17889400-17890400	Enhancers	Stomach Smooth Muscle	stomach
5	chr3:17889600-17890400	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links