Variant report

Variant	rs4348928
Chromosome Location	chr11:70889037-70889038
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:70888498..70892014-chr11:70961351..70964884,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162105	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10897725	0.88[EUR][1000 genomes]
rs10897726	0.86[CEU][hapmap];0.82[CHB][hapmap];0.88[EUR][1000 genomes]
rs11232300	0.82[EUR][1000 genomes]
rs11232301	0.81[EUR][1000 genomes]
rs11232304	0.81[EUR][1000 genomes]
rs12271307	0.86[EUR][1000 genomes]
rs12272223	0.84[EUR][1000 genomes]
rs12273513	0.81[EUR][1000 genomes]
rs12273863	0.81[EUR][1000 genomes]
rs12274896	0.82[EUR][1000 genomes]
rs12282822	0.86[EUR][1000 genomes]
rs12289383	0.81[EUR][1000 genomes]
rs17431746	0.81[EUR][1000 genomes]
rs28811899	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28876818	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34402475	0.96[EUR][1000 genomes]
rs35136877	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245462	0.87[EUR][1000 genomes]
rs4304805	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs4334036	0.87[EUR][1000 genomes]
rs4944245	0.88[EUR][1000 genomes]
rs4944282	0.92[ASN][1000 genomes]
rs55664123	0.84[EUR][1000 genomes]
rs55726773	0.84[EUR][1000 genomes]
rs55988920	0.84[EUR][1000 genomes]
rs56035448	0.84[EUR][1000 genomes]
rs56144630	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181437	0.96[EUR][1000 genomes]
rs56291131	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56341503	0.84[EUR][1000 genomes]
rs56393668	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58093994	0.84[EUR][1000 genomes]
rs59052115	0.94[EUR][1000 genomes]
rs60079515	0.94[EUR][1000 genomes]
rs60524701	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61582992	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66521164	0.84[EUR][1000 genomes]
rs7116150	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7123898	0.86[EUR][1000 genomes]
rs7125114	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957115	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72957676	0.82[EUR][1000 genomes]
rs72957677	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72957679	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72957686	0.83[EUR][1000 genomes]
rs72957688	0.83[EUR][1000 genomes]
rs72957690	0.84[EUR][1000 genomes]
rs72957699	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959503	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959507	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959509	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959517	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72959521	0.96[EUR][1000 genomes]
rs72959524	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7931474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932968	0.87[EUR][1000 genomes]
rs7933736	0.87[TSI][hapmap]
rs7933912	0.86[EUR][1000 genomes]
rs7945968	0.86[EUR][1000 genomes]
rs7949824	0.86[EUR][1000 genomes]
rs7950101	0.86[EUR][1000 genomes]
rs9888294	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4348928	CDK2AP2	cis	cerebellum	SCAN
rs4348928	CABP4	cis	parietal	SCAN
rs4348928	TCIRG1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:70858200-70891000	Weak transcription	Gastric	stomach
2	chr11:70877400-70890200	Weak transcription	Liver	Liver
3	chr11:70882600-70892200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:70885400-70889200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr11:70886600-70891000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:70887000-70891000	Weak transcription	Pancreas	Pancrea
7	chr11:70887200-70891000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:70887200-70892200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:70887200-70892400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:70887400-70890600	Weak transcription	Fetal Intestine Small	intestine
11	chr11:70888800-70890000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:70889000-70889600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:70889000-70889800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:70889000-70890400	Weak transcription	HepG2	liver

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