Variant report

Variant	rs56093858
Chromosome Location	chr3:46230091-46230092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46203859..46207087-chr3:46229501..46231810,3	MCF-7	breast:
2	chr3:46154708..46157691-chr3:46229895..46231641,2	MCF-7	breast:
3	chr3:46224582..46227579-chr3:46229207..46231436,3	MCF-7	breast:
4	chr3:46228969..46230539-chr3:46241094..46242941,2	MCF-7	breast:
5	chr3:46221407..46223602-chr3:46228126..46230272,2	MCF-7	breast:
6	chr3:46229589..46231400-chr3:46238254..46240186,2	K562	blood:

Variant related genes	Relation type
ENSG00000183625	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11914967	0.85[AMR][1000 genomes]
rs11918542	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922302	1.00[EUR][1000 genomes]
rs11929424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11929460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17078685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17078689	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17078694	1.00[EUR][1000 genomes]
rs17078698	1.00[EUR][1000 genomes]
rs3136663	0.92[AMR][1000 genomes]
rs3136672	0.83[AFR][1000 genomes]
rs34611049	0.96[AFR][1000 genomes]
rs41405546	1.00[EUR][1000 genomes]
rs41434946	1.00[EUR][1000 genomes]
rs41491548	1.00[EUR][1000 genomes]
rs41491747	1.00[EUR][1000 genomes]
rs41511545	1.00[EUR][1000 genomes]
rs41537245	1.00[EUR][1000 genomes]
rs56277808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56698532	0.89[AMR][1000 genomes]
rs57560436	0.85[AMR][1000 genomes]
rs59340338	0.85[AMR][1000 genomes]
rs60714453	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830796	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833005	0.89[AMR][1000 genomes]
rs73833018	0.89[AMR][1000 genomes]
rs73833020	0.89[AMR][1000 genomes]
rs7610869	1.00[EUR][1000 genomes]
rs7615337	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618935	0.85[AMR][1000 genomes]
rs7631658	0.85[AMR][1000 genomes]
rs7653045	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46223600-46231400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:46226200-46230600	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:46227200-46230200	Enhancers	Primary B cells from cord blood	blood
4	chr3:46228600-46232800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr3:46229200-46230200	Enhancers	HMEC	breast
6	chr3:46229600-46230600	Enhancers	GM12878-XiMat	blood
7	chr3:46229600-46233200	Weak transcription	Spleen	Spleen
8	chr3:46229800-46230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46229800-46230200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:46229800-46230400	Weak transcription	Pancreas	Pancrea
11	chr3:46229800-46233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:46229800-46234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:46230000-46232800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:46230000-46234800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links