Variant report

Variant	rs11063189
Chromosome Location	chr12:4588248-4588249
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	chr12:4583407..4585013-chr12:4587420..4590111,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1029769	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10849083	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10849085	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10849086	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10849089	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10849090	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11063177	0.87[EUR][1000 genomes]
rs11063179	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063181	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063182	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11063188	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063193	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063194	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063195	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063196	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11063197	0.82[AMR][1000 genomes]
rs11063198	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11063199	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063202	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11063205	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063206	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11063207	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11063213	0.97[EUR][1000 genomes]
rs11063214	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063215	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11063217	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12366731	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12367035	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2907494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2907495	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2907498	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2907499	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2909380	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2909381	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2970808	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2970810	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2970812	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2970818	0.90[CEU][hapmap]
rs4238020	0.96[EUR][1000 genomes]
rs4323977	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60388479	0.96[EUR][1000 genomes]
rs61909580	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73037770	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7304949	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9971700	0.93[EUR][1000 genomes]
rs9971728	1.00[GIH][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription 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	43 gene(s)	inside rSNPs	diseases
2	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11063189	DYRK4	cis	cerebellum	SCAN
rs11063189	SCARNA10	cis	parietal	SCAN
rs11063189	AKAP3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4586800-4591800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:4586800-4596400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:4587200-4597200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr12:4587200-4597200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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