Variant report

Variant	rs1701946
Chromosome Location	chr19:51503524-51503525
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	chr19:51432897..51433716-chr19:51502734..51503640,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10420303	0.88[CEU][hapmap]
rs1612902	0.85[EUR][1000 genomes]
rs1654519	0.86[ASN][1000 genomes]
rs1654520	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1654521	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1654539	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs1654542	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1654543	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1701914	0.92[EUR][1000 genomes]
rs1701915	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1701947	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1701948	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1722545	0.86[ASN][1000 genomes]
rs1722546	0.87[ASN][1000 genomes]
rs1722547	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1722550	0.82[CEU][hapmap]
rs1722559	0.92[EUR][1000 genomes]
rs1722560	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1722561	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1722563	0.85[EUR][1000 genomes]
rs1897605	0.85[EUR][1000 genomes]
rs1897606	0.85[EUR][1000 genomes]
rs2075802	0.84[CEU][hapmap]
rs2569478	0.84[CEU][hapmap]
rs2659071	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs268893	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs268894	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs268895	0.87[ASN][1000 genomes]
rs268896	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs268897	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs268898	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs268899	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6509509	0.81[CEU][hapmap]
rs906191	0.85[EUR][1000 genomes];0.96[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	nsv1058277	chr19:51488544-51509847	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51503000-51503800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:51503200-51504200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:51503200-51506000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:51503200-51506000	Flanking Active TSS	HMEC	breast
5	chr19:51503400-51503600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:51503400-51506000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr19:51503400-51506000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:51503400-51506000	Flanking Active TSS	NHEK	skin

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