Variant report

Variant	rs17500406
Chromosome Location	chr2:98905554-98905555
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	chr2:98903777..98907619-chr2:98918307..98922639,4	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010387	0.83[CEU][hapmap];0.93[GIH][hapmap];1.00[MKK][hapmap]
rs11691306	0.82[CEU][hapmap]
rs13402201	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13430738	0.83[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs17427608	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17427825	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17428745	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17428990	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17429379	0.82[EUR][1000 genomes]
rs17501094	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4564827	0.83[CEU][hapmap]
rs62155312	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62155317	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155347	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62155354	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62155355	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62155358	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156265	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156266	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156268	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156269	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62156681	0.90[AMR][1000 genomes]
rs62156686	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62156724	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62156744	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62157892	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62157901	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62157907	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62157908	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62157916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72817785	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72817792	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72817793	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72819903	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72819917	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72819919	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72819921	0.82[EUR][1000 genomes]
rs72819925	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72819927	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98898800-98913200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:98905000-98908400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:98905000-98915600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:98905400-98905600	Enhancers	HMEC	breast
5	chr2:98905400-98905800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links