Variant report

Variant	rs10206575
Chromosome Location	chr2:47725842-47725843
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	chr2:47723653..47725283-chr2:47725374..47727598,2	K562	blood:
2	chr2:47721161..47722792-chr2:47725179..47726873,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10175959	0.82[ASN][1000 genomes]
rs10175972	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10179452	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10188090	0.85[ASN][1000 genomes]
rs10197011	0.81[ASN][1000 genomes]
rs10206782	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10495945	0.81[ASN][1000 genomes]
rs11684661	0.85[ASN][1000 genomes]
rs11684737	0.85[ASN][1000 genomes]
rs11886591	0.84[ASN][1000 genomes]
rs11901645	0.93[ASN][1000 genomes]
rs12712994	0.97[ASN][1000 genomes]
rs12991125	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031342	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1981928	0.89[EUR][1000 genomes]
rs2059520	0.83[ASN][1000 genomes]
rs2303424	0.85[ASN][1000 genomes]
rs3732182	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3732183	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764959	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764960	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771278	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771279	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771280	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771281	0.81[ASN][1000 genomes]
rs3821227	0.83[ASN][1000 genomes]
rs4583514	0.83[ASN][1000 genomes]
rs6544992	0.90[EUR][1000 genomes]
rs6711675	0.81[ASN][1000 genomes]
rs6718364	0.85[ASN][1000 genomes]
rs6720549	0.90[EUR][1000 genomes]
rs6725042	0.85[EUR][1000 genomes]
rs6726691	0.88[EUR][1000 genomes]
rs6737303	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6746426	0.84[ASN][1000 genomes]
rs6748435	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6757035	0.89[EUR][1000 genomes]
rs6759990	0.82[ASN][1000 genomes]
rs7565513	0.81[ASN][1000 genomes]
rs7585174	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7588420	0.81[EUR][1000 genomes]
rs7596629	0.81[ASN][1000 genomes]
rs7599880	0.96[ASN][1000 genomes]
rs7607076	0.87[EUR][1000 genomes]
rs876936	0.85[ASN][1000 genomes]
rs876937	0.85[ASN][1000 genomes]
rs879722	0.84[ASN][1000 genomes]
rs9784092	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv998314	chr2:47720420-47959168	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10206575	MSH2	cis	lung	GTEx
rs10206575	MSH2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47714600-47727200	Weak transcription	Primary T cells from cord blood	blood
3	chr2:47717000-47726200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:47725000-47726600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:47725000-47726600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:47725000-47728600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:47725400-47727800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
8	chr2:47725600-47726200	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links