Variant report

Variant	rs10887831
Chromosome Location	chr10:90268918-90268919
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	chr10:89621134..89622891-chr10:90266765..90269428,2	MCF-7	breast:
2	chr10:90266844..90269778-chr10:90274233..90275948,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171862	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10509551	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10887822	0.82[AMR][1000 genomes]
rs11202746	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11202748	0.95[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs11202752	0.82[AMR][1000 genomes]
rs11202754	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs11202757	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11202761	0.81[AMR][1000 genomes]
rs11202766	0.90[ASW][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap]
rs11202767	0.95[YRI][hapmap]
rs12357364	0.91[YRI][hapmap]
rs12357948	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12359950	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12413139	0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12413825	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12572235	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1325900	1.00[ASW][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap]
rs1325906	0.90[ASW][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1342455	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1342458	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418482	0.84[ASW][hapmap]
rs1536252	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17111999	0.89[ASW][hapmap]
rs17112571	0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17112575	1.00[CHB][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891431	0.90[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153855	0.82[AMR][1000 genomes]
rs2185785	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs2437871	0.83[YRI][hapmap]
rs2477952	0.86[YRI][hapmap]
rs2576174	0.81[LWK][hapmap]
rs28794023	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3891849	0.89[ASW][hapmap]
rs4145084	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4520503	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4933482	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4933483	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934406	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934410	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934414	0.81[YRI][hapmap]
rs7076491	1.00[ASW][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs725684	0.92[LWK][hapmap]
rs9664569	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10887831	PTEN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90260400-90277600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr10:90265800-90269000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr10:90266600-90269000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:90266600-90269000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:90266600-90269000	Enhancers	Fetal Lung	lung
6	chr10:90268600-90269600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr10:90268800-90269200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:90268800-90269800	Weak transcription	Brain Germinal Matrix	brain

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