Variant report

Variant	rs10509551
Chromosome Location	chr10:90254417-90254418
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90253538..90255456-chr10:90264130..90266420,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10887822	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10887831	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]
rs11202746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11202748	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202752	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11202754	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11202757	1.00[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11202761	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11202766	0.81[ASW][hapmap];0.85[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12357364	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12357948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12359950	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12360281	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12413139	0.84[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12413825	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12572235	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1325900	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap]
rs1325906	0.81[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1342455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1342458	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1536252	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112571	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17112575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891431	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153855	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2185785	1.00[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28794023	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4145084	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4520503	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4933482	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4933483	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4934414	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs61640455	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7076491	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs725684	0.90[LWK][hapmap]
rs73355485	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73355487	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9664569	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10509551	PTEN	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90251200-90258800	Weak transcription	Fetal Thymus	thymus
2	chr10:90253400-90254600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:90253400-90256200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr10:90253400-90256400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:90253400-90258000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr10:90253600-90254600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr10:90253600-90254600	Enhancers	Primary B cells from cord blood	blood
8	chr10:90253600-90254800	Enhancers	Primary hematopoietic stem cells	blood
9	chr10:90253600-90254800	Enhancers	GM12878-XiMat	blood
10	chr10:90253600-90255000	Enhancers	Liver	Liver
11	chr10:90253600-90255400	Weak transcription	Fetal Kidney	kidney
12	chr10:90253800-90254600	Enhancers	Primary B cells from peripheral blood	blood
13	chr10:90254000-90255000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:90254000-90255200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr10:90254000-90255400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr10:90254000-90256400	Weak transcription	Fetal Lung	lung
17	chr10:90254000-90256600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:90254000-90259400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:90254000-90259600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr10:90254200-90257400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:90254200-90259200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr10:90254200-90259400	Weak transcription	Osteobl	bone
23	chr10:90254200-90259600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr10:90254200-90259600	Weak transcription	NHDF-Ad	bronchial
25	chr10:90254400-90254600	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr10:90254400-90254800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:90254400-90255000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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