Variant report

Variant	rs11202766
Chromosome Location	chr10:90295773-90295774
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	chr10:90284453..90286680-chr10:90293279..90295834,2	MCF-7	breast:
2	chr10:89622081..89624106-chr10:90294279..90296284,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227268	Chromatin interaction
ENSG00000171862	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10509551	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]
rs10887822	0.85[AMR][1000 genomes]
rs10887831	0.90[ASW][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[YRI][hapmap]
rs11202746	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11202748	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11202752	0.85[AMR][1000 genomes]
rs11202754	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs11202757	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11202761	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11202767	0.82[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11202776	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs12357364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12357948	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12359950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12360281	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12413139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12413825	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12572235	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1325900	0.90[ASW][hapmap];0.85[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1325906	0.81[ASW][hapmap];0.85[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1342455	0.85[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1342458	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1536252	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17111999	0.81[ASW][hapmap]
rs17112571	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17112575	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1891431	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2153855	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs2185785	0.85[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs2437871	0.91[YRI][hapmap]
rs2477952	0.95[YRI][hapmap]
rs2576164	0.80[LWK][hapmap]
rs2576166	0.87[YRI][hapmap]
rs28794023	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3891849	0.81[ASW][hapmap]
rs4145084	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4520503	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4933482	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4933483	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4934406	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4934410	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4934414	0.84[CEU][hapmap]
rs61640455	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7076491	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7077844	0.83[ASN][1000 genomes]
rs73355485	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73355487	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9664569	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
3	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
4	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
5	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
rs11202766	PTEN	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90288600-90296400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:90289000-90297200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:90289200-90296000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:90289200-90296400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:90289400-90296400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:90290000-90296600	Weak transcription	HSMM	muscle
7	chr10:90290000-90297000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:90291600-90297000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:90291800-90296200	Weak transcription	Fetal Lung	lung
10	chr10:90292000-90296800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr10:90292000-90297400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:90293800-90296400	Weak transcription	Psoas Muscle	Psoas
13	chr10:90294800-90298000	Weak transcription	Liver	Liver
14	chr10:90295600-90296000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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