Variant report

Variant	rs1325906
Chromosome Location	chr10:90237426-90237427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10509551	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]
rs10887822	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10887830	1.00[ASN][1000 genomes]
rs10887831	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]
rs11202746	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11202748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11202752	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11202754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11202757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202761	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11202766	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]
rs12356177	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12357364	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12357948	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12359950	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12360281	0.89[AMR][1000 genomes]
rs12413139	0.84[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12413825	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12572235	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1325900	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1342455	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1342458	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1536252	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17111999	0.81[ASW][hapmap]
rs17112571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17112575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1891431	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2153855	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]
rs2185785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2437872	0.85[YRI][hapmap]
rs2437877	0.81[AFR][1000 genomes]
rs2477957	0.85[YRI][hapmap]
rs2488271	0.85[YRI][hapmap]
rs28794023	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2986118	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs3891849	0.81[ASW][hapmap]
rs4145084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520503	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4933482	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4933483	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934406	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934407	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4934410	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4934414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs61640455	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7076491	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725684	0.85[LWK][hapmap];0.85[YRI][hapmap]
rs73355485	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73355487	0.86[AMR][1000 genomes]
rs9664569	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][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
rs1325906	PTEN	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90233800-90239200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr10:90234400-90238200	Weak transcription	Right Ventricle	heart
3	chr10:90235000-90240400	Weak transcription	Aorta	Aorta
4	chr10:90235400-90237800	Weak transcription	Fetal Heart	heart
5	chr10:90235400-90238200	Weak transcription	HSMM	muscle
6	chr10:90235600-90238600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:90235600-90238800	Weak transcription	Ovary	ovary
8	chr10:90236400-90238600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr10:90237000-90238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:90237000-90238400	Enhancers	Psoas Muscle	Psoas
11	chr10:90237000-90238600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr10:90237000-90239200	Enhancers	HMEC	breast
13	chr10:90237200-90237800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr10:90237200-90238400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:90237200-90239000	Enhancers	NHEK	skin
16	chr10:90237400-90238400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:90237400-90238800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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