Variant report

Variant	rs1538056
Chromosome Location	chr13:86249446-86249447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1011902	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1337261	0.88[AFR][1000 genomes]
rs1415396	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538049	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1538050	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1538051	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1538062	0.88[AFR][1000 genomes]
rs1538063	0.87[AFR][1000 genomes]
rs1556773	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1753738	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1753741	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1753764	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1753768	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1753771	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1753772	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1753780	0.85[EUR][1000 genomes]
rs1753782	0.95[ASN][1000 genomes]
rs1753783	0.95[ASN][1000 genomes]
rs1753789	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1753795	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1764940	0.84[EUR][1000 genomes]
rs1764947	0.96[ASN][1000 genomes]
rs1764948	0.93[ASN][1000 genomes]
rs1764949	0.93[ASN][1000 genomes]
rs1764951	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764953	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1764954	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1764958	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1764959	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1764961	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1764963	0.92[ASN][1000 genomes]
rs1764964	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1764966	0.93[ASN][1000 genomes]
rs1764968	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764969	0.93[ASN][1000 genomes]
rs1764970	0.93[ASN][1000 genomes]
rs1764972	0.92[ASN][1000 genomes]
rs2039658	0.86[AFR][1000 genomes]
rs2039659	0.88[AFR][1000 genomes]
rs2243633	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2245400	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255983	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2343058	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4542551	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4911018	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7342473	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7982006	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9531827	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9547325	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9547327	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9547328	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9547334	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9602804	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752724	chr13:85810499-86320999	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1037563	chr13:85830511-86414012	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv471162	chr13:85994700-86296819	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv456051	chr13:85994700-86306452	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv562609	chr13:85994700-86306452	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv428608	chr13:86109178-86262577	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv900733	chr13:86192376-86309366	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv832668	chr13:86234885-86364254	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1044417	chr13:86239152-86344862	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86249400-86249800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:86249400-86250600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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