Variant report

Variant	rs1538052
Chromosome Location	chr13:86275259-86275260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11149377	0.93[ASN][1000 genomes]
rs12864864	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868045	0.95[ASN][1000 genomes]
rs12871499	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12875807	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337253	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1337254	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1337255	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1337261	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1415396	0.96[AFR][1000 genomes]
rs1538049	0.83[AFR][1000 genomes]
rs1538050	0.96[AFR][1000 genomes]
rs1538051	0.94[AFR][1000 genomes]
rs1538060	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538062	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538063	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538064	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1538067	0.81[ASN][1000 genomes]
rs1538068	0.86[ASN][1000 genomes]
rs1556770	0.90[ASN][1000 genomes]
rs1556773	0.96[AFR][1000 genomes]
rs1556774	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603088	0.90[ASN][1000 genomes]
rs1953675	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953676	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999041	0.86[ASN][1000 genomes]
rs2039658	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2039659	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2039660	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2225858	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342957	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35492271	0.83[ASN][1000 genomes]
rs4996713	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6650466	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7491615	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7981524	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7983704	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7988996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7996126	0.85[ASN][1000 genomes]
rs7998235	0.81[ASN][1000 genomes]
rs7998474	0.87[ASN][1000 genomes]
rs9531822	0.80[EUR][1000 genomes]
rs9531825	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9531826	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9531827	0.96[AFR][1000 genomes]
rs9531830	0.96[ASN][1000 genomes]
rs9531831	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9531832	0.87[ASN][1000 genomes]
rs9531834	0.86[ASN][1000 genomes]
rs9547306	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9547320	0.84[ASN][1000 genomes]
rs9547322	0.82[EUR][1000 genomes]
rs9547324	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9547327	0.96[AFR][1000 genomes]
rs9547328	0.96[AFR][1000 genomes]
rs9547329	0.96[ASN][1000 genomes]
rs9547332	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9547333	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9547334	0.81[AFR][1000 genomes]
rs9547335	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9547339	0.90[ASN][1000 genomes]
rs9594050	0.83[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	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	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
7	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
8	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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86273000-86275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:86274000-86313200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:86274800-86275400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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