Variant report

Variant	rs1538061
Chromosome Location	chr13:86240703-86240704
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12864864	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12871499	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12875807	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1337253	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1337254	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1337255	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1337261	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1337262	0.80[ASN][1000 genomes]
rs1337263	0.80[ASN][1000 genomes]
rs1337264	0.80[ASN][1000 genomes]
rs1415397	0.80[ASN][1000 genomes]
rs1538052	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538062	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538064	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1538065	0.87[ASN][1000 genomes]
rs1556774	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1953675	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1953676	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2039658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2039659	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2039660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2225858	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2342957	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2343054	0.80[ASN][1000 genomes]
rs2343055	0.80[ASN][1000 genomes]
rs4996713	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6650466	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs722952	0.80[ASN][1000 genomes]
rs7491615	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7981524	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7988996	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9531814	0.80[ASN][1000 genomes]
rs9531815	0.80[ASN][1000 genomes]
rs9531816	0.87[ASN][1000 genomes]
rs9531817	0.87[ASN][1000 genomes]
rs9531825	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9531826	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9531831	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9547297	0.80[ASN][1000 genomes]
rs9547300	0.80[ASN][1000 genomes]
rs9547301	0.80[ASN][1000 genomes]
rs9547302	0.80[ASN][1000 genomes]
rs9547303	0.80[ASN][1000 genomes]
rs9547306	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9547324	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9547332	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9547333	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9547335	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916866	chr13:85505771-86241562	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86239200-86240800	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr13:86239400-86240800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:86240200-86240800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr13:86240600-86240800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:86240600-86241000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr13:86240600-86241200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr13:86240600-86241600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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