Variant report

Variant	rs9540729
Chromosome Location	chr13:66947124-66947125
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:66918574..66921439-chr13:66945401..66948264,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1158646	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1158647	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12864905	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1334398	0.81[CEU][hapmap]
rs1413573	1.00[CEU][hapmap];0.80[JPT][hapmap];0.99[EUR][1000 genomes]
rs1444387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831972	1.00[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2324888	0.99[EUR][1000 genomes]
rs2875472	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4635220	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7319883	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7983403	0.92[CEU][hapmap]
rs7988498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7996220	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs930573	0.99[EUR][1000 genomes]
rs9317585	0.99[EUR][1000 genomes]
rs9529052	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9529055	1.00[CEU][hapmap]
rs9540717	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9540718	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9540720	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9540724	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9540728	1.00[CEU][hapmap];0.80[JPT][hapmap];0.99[EUR][1000 genomes]
rs9540731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9540732	1.00[CEU][hapmap];0.85[JPT][hapmap];0.99[EUR][1000 genomes]
rs9540734	1.00[CEU][hapmap]
rs9564313	0.96[EUR][1000 genomes]
rs9571576	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs9571577	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9592461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv530416	chr13:66198235-67126195	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1053763	chr13:66210166-67184972	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541811	chr13:66210166-67184972	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv932195	chr13:66215786-67215733	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv530723	chr13:66219650-67200316	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1052017	chr13:66232288-67213033	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv534503	chr13:66287963-67126195	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv915828	chr13:66544825-67212201	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv900389	chr13:66867794-66961006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:66946800-66953000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr13:66947000-66950600	Weak transcription	Brain Angular Gyrus	brain

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