Variant report

Variant	rs28360536
Chromosome Location	chr6:56831647-56831648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56827463..56830023-chr6:56830661..56832302,2	K562	blood:
2	chr6:56820475..56822704-chr6:56829156..56832250,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1020548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193465	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13198484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207800	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13212013	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220575	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.83[AMR][1000 genomes]
rs1451708	0.83[AMR][1000 genomes]
rs17685277	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2613119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817573	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360535	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34009699	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34027274	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34399458	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34616943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.86[AMR][1000 genomes]
rs34979183	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35090265	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336675	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35434542	0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35735810	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35899012	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35961728	0.83[AMR][1000 genomes]
rs36124814	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55952713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56381984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901944	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907143	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564870	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564872	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760385	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28360536	BEND6	cis	Esophagus Muscularis	GTEx
rs28360536	BEND6	cis	Thyroid	GTEx
rs28360536	C6orf65	cis	multi-tissue	Pritchard
rs28360536	BEND6	cis	Heart Left Ventricle	GTEx
rs28360536	BEND6	cis	Muscle Skeletal	GTEx
rs28360536	BEND6	cis	Artery Tibial	GTEx
rs28360536	BEND6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56827800-56831800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr6:56828000-56841600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:56831600-56832400	Weak transcription	H9 Cell Line	embryonic stem cell

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