Variant report

Variant	rs28360538
Chromosome Location	chr6:56827936-56827937
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	chr6:56817328..56823856-chr6:56824167..56831366,18	K562	blood:
2	chr6:56827463..56830023-chr6:56830661..56832302,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1020548	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13195825	0.93[AFR][1000 genomes]
rs13198484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203600	0.93[AFR][1000 genomes]
rs13205022	0.93[AFR][1000 genomes]
rs13207800	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13209099	0.93[AFR][1000 genomes]
rs13212013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13215865	1.00[AFR][1000 genomes]
rs13216793	0.93[AFR][1000 genomes]
rs13218276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220510	1.00[AFR][1000 genomes]
rs13220575	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1451708	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1460561	1.00[AFR][1000 genomes]
rs17685143	1.00[AFR][1000 genomes]
rs17685277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1903330	1.00[AFR][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	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34009699	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34027274	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34232358	1.00[AFR][1000 genomes]
rs34399458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34616943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34714091	1.00[AFR][1000 genomes]
rs34733863	1.00[AFR][1000 genomes]
rs34812189	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34979183	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35090265	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35434542	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35735810	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35899012	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35961728	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36112505	1.00[AFR][1000 genomes]
rs36124814	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55952713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56381984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901944	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904924	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]
rs71550519	1.00[AFR][1000 genomes]
rs71564866	1.00[AFR][1000 genomes]
rs71564868	0.87[AFR][1000 genomes]
rs71564869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564872	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7760385	1.00[AFR][1000 genomes];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	esv3448433	chr6:56827743-56829891	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28360538	BEND6	cis	Artery Tibial	GTEx
rs28360538	BEND6	cis	Esophagus Muscularis	GTEx
rs28360538	BEND6	cis	Muscle Skeletal	GTEx
rs28360538	BEND6	cis	Esophagus Mucosa	GTEx
rs28360538	C6orf65	cis	multi-tissue	Pritchard
rs28360538	BEND6	cis	Thyroid	GTEx
rs28360538	BEND6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56823000-56828000	Enhancers	Osteobl	bone
2	chr6:56824800-56828200	Enhancers	NHDF-Ad	bronchial
3	chr6:56825400-56828200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:56826600-56828000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:56827000-56828000	Enhancers	NH-A	brain
6	chr6:56827200-56828000	Enhancers	NHLF	lung
7	chr6:56827400-56828000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:56827400-56828000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:56827400-56828000	Enhancers	HSMM	muscle
10	chr6:56827400-56828200	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr6:56827600-56828200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:56827600-56828200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:56827600-56828200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr6:56827600-56828400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:56827800-56828200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:56827800-56828400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:56827800-56831800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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