Variant report

Variant	rs2397227
Chromosome Location	chr6:56839507-56839508
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	chr6:56506621..56508645-chr6:56839158..56841779,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1007417	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs1016048	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12154043	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13193465	0.84[TSI][hapmap]
rs13220575	0.84[TSI][hapmap]
rs1451709	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1562908	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1597694	0.81[EUR][1000 genomes]
rs16888222	0.82[JPT][hapmap]
rs17685277	0.84[TSI][hapmap]
rs17685356	0.82[EUR][1000 genomes]
rs2006930	0.82[EUR][1000 genomes]
rs2122958	0.86[CEU][hapmap];0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2167460	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs2817573	0.84[TSI][hapmap]
rs34589109	0.82[EUR][1000 genomes]
rs34703235	0.81[EUR][1000 genomes]
rs34896907	0.82[EUR][1000 genomes]
rs35553446	0.82[EUR][1000 genomes]
rs62417384	0.83[EUR][1000 genomes]
rs62417410	0.82[EUR][1000 genomes]
rs6901192	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6901660	0.81[EUR][1000 genomes]
rs6901944	0.84[TSI][hapmap]
rs6904172	1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6915492	0.82[EUR][1000 genomes]
rs6924882	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6925107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6935636	0.82[EUR][1000 genomes]
rs720884	0.84[TSI][hapmap]
rs720885	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7741507	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7760435	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9296855	0.80[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs9296857	0.82[ASN][1000 genomes]
rs9357934	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9370550	0.85[CHD][hapmap]
rs9370552	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9382669	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9382670	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9382672	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9382674	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9382675	0.82[EUR][1000 genomes]
rs9396240	0.85[CHD][hapmap]
rs9396245	0.85[CHD][hapmap]
rs9396246	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9396249	0.82[EUR][1000 genomes]
rs9396250	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9475758	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs9475760	0.93[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs9475763	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv970124	chr6:56839095-56846057	ZNF genes & repeats Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2397227	BEND6	cis	Muscle Skeletal	GTEx
rs2397227	DST	cis	cerebellum	SCAN
rs2397227	BEND6	cis	Thyroid	GTEx
rs2397227	BEND6	cis	Heart Left Ventricle	GTEx
rs2397227	BEND6	cis	Esophagus Muscularis	GTEx
rs2397227	BEND6	cis	cerebellum	SCAN
rs2397227	BEND6	cis	Esophagus Mucosa	GTEx
rs2397227	BEND6	cis	Artery Tibial	GTEx
rs2397227	BEND6	cis	lymphoblastoid	seeQTL
rs2397227	BEND6	cis	parietal	SCAN
rs2397227	BEND6	cis	lung	GTEx
rs2397227	C6orf65	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56828000-56841600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:56836400-56840600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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