Variant report

Variant	rs2817573
Chromosome Location	chr6:56811124-56811125
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	chr6:56809927..56811973-chr6:56817461..56820564,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1007417	0.84[TSI][hapmap]
rs1020548	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1044670	0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs13193465	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13198484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207800	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13212013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218276	0.91[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220575	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.83[AMR][1000 genomes]
rs1451708	0.83[AMR][1000 genomes]
rs1562908	0.84[TSI][hapmap]
rs1599280	1.00[GIH][hapmap]
rs17685277	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685338	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2397227	0.84[TSI][hapmap]
rs2613119	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];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[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	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	0.83[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	0.83[AMR][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	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904172	0.84[TSI][hapmap]
rs6904924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907143	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];1.00[EUR][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[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs720885	0.84[TSI][hapmap]
rs7760385	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382669	0.84[TSI][hapmap]
rs9382670	0.84[TSI][hapmap]
rs9396246	0.84[TSI][hapmap]
rs9396250	0.84[TSI][hapmap]
rs9475758	0.84[TSI][hapmap]
rs9475760	0.84[TSI][hapmap]
rs9475763	0.84[TSI][hapmap]

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	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2817573	BEND6	cis	Esophagus Muscularis	GTEx
rs2817573	BEND6	cis	cerebellum	SCAN
rs2817573	BEND6	cis	Heart Left Ventricle	GTEx
rs2817573	BEND6	cis	Thyroid	GTEx
rs2817573	C6orf65	cis	multi-tissue	Pritchard
rs2817573	DST	cis	cerebellum	SCAN
rs2817573	BEND6	cis	Artery Tibial	GTEx
rs2817573	BEND6	cis	lymphoblastoid	seeQTL
rs2817573	BEND6	cis	Esophagus Mucosa	GTEx
rs2817573	BEND6	cis	Muscle Skeletal	GTEx
rs2817573	BEND6	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56804200-56813000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:56804200-56818000	Weak transcription	HSMM	muscle
3	chr6:56804400-56813600	Weak transcription	A549	lung
4	chr6:56804400-56814600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:56804400-56815800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:56806600-56812400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:56806600-56817800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:56806600-56818000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:56806600-56818400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:56806800-56812200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:56806800-56812600	Weak transcription	Osteobl	bone
12	chr6:56807000-56812400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:56807000-56812800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:56807000-56813000	Weak transcription	NHLF	lung
15	chr6:56807200-56812600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:56809000-56812400	Weak transcription	NHEK	skin
17	chr6:56809600-56811600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:56809600-56813200	Strong transcription	NHDF-Ad	bronchial
19	chr6:56809800-56813000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:56810000-56818200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:56810200-56814600	Weak transcription	HUVEC	blood vessel
22	chr6:56810800-56813000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:56811000-56811600	Enhancers	NH-A	brain
24	chr6:56811000-56814800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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