Variant report

Variant	rs6907143
Chromosome Location	chr6:56808872-56808873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56807429..56808990-chr6:56818714..56821233,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1020548	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13193465	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13193800	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13198484	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13207800	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13212013	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13214032	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13214255	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13218276	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13220575	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1451707	0.83[AMR][1000 genomes]
rs1451708	0.83[AMR][1000 genomes]
rs17685277	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17685338	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17685380	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2613119	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2817573	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360535	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28360536	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360537	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360538	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34009699	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34027274	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34399458	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34616943	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34812189	0.86[AMR][1000 genomes]
rs34979183	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35090265	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35336675	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35434542	0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35735810	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35899012	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35961728	0.83[AMR][1000 genomes]
rs36124814	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55952713	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56381984	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6901944	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6904924	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6906623	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71564869	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71564870	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71564872	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs720884	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7760385	0.93[AMR][1000 genomes];0.93[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6907143	BEND6	cis	Heart Left Ventricle	GTEx
rs6907143	BEND6	cis	Artery Tibial	GTEx
rs6907143	BEND6	cis	Thyroid	GTEx
rs6907143	BEND6	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 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	chr6:56807000-56809600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:56807000-56809600	Weak transcription	NHDF-Ad	bronchial
14	chr6:56807000-56812400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:56807000-56812800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:56807000-56813000	Weak transcription	NHLF	lung
17	chr6:56807200-56812600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:56808000-56811000	Weak transcription	NH-A	brain

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