Variant report

Variant	rs71550519
Chromosome Location	chr6:56780272-56780273
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56780041..56782514-chr6:56808634..56811006,2	K562	blood:
2	chr6:56779944..56782895-chr6:56786364..56788046,2	MCF-7	breast:
3	chr6:56773281..56775523-chr6:56776609..56780879,5	K562	blood:

Variant related genes	Relation type
ENSG00000200224	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13195825	0.93[AFR][1000 genomes]
rs13198484	0.93[AFR][1000 genomes]
rs13203600	0.93[AFR][1000 genomes]
rs13205022	0.93[AFR][1000 genomes]
rs13209099	0.93[AFR][1000 genomes]
rs13214032	1.00[AFR][1000 genomes]
rs13215865	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13216793	0.93[AFR][1000 genomes]
rs13220510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1451707	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451708	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1460561	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1599280	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1599281	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17450853	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17685143	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685185	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685277	1.00[AFR][1000 genomes]
rs17685338	1.00[AFR][1000 genomes]
rs17685380	1.00[AFR][1000 genomes]
rs17752412	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17752435	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752459	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1903330	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28360537	1.00[AFR][1000 genomes]
rs28360538	1.00[AFR][1000 genomes]
rs34009699	1.00[AFR][1000 genomes]
rs34027274	1.00[AFR][1000 genomes]
rs34232358	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34259328	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34399458	1.00[AFR][1000 genomes]
rs34616943	1.00[AFR][1000 genomes]
rs34714091	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34733863	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34752771	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34812189	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35202312	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35434542	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35527216	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35860642	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35961728	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36112505	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4490669	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55786720	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030203	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58338781	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61340009	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71564866	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564868	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	1.00[AFR][1000 genomes]
rs748996	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7760385	1.00[AFR][1000 genomes]
rs9475752	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71550519	BEND6	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56775800-56780600	Enhancers	NHLF	lung
2	chr6:56775800-56781200	Enhancers	Osteobl	bone
3	chr6:56776600-56781200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:56777000-56780400	Enhancers	HSMMtube	muscle
5	chr6:56777000-56781000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:56777400-56781400	Enhancers	K562	blood
7	chr6:56777400-56781800	Weak transcription	HMEC	breast
8	chr6:56777600-56792600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:56777600-56792600	Weak transcription	NH-A	brain
10	chr6:56777800-56780800	Enhancers	NHDF-Ad	bronchial
11	chr6:56777800-56782200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:56778000-56781000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:56778000-56782200	Enhancers	Fetal Brain Male	brain
14	chr6:56778200-56780800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:56778200-56781200	Enhancers	Brain Anterior Caudate	brain
16	chr6:56778400-56780400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:56778400-56781000	Enhancers	Brain Cingulate Gyrus	brain
18	chr6:56778400-56792800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:56778800-56782000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:56779000-56780400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:56779000-56780400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:56779000-56781000	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:56779200-56780600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:56779200-56780600	Enhancers	Brain Angular Gyrus	brain
25	chr6:56779400-56780400	Enhancers	Brain Substantia Nigra	brain
26	chr6:56779600-56780400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:56779600-56780600	Enhancers	GM12878-XiMat	blood
28	chr6:56779600-56782000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:56779800-56780400	Flanking Active TSS	Fetal Brain Female	brain
30	chr6:56779800-56780800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:56779800-56782200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:56779800-56782800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:56780200-56780400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:56780200-56780400	Enhancers	Brain Hippocampus Middle	brain

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