Variant report

Variant	rs1599280
Chromosome Location	chr6:56792576-56792577
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	chr6:56792046..56794849-chr6:56818085..56820101,2	K562	blood:
2	chr6:56790222..56793074-chr6:56811865..56815272,3	K562	blood:

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:45)

rs_ID	r²[population]
rs1044670	1.00[ASW][hapmap];0.83[GIH][hapmap]
rs13193465	1.00[GIH][hapmap]
rs13207768	1.00[ASW][hapmap]
rs13215865	0.81[EUR][1000 genomes]
rs13220510	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220575	1.00[GIH][hapmap]
rs1451707	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1451708	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1460561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599281	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17450853	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685143	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17685185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685277	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs17752412	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1903330	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2817573	1.00[GIH][hapmap]
rs34232358	0.81[EUR][1000 genomes]
rs34259328	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34714091	0.81[EUR][1000 genomes]
rs34733863	0.81[EUR][1000 genomes]
rs34752771	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35202312	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35434542	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35527216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35860642	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35961728	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36112505	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3957366	1.00[ASW][hapmap]
rs4490669	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55786720	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56030203	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58338781	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61340009	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901944	1.00[GIH][hapmap]
rs71550519	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564866	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564868	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs720884	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs748996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296855	0.82[TSI][hapmap]
rs9475752	1.00[CEU][hapmap];0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1599280	BEND6	cis	cerebellum	SCAN
rs1599280	BEND6	cis	Artery Tibial	GTEx
rs1599280	DST	cis	cerebellum	SCAN
rs1599280	BEND6	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56777600-56792600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:56777600-56792600	Weak transcription	NH-A	brain
3	chr6:56778400-56792800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:56780600-56792600	Weak transcription	NHLF	lung
5	chr6:56781000-56792600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:56782400-56793000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:56790400-56792600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:56790400-56792600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:56790400-56799800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:56791200-56793800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:56791400-56793200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:56791600-56792800	Enhancers	A549	lung
13	chr6:56791600-56793200	Enhancers	Osteobl	bone
14	chr6:56791600-56793400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr6:56791600-56793400	Enhancers	NHDF-Ad	bronchial
16	chr6:56791800-56792600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:56792200-56793000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:56792200-56793000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:56792400-56792600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:56792400-56792600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:56792400-56793000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:56792400-56793000	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:56792400-56793000	Enhancers	HSMM	muscle
24	chr6:56792400-56793400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:56792400-56793400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:56792400-56793400	Enhancers	HMEC	breast
27	chr6:56792400-56793400	Enhancers	NHEK	skin

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