Variant report

Variant	rs6504280
Chromosome Location	chr17:46560069-46560070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46554419..46558240-chr17:46559048..46562749,5	K562	blood:
2	chr17:46549355..46551508-chr17:46558983..46560720,2	K562	blood:
3	chr17:46554419..46557845-chr17:46559048..46562749,6	K562	blood:

Variant related genes	Relation type
ENSG00000206805	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1022086	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1553748	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1553755	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4793564	0.81[JPT][hapmap]
rs60944926	0.92[EUR][1000 genomes]
rs8074239	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078201	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8078849	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6504280	ATXN7L3	cis	cerebellum	SCAN
rs6504280	HOXB6	cis	cerebellum	SCAN
rs6504280	FLJ40194	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46554200-46564600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr17:46555000-46566000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr17:46556200-46560400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr17:46556200-46560400	Weak transcription	Fetal Thymus	thymus
5	chr17:46556200-46560800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr17:46556200-46561000	Weak transcription	Primary B cells from cord blood	blood
7	chr17:46556400-46560400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:46556400-46560600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr17:46556600-46560400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:46556600-46560400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:46557400-46560200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr17:46558400-46561200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:46558600-46561000	Enhancers	HSMMtube	muscle
14	chr17:46558800-46560200	Enhancers	HSMM	muscle
15	chr17:46558800-46560200	Enhancers	NHDF-Ad	bronchial
16	chr17:46558800-46560800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr17:46559000-46560400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:46559000-46560600	Enhancers	NHEK	skin
19	chr17:46559000-46561000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:46559000-46561000	Enhancers	NH-A	brain
21	chr17:46559200-46560200	Enhancers	K562	blood
22	chr17:46559200-46560200	Enhancers	Osteobl	bone
23	chr17:46559200-46560400	Enhancers	HMEC	breast
24	chr17:46559200-46561000	Enhancers	NHLF	lung
25	chr17:46559200-46566200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:46559400-46560400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:46559400-46561200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:46559400-46562200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:46559400-46562400	Enhancers	GM12878-XiMat	blood
30	chr17:46559800-46562000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:46560000-46561400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:46560000-46562200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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