Variant report

Variant	rs4562008
Chromosome Location	chr5:57159395-57159396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57158482..57160227-chr5:57754453..57756004,2	MCF-7	breast:
2	chr5:57159004..57160739-chr5:57754987..57756954,2	MCF-7	breast:
3	chr5:57157132..57161136-chr5:57747678..57750826,3	MCF-7	breast:
4	chr5:57158247..57160209-chr5:57752409..57754364,2	MCF-7	breast:
5	chr5:57158588..57161134-chr5:57757060..57758676,2	MCF-7	breast:
6	chr5:57147307..57149635-chr5:57158498..57160416,2	MCF-7	breast:
7	chr5:57074121..57076922-chr5:57158153..57160204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16887464	0.83[TSI][hapmap]
rs1821211	0.80[EUR][1000 genomes]
rs2408855	0.80[EUR][1000 genomes]
rs6868222	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs7721249	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4562008	PLK2	cis	cerebellum	SCAN
rs4562008	IL6ST	cis	cerebellum	SCAN
rs4562008	DHX29	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57151400-57160000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:57156000-57160000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:57156200-57159800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:57156400-57160600	Enhancers	Placenta	Placenta
5	chr5:57157200-57159800	Enhancers	HMEC	breast
6	chr5:57157600-57159400	Enhancers	Fetal Heart	heart
7	chr5:57157600-57160000	Enhancers	HSMM	muscle
8	chr5:57157800-57160200	Enhancers	HSMMtube	muscle
9	chr5:57157800-57160200	Enhancers	Osteobl	bone
10	chr5:57158000-57160000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:57158000-57160000	Enhancers	NHEK	skin
12	chr5:57158200-57160000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:57158200-57160000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:57158200-57160000	Enhancers	NHDF-Ad	bronchial
15	chr5:57158200-57160600	Enhancers	Adipose Nuclei	Adipose
16	chr5:57158400-57159800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:57158400-57160000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:57158600-57160000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:57159000-57160000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:57159200-57159400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:57159200-57160000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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