Variant report

Variant	rs12497656
Chromosome Location	chr3:111300775-111300776
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	chr3:111296559..111298306-chr3:111299158..111301794,2	MCF-7	breast:
2	chr3:111300439..111301407-chr3:111310086..111311004,2	MCF-7	breast:

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1282090	0.92[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4682288	0.92[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs9836430	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12497656	VASH2	trans	parietal	SCAN
rs12497656	CD200	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111294200-111302000	Strong transcription	Primary T cells fromperipheralblood	blood
2	chr3:111295600-111301600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:111295800-111301400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:111295800-111311400	Strong transcription	Fetal Thymus	thymus
5	chr3:111296000-111314400	Strong transcription	Primary T cells from cord blood	blood
6	chr3:111296400-111314600	Strong transcription	Dnd41	blood
7	chr3:111296600-111301800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:111297000-111301200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:111297000-111302000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:111297200-111300800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:111297200-111300800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:111297200-111307200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:111298000-111301000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:111298200-111302200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:111298600-111305400	Weak transcription	Thymus	Thymus
16	chr3:111299200-111301000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:111299200-111301000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:111299200-111305200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:111299400-111328600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:111299600-111301800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:111299800-111301800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:111299800-111310400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:111300000-111301200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr3:111300200-111301000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:111300200-111301400	Flanking Active TSS	A549	lung
26	chr3:111300200-111301600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:111300200-111301600	Enhancers	Hela-S3	cervix
28	chr3:111300200-111301800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:111300200-111301800	Enhancers	HMEC	breast
30	chr3:111300200-111301800	Enhancers	NHEK	skin
31	chr3:111300200-111302000	Enhancers	Osteobl	bone
32	chr3:111300400-111300800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:111300400-111301400	Enhancers	NHLF	lung
34	chr3:111300400-111301600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:111300600-111301600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:111300600-111301600	Enhancers	HSMMtube	muscle
37	chr3:111300600-111301600	Flanking Active TSS	NH-A	brain
38	chr3:111300600-111302000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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