Variant report

Variant	rs12612665
Chromosome Location	chr2:54908210-54908211
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	chr2:54907957..54910043-chr2:54910399..54913105,2	MCF-7	breast:
2	chr2:54903042..54905906-chr2:54907957..54909608,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1027950	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1052820	0.80[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs12475342	0.88[JPT][hapmap]
rs12611806	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12622340	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1510612	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17045941	0.81[CEU][hapmap]
rs17046153	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17416284	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1848923	0.82[EUR][1000 genomes]
rs2007020	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2567837	0.84[ASN][1000 genomes]
rs354188	0.89[ASN][1000 genomes]
rs354215	0.90[ASN][1000 genomes]
rs3817163	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4671229	0.85[EUR][1000 genomes]
rs4671959	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs4671962	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs4671965	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs4671966	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4671968	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56898160	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545433	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6545438	0.91[CHB][hapmap]
rs6705756	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs6738725	0.80[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72618665	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72618666	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72618667	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72618668	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12612665	C2orf63	cis	cerebellum	SCAN
rs12612665	VRK2	cis	cerebellum	SCAN
rs12612665	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54900000-54908600	Enhancers	NHDF-Ad	bronchial
2	chr2:54901400-54908600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:54903400-54908800	Weak transcription	Spleen	Spleen
4	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
5	chr2:54904800-54908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54905800-54909400	Enhancers	Dnd41	blood
7	chr2:54907000-54908600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:54907200-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:54907600-54908400	Enhancers	HepG2	liver
10	chr2:54907600-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:54907600-54908600	Enhancers	Brain Hippocampus Middle	brain
12	chr2:54907600-54908600	Enhancers	Fetal Thymus	thymus
13	chr2:54907600-54908800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:54907600-54908800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:54907600-54908800	Enhancers	Lung	lung
16	chr2:54907800-54908400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:54907800-54908400	Enhancers	Primary hematopoietic stem cells	blood
18	chr2:54907800-54908600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr2:54907800-54908600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:54907800-54908600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:54907800-54908800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
22	chr2:54908000-54908400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr2:54908000-54908400	Enhancers	Osteobl	bone
24	chr2:54908000-54908600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:54908000-54908800	Enhancers	Primary T cells fromperipheralblood	blood
26	chr2:54908000-54914800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:54908200-54909200	Enhancers	GM12878-XiMat	blood
28	chr2:54908200-54910800	Weak transcription	Fetal Intestine Large	intestine
29	chr2:54908200-54910800	Weak transcription	Pancreas	Pancrea
30	chr2:54908200-54910800	Weak transcription	HMEC	breast
31	chr2:54908200-54914800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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