Variant report

Variant	rs2064061
Chromosome Location	chr3:45871203-45871204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1058961	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs11130076	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13065964	0.91[CHB][hapmap]
rs1386930	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1488369	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1860264	0.81[JPT][hapmap]
rs4683146	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441930	0.81[JPT][hapmap]
rs7613548	0.81[JPT][hapmap]
rs7625839	0.86[CHB][hapmap]
rs9814578	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868455	0.81[JPT][hapmap]
rs9871972	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2064061	CDC25A	cis	cerebellum	SCAN
rs2064061	CCR1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:45857800-45871600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:45858000-45882600	Weak transcription	A549	lung
6	chr3:45858400-45881200	Strong transcription	Dnd41	blood
7	chr3:45859800-45871400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:45860400-45871600	Weak transcription	Esophagus	oesophagus
11	chr3:45860400-45871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:45860400-45871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:45860400-45875800	Weak transcription	Placenta	Placenta
14	chr3:45860400-45877400	Strong transcription	Liver	Liver
15	chr3:45860600-45874400	Weak transcription	HUVEC	blood vessel
16	chr3:45860800-45875200	Weak transcription	Aorta	Aorta
17	chr3:45861000-45882400	Weak transcription	Small Intestine	intestine
18	chr3:45861000-45882400	Weak transcription	NHDF-Ad	bronchial
19	chr3:45861000-45882600	Weak transcription	Stomach Mucosa	stomach
20	chr3:45861000-45882600	Weak transcription	Hela-S3	cervix
21	chr3:45861200-45879600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:45861200-45882400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:45861200-45882600	Weak transcription	Right Ventricle	heart
24	chr3:45861400-45882200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:45861400-45882200	Weak transcription	Fetal Heart	heart
26	chr3:45861800-45882600	Weak transcription	NHLF	lung
27	chr3:45862000-45882800	Weak transcription	Psoas Muscle	Psoas
28	chr3:45862200-45871800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr3:45862200-45879400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:45862200-45882600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:45862400-45879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:45862400-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:45862600-45877400	Strong transcription	Adipose Nuclei	Adipose
34	chr3:45862600-45878400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:45862800-45878400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:45862800-45882400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:45863000-45876600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:45863200-45877200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:45863200-45878400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:45863200-45879600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:45863400-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:45863600-45877000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:45863800-45875400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:45864000-45881000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:45864600-45882600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:45864800-45871600	Weak transcription	Lung	lung
47	chr3:45864800-45882600	Weak transcription	Colonic Mucosa	Colon
48	chr3:45865200-45882200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:45865800-45873200	Strong transcription	Osteobl	bone
50	chr3:45865800-45877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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