Variant report

Variant	rs2046823
Chromosome Location	chr3:56779011-56779012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10222681	0.85[JPT][hapmap]
rs11130536	0.85[GIH][hapmap]
rs2004199	0.85[GIH][hapmap]
rs2029464	0.83[GIH][hapmap]
rs2291501	0.83[GIH][hapmap]
rs3772218	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772219	0.83[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4681794	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4681951	0.85[GIH][hapmap]
rs6445817	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445818	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445819	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6445821	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs68072945	0.83[ASN][1000 genomes]
rs7631008	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7634907	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs808	0.88[GIH][hapmap]
rs9825368	0.85[JPT][hapmap]
rs9842283	0.85[GIH][hapmap]
rs9862490	0.83[GIH][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2046823	CCDC66	cis	cerebellum	SCAN
rs2046823	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL
rs2046823	C3orf51	cis	cerebellum	SCAN
rs2046823	ARHGEF3	cis	cerebellum	SCAN
rs2046823	ERC2	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56754400-56783200	Weak transcription	Stomach Mucosa	stomach
2	chr3:56755200-56781800	Weak transcription	NH-A	brain
3	chr3:56756800-56781000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:56757000-56786400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:56757600-56792200	Weak transcription	Hela-S3	cervix
6	chr3:56758600-56792200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:56758800-56782800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:56759400-56784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:56759800-56790400	Strong transcription	Dnd41	blood
10	chr3:56760800-56783000	Weak transcription	Osteobl	bone
11	chr3:56760800-56788800	Strong transcription	Fetal Thymus	thymus
12	chr3:56762000-56788400	Weak transcription	Colonic Mucosa	Colon
13	chr3:56763600-56781000	Weak transcription	Fetal Brain Male	brain
14	chr3:56763600-56784200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:56763800-56789000	Weak transcription	Small Intestine	intestine
16	chr3:56763800-56790200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:56763800-56792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:56764000-56783200	Weak transcription	HSMMtube	muscle
19	chr3:56764000-56783400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:56764000-56786600	Weak transcription	Aorta	Aorta
21	chr3:56764000-56788800	Weak transcription	Fetal Heart	heart
22	chr3:56764000-56789000	Weak transcription	Psoas Muscle	Psoas
23	chr3:56764000-56793400	Weak transcription	Gastric	stomach
24	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
25	chr3:56766200-56788200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:56766600-56785800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:56766800-56782800	Weak transcription	Fetal Kidney	kidney
28	chr3:56766800-56782800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:56767400-56783000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:56767400-56792600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:56767600-56783000	Weak transcription	NHEK	skin
32	chr3:56768400-56779200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:56768400-56797600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:56769000-56785200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:56770800-56787200	Strong transcription	Primary T cells from cord blood	blood
36	chr3:56771200-56782200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:56771200-56782800	Weak transcription	Fetal Lung	lung
38	chr3:56773800-56781800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:56774400-56785000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:56774600-56784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:56774600-56787400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:56774800-56781200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:56775000-56792600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:56775400-56785400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:56775600-56782600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:56775600-56783400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:56775800-56779600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:56775800-56780400	Strong transcription	Placenta	Placenta
49	chr3:56775800-56783800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:56775800-56788800	Strong transcription	Thymus	Thymus

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