Variant report

Variant	rs3772219
Chromosome Location	chr3:56771251-56771252
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10222681	0.85[JPT][hapmap]
rs11130543	0.82[EUR][1000 genomes]
rs2046823	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]
rs3772218	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4681794	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445817	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445818	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445819	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445821	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68072945	0.85[ASN][1000 genomes]
rs7618024	0.89[GIH][hapmap]
rs7631008	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634907	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9820759	0.80[GIH][hapmap]
rs9825368	0.85[JPT][hapmap]
rs9858728	0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440152	chr3:56764403-56773941	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3772219	CCDC66	cis	cerebellum	SCAN
rs3772219	ARHGEF3	cis	cerebellum	SCAN
rs3772219	ITIH3	cis	cerebellum	SCAN
rs3772219	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 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	chr3:56759000-56774400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:56759400-56784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:56759600-56773200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:56759800-56779000	Weak transcription	Liver	Liver
12	chr3:56759800-56790400	Strong transcription	Dnd41	blood
13	chr3:56760400-56773200	Strong transcription	Primary B cells from cord blood	blood
14	chr3:56760800-56773200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr3:56760800-56783000	Weak transcription	Osteobl	bone
16	chr3:56760800-56788800	Strong transcription	Fetal Thymus	thymus
17	chr3:56762000-56788400	Weak transcription	Colonic Mucosa	Colon
18	chr3:56763600-56781000	Weak transcription	Fetal Brain Male	brain
19	chr3:56763600-56784200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:56763800-56789000	Weak transcription	Small Intestine	intestine
21	chr3:56763800-56790200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:56763800-56792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:56764000-56783200	Weak transcription	HSMMtube	muscle
24	chr3:56764000-56783400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:56764000-56786600	Weak transcription	Aorta	Aorta
26	chr3:56764000-56788800	Weak transcription	Fetal Heart	heart
27	chr3:56764000-56789000	Weak transcription	Psoas Muscle	Psoas
28	chr3:56764000-56793400	Weak transcription	Gastric	stomach
29	chr3:56764000-56815800	Weak transcription	Fetal Intestine Small	intestine
30	chr3:56764200-56777200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:56765200-56778200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:56766200-56771400	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr3:56766200-56788200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:56766400-56776400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:56766400-56777400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:56766400-56777600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:56766400-56777800	Weak transcription	Fetal Brain Female	brain
38	chr3:56766600-56777200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:56766600-56778800	Weak transcription	Brain Angular Gyrus	brain
40	chr3:56766600-56779000	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:56766600-56785800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:56766800-56775800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:56766800-56777200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:56766800-56778200	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:56766800-56779000	Weak transcription	Brain Substantia Nigra	brain
46	chr3:56766800-56782800	Weak transcription	Fetal Kidney	kidney
47	chr3:56766800-56782800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:56767000-56773200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr3:56767400-56777000	Weak transcription	GM12878-XiMat	blood
50	chr3:56767400-56778200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links