Variant report

Variant	rs12611806
Chromosome Location	chr2:54907635-54907636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1027950	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612665	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620195	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12622340	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1510612	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046153	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1848923	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2007020	0.93[ASN][1000 genomes]
rs2567837	0.85[ASN][1000 genomes]
rs354188	0.91[ASN][1000 genomes]
rs354215	0.92[ASN][1000 genomes]
rs4671229	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4671966	0.83[ASN][1000 genomes]
rs4671968	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56898160	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6738725	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72618665	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618666	0.86[EUR][1000 genomes]
rs72618667	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72618668	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72618669	0.83[AMR][1000 genomes];0.89[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12611806	SPTBN1	Cis_1M	lymphoblastoid	RTeQTL
rs12611806	EML6	cis	Artery Tibial	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54897200-54907800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:54898600-54907800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:54900000-54908600	Enhancers	NHDF-Ad	bronchial
4	chr2:54901000-54907800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:54901200-54907800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:54901400-54908600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:54901800-54907800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:54902200-54907800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:54903400-54907800	Weak transcription	Pancreas	Pancrea
10	chr2:54903400-54908800	Weak transcription	Spleen	Spleen
11	chr2:54903400-54915600	Weak transcription	Right Atrium	heart
12	chr2:54904200-54907800	Weak transcription	Fetal Heart	heart
13	chr2:54904800-54907800	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:54904800-54908000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:54904800-54908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:54905800-54909400	Enhancers	Dnd41	blood
17	chr2:54907000-54907800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:54907000-54907800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr2:54907000-54908000	Enhancers	Brain Anterior Caudate	brain
20	chr2:54907000-54908200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:54907000-54908200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:54907000-54908200	Enhancers	Brain Substantia Nigra	brain
23	chr2:54907000-54908600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:54907200-54907800	Weak transcription	Left Ventricle	heart
25	chr2:54907200-54908200	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:54907200-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:54907400-54907800	Active TSS	Osteobl	bone
28	chr2:54907400-54908000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:54907400-54908200	Flanking Active TSS	GM12878-XiMat	blood
30	chr2:54907600-54907800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:54907600-54908000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:54907600-54908000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:54907600-54908000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:54907600-54908000	Enhancers	Brain Angular Gyrus	brain
35	chr2:54907600-54908000	Enhancers	Fetal Muscle Trunk	muscle
36	chr2:54907600-54908200	Enhancers	Primary B cells from peripheral blood	blood
37	chr2:54907600-54908200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:54907600-54908200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr2:54907600-54908200	Enhancers	Liver	Liver
40	chr2:54907600-54908200	Enhancers	Duodenum Mucosa	Duodenum
41	chr2:54907600-54908200	Enhancers	Fetal Intestine Large	intestine
42	chr2:54907600-54908200	Enhancers	HMEC	breast
43	chr2:54907600-54908200	Enhancers	HSMMtube	muscle
44	chr2:54907600-54908200	Enhancers	NHEK	skin
45	chr2:54907600-54908200	Enhancers	NHLF	lung
46	chr2:54907600-54908400	Enhancers	HepG2	liver
47	chr2:54907600-54908600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:54907600-54908600	Enhancers	Brain Hippocampus Middle	brain
49	chr2:54907600-54908600	Enhancers	Fetal Thymus	thymus
50	chr2:54907600-54908800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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