Variant report

Variant	rs12416581
Chromosome Location	chr10:90780440-90780441
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12411452	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12411483	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12412701	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415680	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234768	1.00[ASN][1000 genomes]
rs2862834	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34462240	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34891735	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36206197	1.00[ASN][1000 genomes]
rs3740281	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758483	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55803311	1.00[ASN][1000 genomes]
rs66782588	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7079111	1.00[ASN][1000 genomes]
rs72809352	1.00[ASN][1000 genomes]
rs72809360	1.00[ASN][1000 genomes]
rs72810908	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908760	1.00[CHB][hapmap]
rs7909414	1.00[ASN][1000 genomes]
rs9325604	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658691	1.00[ASN][1000 genomes]
rs9658727	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658750	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9658757	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658766	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658786	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658788	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9658791	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12416581	TNKS2	cis	cerebellum	SCAN
rs12416581	BRCC3	trans	parietal	SCAN
rs12416581	LIPA	cis	parietal	SCAN
rs12416581	LIPN	cis	cerebellum	SCAN
rs12416581	RPP30	cis	parietal	SCAN
rs12416581	ACTA2	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90754000-90789600	Weak transcription	A549	lung
2	chr10:90756200-90781800	Weak transcription	Stomach Mucosa	stomach
3	chr10:90761800-90783800	Weak transcription	Gastric	stomach
4	chr10:90761800-90786200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:90762400-90785800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr10:90762600-90786000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr10:90762800-90781000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:90762800-90782000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr10:90763600-90780800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:90766200-90785600	Strong transcription	GM12878-XiMat	blood
11	chr10:90767400-90781000	Strong transcription	Osteobl	bone
12	chr10:90767600-90780800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:90767600-90786600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:90767800-90781800	Weak transcription	Small Intestine	intestine
15	chr10:90768400-90785000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr10:90769400-90781400	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr10:90771600-90782600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr10:90771600-90784800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:90771600-90789600	Weak transcription	Brain Anterior Caudate	brain
20	chr10:90771800-90808600	Weak transcription	Primary T cells from cord blood	blood
21	chr10:90772400-90795000	Weak transcription	Placenta	Placenta
22	chr10:90772600-90784600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr10:90772600-90789600	Weak transcription	Fetal Stomach	stomach
24	chr10:90772600-90791800	Weak transcription	Esophagus	oesophagus
25	chr10:90772600-90792000	Weak transcription	Colonic Mucosa	Colon
26	chr10:90772600-90795800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr10:90773800-90780800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr10:90774400-90780800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:90774400-90781200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:90774600-90784800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:90774800-90781600	Strong transcription	Ovary	ovary
32	chr10:90775000-90789400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:90775200-90789400	Weak transcription	NH-A	brain
34	chr10:90776000-90781000	Strong transcription	Aorta	Aorta
35	chr10:90776000-90781000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:90776200-90781000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:90776200-90789400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:90776600-90781400	Weak transcription	Pancreas	Pancrea
39	chr10:90776600-90792600	Weak transcription	Right Ventricle	heart
40	chr10:90776800-90789400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr10:90777800-90781400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:90778000-90791200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:90778400-90780600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr10:90778800-90780600	Strong transcription	HSMM	muscle
45	chr10:90778800-90780800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr10:90778800-90781000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr10:90778800-90781200	Strong transcription	NHDF-Ad	bronchial
48	chr10:90779000-90780600	ZNF genes & repeats	Liver	Liver
49	chr10:90779000-90780800	ZNF genes & repeats	Dnd41	blood
50	chr10:90779000-90781000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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