Variant report

Variant	rs12881652
Chromosome Location	chr14:64400120-64400121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10149728	0.91[CEU][hapmap]
rs10873172	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11623650	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1255856	0.86[EUR][1000 genomes]
rs1255867	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255869	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255872	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255873	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255874	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255875	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255876	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1255877	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1255878	0.80[EUR][1000 genomes]
rs1255879	0.80[EUR][1000 genomes]
rs1255880	0.80[EUR][1000 genomes]
rs1255883	0.80[EUR][1000 genomes]
rs1255885	0.80[EUR][1000 genomes]
rs1255887	0.80[EUR][1000 genomes]
rs1262235	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1266870	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1270526	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1271567	0.95[CEU][hapmap]
rs1272156	0.82[ASW][hapmap];0.95[CEU][hapmap]
rs1272714	0.81[AMR][1000 genomes]
rs1273192	0.80[EUR][1000 genomes]
rs12878653	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1953241	0.82[GIH][hapmap]
rs2184292	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2357175	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2792201	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2884111	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2994421	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2994422	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35224808	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4027383	0.82[CHB][hapmap]
rs61984073	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7156570	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9323442	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9323443	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs945027	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs945028	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12881652	DAAM1	cis	cerebellum	SCAN
rs12881652	SYNE2	cis	cerebellum	SCAN
rs12881652	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
3	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr14:64378000-64404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
6	chr14:64378400-64416000	Weak transcription	Primary B cells from cord blood	blood
7	chr14:64378800-64401200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:64379800-64409000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr14:64386400-64403800	Weak transcription	Esophagus	oesophagus
10	chr14:64386400-64405600	Weak transcription	Pancreas	Pancrea
11	chr14:64386600-64403400	Weak transcription	Gastric	stomach
12	chr14:64387000-64404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:64387000-64416400	Weak transcription	Aorta	Aorta
14	chr14:64390200-64400600	Weak transcription	Right Atrium	heart
15	chr14:64390200-64416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr14:64390600-64418800	Weak transcription	HepG2	liver
17	chr14:64390800-64404000	Weak transcription	Placenta	Placenta
18	chr14:64390800-64408600	Weak transcription	Fetal Intestine Large	intestine
19	chr14:64392000-64405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr14:64392000-64409000	Weak transcription	Fetal Intestine Small	intestine
21	chr14:64393200-64419800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr14:64393800-64403200	Weak transcription	Spleen	Spleen
23	chr14:64393800-64414800	Weak transcription	Fetal Muscle Leg	muscle
24	chr14:64394200-64403400	Weak transcription	Right Ventricle	heart
25	chr14:64395000-64403200	Weak transcription	Left Ventricle	heart
26	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
27	chr14:64395600-64408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:64396000-64400600	Weak transcription	Ovary	ovary
29	chr14:64396000-64405000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:64396000-64408400	Weak transcription	Fetal Kidney	kidney
31	chr14:64396000-64418600	Weak transcription	Fetal Heart	heart
32	chr14:64396800-64407200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:64397000-64403200	Weak transcription	Dnd41	blood
34	chr14:64397400-64409000	Weak transcription	Fetal Stomach	stomach
35	chr14:64399400-64400400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr14:64399400-64400800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr14:64399400-64400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr14:64399400-64401200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr14:64399400-64401400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr14:64399400-64401400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:64399600-64400200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr14:64399600-64400200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:64399600-64400400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:64399600-64400400	Enhancers	Brain Germinal Matrix	brain
45	chr14:64399600-64400400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr14:64399600-64400400	Flanking Active TSS	NHEK	skin
47	chr14:64399600-64400600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr14:64399600-64400800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr14:64399600-64400800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:64399600-64400800	Flanking Active TSS	GM12878-XiMat	blood

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