Variant report

Variant	rs2275018
Chromosome Location	chr14:64375985-64375986
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11158512	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11158516	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12435958	0.87[CHB][hapmap];0.85[MEX][hapmap]
rs12587472	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12588087	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12894053	0.86[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12894864	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1953241	0.86[CEU][hapmap];0.87[CHB][hapmap]
rs1959034	0.87[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1959035	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2150288	0.81[ASN][1000 genomes]
rs2150291	0.86[JPT][hapmap]
rs2210650	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2357001	0.87[CHB][hapmap];0.81[MEX][hapmap]
rs2357002	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2357003	0.95[CEU][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34780876	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902247	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4902248	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6573534	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6573535	0.87[CHB][hapmap]
rs7145302	0.91[CHB][hapmap];0.81[MEX][hapmap]
rs7145657	0.84[ASN][1000 genomes]
rs7146821	0.87[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7149766	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7153101	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7157314	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7157323	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7158974	0.88[ASN][1000 genomes]
rs7160127	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7493416	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8005899	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8013611	0.83[CHB][hapmap]
rs8015158	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8015354	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8022917	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs945030	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs951250	0.87[CHB][hapmap]
rs954730	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9707224	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998241	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2275018	FLJ43390	cis	cerebellum	SCAN
rs2275018	HIF1A	cis	parietal	SCAN
rs2275018	SYT16	cis	parietal	SCAN
rs2275018	SYNE2	cis	parietal	SCAN
rs2275018	SYNE2	cis	cerebellum	SCAN
rs2275018	ADORA3	trans	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64358200-64377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:64358800-64377600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:64360600-64382200	Weak transcription	Psoas Muscle	Psoas
5	chr14:64360800-64377800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:64364400-64385200	Weak transcription	Pancreas	Pancrea
7	chr14:64364600-64387800	Weak transcription	HMEC	breast
8	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
9	chr14:64365200-64386200	Weak transcription	Gastric	stomach
10	chr14:64365400-64376600	Weak transcription	Placenta	Placenta
11	chr14:64365400-64379800	Weak transcription	Fetal Thymus	thymus
12	chr14:64365400-64393600	Weak transcription	Right Ventricle	heart
13	chr14:64367400-64378000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr14:64367800-64377400	Weak transcription	Primary B cells from cord blood	blood
15	chr14:64369600-64377600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:64369800-64376200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:64369800-64376400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr14:64369800-64386200	Weak transcription	Esophagus	oesophagus
19	chr14:64372200-64378000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:64373000-64376000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr14:64373200-64376400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr14:64373600-64376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr14:64374000-64376000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr14:64374200-64376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr14:64374400-64376000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr14:64374400-64376000	Enhancers	Small Intestine	intestine
27	chr14:64374600-64376400	Enhancers	Liver	Liver
28	chr14:64374600-64377400	Weak transcription	Brain Germinal Matrix	brain
29	chr14:64374600-64399600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr14:64374800-64376000	Enhancers	Fetal Heart	heart
31	chr14:64375000-64376000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr14:64375000-64377400	Weak transcription	Fetal Intestine Small	intestine
33	chr14:64375200-64376000	Active TSS	Stomach Smooth Muscle	stomach
34	chr14:64375200-64376200	Weak transcription	Lung	lung
35	chr14:64375200-64385000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr14:64375200-64395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:64375200-64395200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr14:64375400-64376000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:64375400-64376000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr14:64375400-64376000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr14:64375400-64376000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:64375400-64376000	Active TSS	Aorta	Aorta
43	chr14:64375400-64376000	Active TSS	Brain Substantia Nigra	brain
44	chr14:64375400-64376000	Flanking Active TSS	Fetal Lung	lung
45	chr14:64375400-64376000	Enhancers	Left Ventricle	heart
46	chr14:64375400-64376000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr14:64375400-64376000	Flanking Active TSS	Osteobl	bone
48	chr14:64375400-64377400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr14:64375400-64380000	Strong transcription	Dnd41	blood
50	chr14:64375600-64376000	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links