Variant report

Variant	rs2280596
Chromosome Location	chr3:138213166-138213167
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10935282	0.82[JPT][hapmap]
rs11709290	0.82[JPT][hapmap]
rs11916525	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12054428	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490633	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12630060	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12630144	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630351	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12631438	0.81[JPT][hapmap]
rs12632793	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12635354	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635490	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12635904	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636936	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637638	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13062423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13067095	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13067864	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069355	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072751	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13073978	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13077766	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13084780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13093668	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13095122	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13095125	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13098554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546758	1.00[CEU][hapmap]
rs1563615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1625751	0.80[ASN][1000 genomes]
rs1672927	0.82[JPT][hapmap]
rs1672928	0.87[CHD][hapmap]
rs1672932	0.81[JPT][hapmap]
rs1673608	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1673622	0.82[JPT][hapmap]
rs1679181	0.81[JPT][hapmap]
rs1720829	0.80[JPT][hapmap]
rs1720833	0.80[ASN][1000 genomes]
rs2085446	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2085447	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2086351	0.80[ASN][1000 genomes]
rs2305269	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs34011134	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153951	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34284415	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34316974	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34377792	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34416776	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34482601	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34583117	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34607531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34640717	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34652182	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34878008	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35034861	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35269190	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35270255	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35340237	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35489558	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35537868	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35549884	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35597846	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35834585	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35876758	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35906980	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3773748	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3813264	0.82[JPT][hapmap]
rs3884240	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3884241	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs497334	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs503922	0.82[JPT][hapmap]
rs529615	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs542010	0.81[CHB][hapmap]
rs56028542	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56654955	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57516770	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58873565	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59184769	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59371015	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60371967	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60426689	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs609797	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs61258082	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61662147	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6439809	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6439810	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs66775405	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67390774	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67666216	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768963	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs6784770	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7645920	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs773450	0.82[JPT][hapmap]
rs774011	0.80[ASN][1000 genomes]
rs774012	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs811794	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs812277	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs814022	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936316	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9848938	0.81[JPT][hapmap]
rs9855306	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs9880928	0.94[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	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280596	CEP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:138208600-138215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:138208800-138213400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:138209200-138218400	Weak transcription	Gastric	stomach
7	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
8	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
9	chr3:138210000-138218400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:138210000-138230200	Weak transcription	Fetal Brain Male	brain
11	chr3:138210200-138215000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:138210200-138222000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:138210400-138215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:138210400-138218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:138210800-138213200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:138210800-138213200	Strong transcription	Stomach Smooth Muscle	stomach
19	chr3:138210800-138214400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
21	chr3:138211000-138213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:138211000-138229400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:138211000-138231000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:138211000-138236600	Weak transcription	Spleen	Spleen
25	chr3:138211200-138213200	Strong transcription	Dnd41	blood
26	chr3:138211200-138213600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:138211200-138213600	Strong transcription	Liver	Liver
28	chr3:138211200-138213600	Strong transcription	Fetal Thymus	thymus
29	chr3:138211200-138215000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:138211200-138215000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:138211200-138215000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr3:138211200-138227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
34	chr3:138211400-138213200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:138211400-138230400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:138211600-138213200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:138211600-138213200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:138211600-138213400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:138211600-138215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:138211600-138227400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:138211800-138213200	Strong transcription	Adipose Nuclei	Adipose
42	chr3:138211800-138213200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr3:138211800-138214400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:138211800-138214800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:138211800-138215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:138212000-138214400	Enhancers	NHDF-Ad	bronchial
48	chr3:138212000-138235000	Weak transcription	Brain Germinal Matrix	brain
49	chr3:138212000-138235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:138212200-138213600	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links