Variant report

Variant	rs13084780
Chromosome Location	chr3:138260236-138260237
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1082034	0.80[ASN][1000 genomes]
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];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054428	0.82[EUR][1000 genomes]
rs12487694	0.80[ASN][1000 genomes]
rs12490633	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12630060	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12630144	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630351	0.87[EUR][1000 genomes]
rs12631438	0.81[JPT][hapmap]
rs12632793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632794	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635354	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635490	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12635904	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12636936	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637638	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062423	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067095	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067864	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069355	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072751	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073978	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077766	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13093668	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095122	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095125	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098554	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1546758	1.00[CEU][hapmap]
rs1563615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672927	0.82[JPT][hapmap]
rs1672928	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs1672931	0.82[ASN][1000 genomes]
rs1672932	0.81[JPT][hapmap]
rs1672936	0.81[ASN][1000 genomes]
rs1672963	0.80[ASN][1000 genomes]
rs1673608	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1673622	0.82[JPT][hapmap]
rs1679181	0.81[JPT][hapmap]
rs1720829	0.80[JPT][hapmap]
rs2085446	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085447	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280596	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305269	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs2607790	0.80[ASN][1000 genomes]
rs34011134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34153951	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34284415	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34316974	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34377792	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34416776	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34482601	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34583117	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34607531	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34640717	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34652182	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34878008	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35034861	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35269190	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35270255	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35340237	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35489558	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35537868	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35549884	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35597846	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35834585	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35876758	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35906980	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773748	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.86[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]
rs4894389	0.80[ASN][1000 genomes]
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];0.80[ASN][1000 genomes]
rs56028542	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564800	0.80[ASN][1000 genomes]
rs56654955	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57516770	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582386	0.80[ASN][1000 genomes]
rs58873565	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59184769	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59371015	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60371967	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60426689	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609797	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs61258082	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61662147	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs620035	0.80[ASN][1000 genomes]
rs6439809	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs6439810	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs654528	0.82[ASN][1000 genomes]
rs66775405	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67390774	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67666216	0.93[ASN][1000 genomes]
rs6768963	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs6784770	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73229540	0.85[ASN][1000 genomes]
rs7645920	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs773450	0.82[JPT][hapmap]
rs773455	0.84[ASN][1000 genomes]
rs774012	0.81[CHB][hapmap];0.82[JPT][hapmap]
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];0.80[ASN][1000 genomes]
rs9049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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]
rs9880928	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active 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
7	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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	38 gene(s)	inside rSNPs	diseases
8	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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
10	nsv877539	chr3:138224220-138261288	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
13	esv1805538	chr3:138255198-138266635	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases
14	esv1812294	chr3:138255198-138266635	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13084780	CEP70	cis	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
2	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:138214400-138260600	Weak transcription	Right Ventricle	heart
5	chr3:138219400-138263200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:138231200-138260600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:138232000-138260600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:138232200-138260600	Weak transcription	Left Ventricle	heart
9	chr3:138232200-138260600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:138235600-138260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:138236000-138264800	Weak transcription	Fetal Heart	heart
12	chr3:138237200-138260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:138237400-138260400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:138237400-138260600	Weak transcription	Aorta	Aorta
15	chr3:138237600-138260600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:138239800-138277200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:138240600-138260600	Weak transcription	Pancreas	Pancrea
18	chr3:138240800-138260600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:138241000-138260600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:138246800-138260600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:138247800-138260600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:138254200-138260600	Weak transcription	Ovary	ovary
23	chr3:138254600-138260600	Weak transcription	Fetal Thymus	thymus
24	chr3:138255800-138282000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:138256000-138261000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:138256400-138274200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:138258000-138269000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr3:138258200-138260600	Weak transcription	Fetal Stomach	stomach
29	chr3:138258200-138260800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:138258200-138271000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:138258600-138260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:138258600-138262000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
33	chr3:138258600-138263800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr3:138258600-138268800	Weak transcription	K562	blood
35	chr3:138259000-138260800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:138259000-138261200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr3:138259200-138269600	Weak transcription	NHLF	lung
38	chr3:138259400-138260600	Weak transcription	Lung	lung
39	chr3:138259400-138260600	Weak transcription	Thymus	Thymus
40	chr3:138259400-138262000	ZNF genes & repeats	Fetal Lung	lung
41	chr3:138259400-138270200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:138259400-138270200	Weak transcription	A549	lung
43	chr3:138259600-138260800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:138259600-138260800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:138259600-138262000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
46	chr3:138259600-138262200	ZNF genes & repeats	Brain Anterior Caudate	brain
47	chr3:138259600-138262600	ZNF genes & repeats	Adipose Nuclei	Adipose
48	chr3:138259600-138263800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr3:138259600-138264200	ZNF genes & repeats	Dnd41	blood
50	chr3:138259800-138260600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links