Variant report

Variant	rs59371015
Chromosome Location	chr3:138268993-138268994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1082034	0.80[ASN][1000 genomes]
rs11916525	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487694	0.80[ASN][1000 genomes]
rs12630060	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12630144	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630351	0.83[EUR][1000 genomes]
rs12632793	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632794	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635354	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12635490	0.87[EUR][1000 genomes]
rs12635904	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12636936	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637638	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12637679	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059817	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13062423	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067095	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067864	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072751	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13073978	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077766	0.88[ASN][1000 genomes]
rs13084780	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095122	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095125	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13098554	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1563615	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672928	0.80[ASN][1000 genomes]
rs1672931	0.82[ASN][1000 genomes]
rs1672936	0.81[ASN][1000 genomes]
rs1672963	0.80[ASN][1000 genomes]
rs2085446	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2085447	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2280596	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2607790	0.80[ASN][1000 genomes]
rs34011134	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34153951	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34284415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34316974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34377792	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34416776	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34482601	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34583117	0.96[ASN][1000 genomes]
rs34607531	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34640717	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34652182	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34878008	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35034861	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35269190	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35270255	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35340237	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35489558	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35537868	0.87[EUR][1000 genomes]
rs35549884	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35597846	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35834585	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35876758	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35906980	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773748	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4894389	0.80[ASN][1000 genomes]
rs542010	0.80[ASN][1000 genomes]
rs56028542	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564800	0.80[ASN][1000 genomes]
rs56654955	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57516770	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582386	0.80[ASN][1000 genomes]
rs58873565	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59184769	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60371967	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60426689	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61258082	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61662147	0.86[ASN][1000 genomes]
rs620035	0.80[ASN][1000 genomes]
rs654528	0.82[ASN][1000 genomes]
rs66775405	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67390774	0.88[ASN][1000 genomes]
rs67666216	0.93[ASN][1000 genomes]
rs6784770	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73229540	0.85[ASN][1000 genomes]
rs773455	0.84[ASN][1000 genomes]
rs814022	0.80[ASN][1000 genomes]
rs9049	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880928	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
11	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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138239800-138277200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:138255800-138282000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:138256400-138274200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:138258000-138269000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr3:138258200-138271000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:138259200-138269600	Weak transcription	NHLF	lung
7	chr3:138259400-138270200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:138259400-138270200	Weak transcription	A549	lung
9	chr3:138261600-138269400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:138262000-138281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:138262400-138270200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:138263800-138273800	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:138264600-138269000	ZNF genes & repeats	Fetal Brain Female	brain
14	chr3:138264600-138269000	ZNF genes & repeats	Thymus	Thymus
15	chr3:138264800-138269000	ZNF genes & repeats	Dnd41	blood
16	chr3:138265000-138270600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr3:138265600-138269000	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr3:138265600-138269200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:138265600-138270200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr3:138266400-138270600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:138266600-138269600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:138267200-138269400	Strong transcription	Liver	Liver
23	chr3:138267400-138269000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr3:138267400-138269600	ZNF genes & repeats	Fetal Intestine Small	intestine
25	chr3:138267600-138269000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:138267600-138269600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:138267600-138276000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:138267600-138292000	Weak transcription	Fetal Heart	heart
29	chr3:138267800-138269200	ZNF genes & repeats	Fetal Thymus	thymus
30	chr3:138267800-138271000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:138268000-138269000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:138268000-138269800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:138268200-138269000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:138268200-138269600	Weak transcription	NHEK	skin
35	chr3:138268200-138278400	Weak transcription	Brain Anterior Caudate	brain
36	chr3:138268400-138269000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:138268400-138269000	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:138268400-138269000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr3:138268400-138269600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr3:138268400-138269800	Weak transcription	Brain Substantia Nigra	brain
41	chr3:138268400-138271600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:138268400-138278200	Weak transcription	Aorta	Aorta
43	chr3:138268600-138269000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:138268600-138270600	Weak transcription	Primary T cells from cord blood	blood
45	chr3:138268600-138270800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:138268600-138278200	Weak transcription	Esophagus	oesophagus
47	chr3:138268600-138278200	Weak transcription	Pancreas	Pancrea
48	chr3:138268600-138279000	Weak transcription	Colonic Mucosa	Colon
49	chr3:138268600-138291200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:138268600-138297800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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