Variant report

Variant	rs13071857
Chromosome Location	chr3:139152153-139152154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1044826	1.00[CEU][hapmap]
rs10935323	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12494806	1.00[CEU][hapmap]
rs12695698	1.00[CEU][hapmap];0.89[CHB][hapmap];0.80[EUR][1000 genomes]
rs12695699	0.80[EUR][1000 genomes]
rs13060697	0.82[EUR][1000 genomes]
rs13083195	1.00[CEU][hapmap]
rs13085888	0.80[EUR][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs13092507	0.82[EUR][1000 genomes]
rs13092935	0.80[EUR][1000 genomes]
rs1586863	0.82[EUR][1000 genomes]
rs1586864	0.82[EUR][1000 genomes]
rs167184	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1907687	0.82[EUR][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs2233815	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs2349059	0.80[EUR][1000 genomes]
rs295488	0.82[JPT][hapmap]
rs3772877	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs3772878	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs3772879	0.89[CHB][hapmap]
rs3821544	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs3821545	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs4544576	0.82[EUR][1000 genomes]
rs4683799	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9289578	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs964227	0.82[EUR][1000 genomes]
rs9818691	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9825064	1.00[CEU][hapmap]
rs9831108	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9835241	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9848241	0.82[EUR][1000 genomes]
rs9849039	0.82[EUR][1000 genomes]
rs9849578	1.00[CEU][hapmap]
rs9860201	0.90[CEU][hapmap]
rs9882014	0.95[CEU][hapmap];0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv2760754	chr3:139144615-139164874	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139114200-139153800	Weak transcription	Left Ventricle	heart
2	chr3:139136400-139166200	Weak transcription	Fetal Brain Female	brain
3	chr3:139137800-139153200	Weak transcription	Esophagus	oesophagus
4	chr3:139138200-139153600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:139138600-139166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:139138600-139170400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:139139600-139160000	Weak transcription	Fetal Brain Male	brain
8	chr3:139140800-139152800	Weak transcription	Placenta	Placenta
9	chr3:139140800-139153200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:139140800-139153200	Weak transcription	HSMMtube	muscle
11	chr3:139140800-139153800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:139141200-139160000	Weak transcription	Lung	lung
13	chr3:139141400-139167000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:139142200-139152800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:139142200-139172200	Weak transcription	Fetal Heart	heart
16	chr3:139142400-139154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:139142600-139158200	Weak transcription	Gastric	stomach
18	chr3:139142800-139162600	Weak transcription	Psoas Muscle	Psoas
19	chr3:139142800-139169000	Weak transcription	Aorta	Aorta
20	chr3:139142800-139176800	Weak transcription	Fetal Stomach	stomach
21	chr3:139143000-139153800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:139143600-139153800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:139144800-139173200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:139145000-139153400	Weak transcription	Ovary	ovary
25	chr3:139145000-139153800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:139145200-139152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:139145200-139153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:139145200-139158000	Weak transcription	Brain Substantia Nigra	brain
29	chr3:139145200-139158200	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:139145200-139164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:139145200-139170400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:139145400-139153400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:139146800-139153400	Weak transcription	Fetal Lung	lung
34	chr3:139147200-139158200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:139147400-139153000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:139147400-139153000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr3:139147400-139160200	Weak transcription	Brain Angular Gyrus	brain
38	chr3:139147800-139153200	Weak transcription	Fetal Intestine Small	intestine
39	chr3:139148000-139160000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:139148800-139153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:139149600-139152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:139149800-139153600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr3:139149800-139170600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:139150600-139152200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:139151800-139152600	Weak transcription	Adipose Nuclei	Adipose
46	chr3:139151800-139158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:139152000-139152200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
48	chr3:139152000-139152400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links