Variant report

Variant	rs13074884
Chromosome Location	chr3:46993143-46993144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46988980..46994216-chr3:47016439..47022535,7	K562	blood:
2	chr3:46987488..46994423-chr3:47016253..47019914,6	MCF-7	breast:
3	chr3:46988418..46991129-chr3:46992863..46994642,3	MCF-7	breast:
4	chr3:46992891..46995361-chr3:47004607..47007374,2	MCF-7	breast:
5	chr3:46993041..46995087-chr3:46996208..46998631,3	K562	blood:
6	chr3:46992711..46994503-chr3:47010548..47012316,2	K562	blood:

Variant related genes	Relation type
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11130109	0.87[AFR][1000 genomes]
rs11709876	0.82[AFR][1000 genomes]
rs13062516	0.81[AFR][1000 genomes]
rs1463394	0.87[AFR][1000 genomes]
rs1563431	0.80[AFR][1000 genomes]
rs2124510	0.81[AFR][1000 genomes]
rs2385868	0.82[AFR][1000 genomes]
rs2891893	0.87[AFR][1000 genomes]
rs4324490	0.82[AFR][1000 genomes]
rs4378998	0.82[AFR][1000 genomes]
rs4389512	0.82[AFR][1000 genomes]
rs4543047	0.82[AFR][1000 genomes]
rs4682834	0.80[AFR][1000 genomes]
rs4682835	0.87[AFR][1000 genomes]
rs4682836	0.87[AFR][1000 genomes]
rs4682838	0.80[AFR][1000 genomes]
rs4683285	0.86[AFR][1000 genomes]
rs6442043	0.80[AFR][1000 genomes]
rs6442044	0.87[AFR][1000 genomes]
rs6442047	0.82[AFR][1000 genomes]
rs6442048	0.81[AFR][1000 genomes]
rs6766676	0.87[AFR][1000 genomes]
rs6806521	0.82[AFR][1000 genomes]
rs7624549	0.87[AFR][1000 genomes]
rs7627241	0.82[AFR][1000 genomes]
rs7630904	0.83[AFR][1000 genomes]
rs7646076	0.86[AFR][1000 genomes]
rs7649941	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012682	chr3:46973552-47016357	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46977000-47000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:46979600-46994600	Genic enhancers	Fetal Thymus	thymus
3	chr3:46983600-46994000	Enhancers	HUVEC	blood vessel
4	chr3:46984200-46996400	Enhancers	Liver	Liver
5	chr3:46985600-46995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:46985800-46994200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:46985800-47004400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:46987600-46994800	Enhancers	Fetal Intestine Large	intestine
9	chr3:46988000-46994200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:46988000-47003200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:46988400-46994600	Genic enhancers	Dnd41	blood
12	chr3:46988600-46994400	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:46989200-46995400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:46989600-46993200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:46989800-46993200	Enhancers	Adipose Nuclei	Adipose
16	chr3:46989800-46993800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:46989800-46995200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:46989800-46998600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:46989800-47000600	Weak transcription	Brain Germinal Matrix	brain
20	chr3:46989800-47000600	Weak transcription	NHDF-Ad	bronchial
21	chr3:46989800-47001200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:46990000-46995400	Weak transcription	HSMMtube	muscle
23	chr3:46990000-47006800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:46990200-46995200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:46990200-46995400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:46990200-46998200	Weak transcription	Aorta	Aorta
27	chr3:46990200-47000800	Weak transcription	Fetal Brain Female	brain
28	chr3:46990400-47000000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:46990800-46993600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:46991000-46995200	Weak transcription	NH-A	brain
31	chr3:46991000-46996800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:46991000-46998800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:46991000-47000200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:46991000-47001400	Weak transcription	Osteobl	bone
35	chr3:46991200-46993200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:46991200-46993400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:46991200-46993600	Weak transcription	Fetal Stomach	stomach
38	chr3:46991200-46993600	Weak transcription	Thymus	Thymus
39	chr3:46991200-46993800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:46991200-46993800	Enhancers	GM12878-XiMat	blood
41	chr3:46991200-46994000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:46991200-46994200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:46991200-46994400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:46991200-46994400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:46991200-46994400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:46991200-46994600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:46991200-46994600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:46991200-46994600	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr3:46991200-46994800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:46991200-46994800	Weak transcription	Placenta Amnion	Placenta Amnion

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