Variant report

Variant	rs3809269
Chromosome Location	chr12:1725545-1725546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr12:1725330-1725680	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:1725401-1725734	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr12:1725402-1725687	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr12:1725309-1725703	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:1725301-1725681	MCF10A-Er-Src	breast:	n/a	n/a
6	SPI1	chr12:1725501-1726053	HL-60	blood:	n/a	n/a
7	FOS	chr12:1725404-1725711	MCF10A-Er-Src	breast:	n/a	n/a
8	RUNX3	chr12:1725398-1726122	GM12878	blood:	n/a	n/a
9	SPI1	chr12:1725514-1726003	GM12891	blood:	n/a	n/a
10	MYC	chr12:1725414-1725718	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr12:1725447-1725703	MCF10A-Er-Src	breast:	n/a	n/a
12	SP1	chr12:1725490-1725873	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:1725390-1726054	GM12878	blood:	n/a	n/a
14	STAT3	chr12:1725483-1725637	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr12:1725470-1725595	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
WNT5B	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1476709	0.86[EUR][1000 genomes]
rs35524129	0.86[EUR][1000 genomes]
rs4766420	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	16 gene(s)	inside rSNPs	diseases
5	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv898586	chr12:1690140-1734365	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv1834423	chr12:1703324-1727170	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1715200-1725800	Weak transcription	Esophagus	oesophagus
2	chr12:1715400-1738600	Weak transcription	Right Atrium	heart
3	chr12:1716200-1734600	Weak transcription	Fetal Stomach	stomach
4	chr12:1717000-1728800	Weak transcription	Lung	lung
5	chr12:1719600-1725600	Weak transcription	Thymus	Thymus
6	chr12:1719600-1728000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:1720000-1725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:1720200-1727200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:1720200-1727200	Weak transcription	Stomach Mucosa	stomach
10	chr12:1720800-1725600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:1721000-1734400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:1721600-1727400	Weak transcription	Adipose Nuclei	Adipose
13	chr12:1721800-1727200	Weak transcription	NHLF	lung
14	chr12:1721800-1727800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:1721800-1734600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:1721800-1738600	Weak transcription	Fetal Brain Female	brain
17	chr12:1722200-1725800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:1722200-1727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:1722200-1727400	Weak transcription	Osteobl	bone
20	chr12:1722200-1727600	Weak transcription	NH-A	brain
21	chr12:1722400-1725800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:1723000-1725800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr12:1723000-1727600	Enhancers	K562	blood
24	chr12:1724000-1725800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:1724000-1727000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:1724000-1727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:1724000-1731600	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:1724000-1737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:1724400-1727600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:1724400-1727600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:1724600-1725800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:1724800-1725600	Bivalent Enhancer	NHEK	skin
33	chr12:1724800-1726000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:1724800-1726400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:1724800-1727000	Enhancers	HMEC	breast
36	chr12:1724800-1727800	Weak transcription	NHDF-Ad	bronchial
37	chr12:1724800-1734200	Weak transcription	HSMM	muscle
38	chr12:1725000-1726000	Enhancers	GM12878-XiMat	blood
39	chr12:1725000-1729600	Enhancers	Primary hematopoietic stem cells	blood
40	chr12:1725200-1725600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:1725200-1725800	Enhancers	Primary B cells from cord blood	blood
42	chr12:1725200-1725800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:1725200-1726200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:1725200-1726200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:1725200-1726400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr12:1725200-1727400	Enhancers	Fetal Thymus	thymus
47	chr12:1725200-1729200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links