Variant report

Variant	rs538924471
Chromosome Location	chr3:52092405-52092406
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	MAZ	chr3:52088560-52092528	IMR90	lung:	n/a	chr3:52091334-52091347 chr3:52091339-52091347 chr3:52091535-52091545 chr3:52091336-52091345 chr3:52091336-52091345 chr3:52091331-52091350 chr3:52091335-52091346
2	EBF1	chr3:52092291-52092420	GM12878	blood:	n/a	chr3:52092350-52092363 chr3:52092351-52092362 chr3:52092352-52092362 chr3:52092352-52092361
3	KAP1	chr3:52092132-52092441	U2OS	brain:	n/a	n/a
4	EBF1	chr3:52092226-52092494	GM12878	blood:	n/a	chr3:52092350-52092363 chr3:52092351-52092362 chr3:52092352-52092362 chr3:52092352-52092361

No.	Distal block	Cell Line	Cell type
1	chr3:52028061..52031321-chr3:52088873..52092735,5	MCF-7	breast:
2	chr3:52091359..52093112-chr3:52104568..52106950,2	K562	blood:
3	chr3:52088485..52093169-chr3:52093699..52100396,11	MCF-7	breast:
4	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:

Variant related genes	Relation type
DUSP7	TF binding region
ENSG00000114779	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000256097	Chromatin interaction
ENSG00000243989	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv1797189	chr3:52070955-52101799	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
12	esv1798365	chr3:52070955-52101799	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
13	nsv590282	chr3:52088204-52097060	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv1836489	chr3:52089837-52101799	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv1838771	chr3:52089837-52101799	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv590293	chr3:52089889-52097060	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv590299	chr3:52090344-52096432	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv590300	chr3:52090597-52096432	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52091200-52092600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:52091200-52092800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:52091400-52092600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:52091800-52092600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:52091800-52101800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:52091800-52106000	Enhancers	Esophagus	oesophagus
7	chr3:52092000-52092600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:52092000-52092600	Enhancers	Fetal Muscle Leg	muscle
9	chr3:52092000-52092800	Weak transcription	A549	lung
10	chr3:52092000-52095800	Weak transcription	Left Ventricle	heart
11	chr3:52092000-52096200	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:52092000-52096400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:52092000-52096400	Weak transcription	HUVEC	blood vessel
14	chr3:52092000-52096400	Weak transcription	NH-A	brain
15	chr3:52092000-52096800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:52092000-52097600	Enhancers	GM12878-XiMat	blood
17	chr3:52092000-52099200	Weak transcription	Right Atrium	heart
18	chr3:52092000-52102200	Enhancers	HMEC	breast
19	chr3:52092000-52106400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:52092200-52092600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:52092200-52092600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:52092200-52093400	Enhancers	NHEK	skin
23	chr3:52092200-52093600	Enhancers	Fetal Muscle Trunk	muscle
24	chr3:52092200-52093800	Weak transcription	Spleen	Spleen
25	chr3:52092200-52094800	Weak transcription	Lung	lung
26	chr3:52092200-52094800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:52092200-52095200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:52092200-52095600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:52092200-52095800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:52092200-52095800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:52092200-52095800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:52092200-52096200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:52092200-52096400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:52092200-52096400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:52092200-52096400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:52092200-52096400	Weak transcription	Pancreas	Pancrea
37	chr3:52092200-52096400	Weak transcription	NHLF	lung
38	chr3:52092200-52096400	Weak transcription	Osteobl	bone
39	chr3:52092200-52096600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52092200-52096600	Weak transcription	Brain Anterior Caudate	brain
41	chr3:52092200-52096600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:52092200-52096600	Weak transcription	Brain Substantia Nigra	brain
43	chr3:52092200-52096600	Weak transcription	Right Ventricle	heart
44	chr3:52092200-52096800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52092200-52096800	Weak transcription	Fetal Brain Male	brain
46	chr3:52092200-52099200	Weak transcription	Gastric	stomach
47	chr3:52092200-52101400	Weak transcription	Fetal Intestine Large	intestine
48	chr3:52092200-52102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:52092200-52102800	Weak transcription	Thymus	Thymus
50	chr3:52092200-52104200	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links