Variant report

Variant	rs557515860
Chromosome Location	chr5:119950300-119950301
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	POLR2A	chr5:119950271-119950534	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr5:119950226-119950846	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr5:119950254-119950534	MCF10A-Er-Src	breast:	n/a	n/a
4	PBX3	chr5:119950171-119950849	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr5:119950086-119950549	SK-N-SH	brain:	n/a	n/a
6	NFIC	chr5:119949891-119950748	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr5:119949576-119950746	SK-N-SH	brain:	n/a	n/a
8	STAT3	chr5:119950258-119950491	MCF10A-Er-Src	breast:	n/a	n/a
9	PBX3	chr5:119950107-119950770	SK-N-SH	brain:	n/a	n/a
10	EP300	chr5:119949959-119950739	SK-N-SH	brain:	n/a	n/a
11	TEAD4	chr5:119950011-119950746	SK-N-SH	brain:	n/a	n/a
12	CEBPB	chr5:119950210-119950705	IMR90	lung:	n/a	n/a
13	GATA3	chr5:119949512-119950694	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr5:119950137-119950571	ECC-1	luminal epithelium:	n/a	n/a
15	MYC	chr5:119950265-119950564	MCF10A-Er-Src	breast:	n/a	n/a
16	TCF12	chr5:119950010-119950773	SK-N-SH	brain:	n/a	n/a
17	MYC	chr5:119950280-119950563	MCF10A-Er-Src	breast:	n/a	n/a
18	FOSL2	chr5:119949965-119950740	SK-N-SH	brain:	n/a	n/a
19	FOS	chr5:119950200-119950575	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PRR16	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv830464	chr5:119950090-120106717	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119942600-119952800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:119948200-119952000	Enhancers	Osteobl	bone
3	chr5:119948600-119950400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:119948600-119952000	Enhancers	HSMM	muscle
5	chr5:119949200-119950400	Enhancers	NH-A	brain
6	chr5:119949200-119953000	Enhancers	NHLF	lung
7	chr5:119949400-119950600	Enhancers	Brain Cingulate Gyrus	brain
8	chr5:119949400-119951000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:119949400-119951800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:119949400-119952400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:119949400-119953000	Enhancers	HMEC	breast
12	chr5:119949400-119953000	Enhancers	NHEK	skin
13	chr5:119949600-119950400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:119949600-119950600	Enhancers	Fetal Lung	lung
15	chr5:119949600-119950600	Flanking Active TSS	NHDF-Ad	bronchial
16	chr5:119949600-119950800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:119949600-119951000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:119949600-119951200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:119949600-119951200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:119949600-119952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:119949800-119950600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:119949800-119950600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr5:119949800-119950600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:119949800-119950600	Enhancers	Brain Substantia Nigra	brain
25	chr5:119949800-119950600	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:119949800-119950600	Enhancers	Fetal Brain Female	brain
27	chr5:119949800-119950600	Enhancers	Rectal Smooth Muscle	rectum
28	chr5:119949800-119950800	Enhancers	Fetal Brain Male	brain
29	chr5:119949800-119951600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:119949800-119953000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:119950000-119950600	Enhancers	Aorta	Aorta
32	chr5:119950000-119950600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr5:119950000-119950600	Flanking Active TSS	HSMMtube	muscle
34	chr5:119950000-119950800	Enhancers	Brain Germinal Matrix	brain
35	chr5:119950000-119950800	Enhancers	Brain Hippocampus Middle	brain
36	chr5:119950000-119951000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:119950000-119951400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:119950200-119950600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr5:119950200-119951000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links