Variant report

Variant	rs550526497
Chromosome Location	chr3:119012439-119012440
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	RUNX3	chr3:119012385-119013728	GM12878	blood:	n/a	n/a
2	EP300	chr3:119012412-119012822	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr3:119012436-119013312	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr3:119012408-119012871	SK-N-SH_RA	brain:	n/a	n/a
5	POLR2A	chr3:119012347-119014210	GM12878	blood:	n/a	n/a
6	MXI1	chr3:119012051-119014329	IMR90	lung:	n/a	n/a
7	RUNX3	chr3:119012370-119013672	GM12878	blood:	n/a	n/a
8	MXI1	chr3:119011830-119016982	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:119012420-119013504	SK-N-MC	brain:	n/a	n/a
10	TCF7L2	chr3:119012379-119013528	HEK293	kidney:	n/a	chr3:119012928-119012937 chr3:119012925-119012939
11	STAT3	chr3:119012250-119012447	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:119012410-119014350	GM12878	blood:	n/a	n/a
13	MTA3	chr3:119012380-119014309	GM12878	blood:	n/a	n/a
14	FOXM1	chr3:119012413-119013778	GM12878	blood:	n/a	n/a
15	TCF7L2	chr3:119012295-119014165	PANC-1	pancreas:	n/a	chr3:119012928-119012937 chr3:119012925-119012939
16	EP300	chr3:119012427-119013617	GM12878	blood:	n/a	chr3:119013303-119013319 chr3:119013538-119013554 chr3:119012940-119012956 chr3:119013536-119013545 chr3:119013474-119013488
17	MTA3	chr3:119012423-119013674	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:119012253-119014459	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr3:119012432-119013672	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119011699..119014378-chr3:119015999..119019083,3	MCF-7	breast:
2	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
3	chr3:119011961..119014558-chr3:119015081..119019200,4	MCF-7	breast:
4	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:

Variant related genes	Relation type
ARHGAP31	TF binding region
ENSG00000241155	Chromatin interaction
ENSG00000242829	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119008800-119012600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119008800-119012600	Weak transcription	Esophagus	oesophagus
3	chr3:119008800-119012800	Weak transcription	Spleen	Spleen
4	chr3:119011400-119012600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:119011400-119012600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:119011400-119012600	Bivalent Enhancer	HepG2	liver
7	chr3:119011400-119012800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:119011600-119012600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:119011600-119012600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:119011600-119012600	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr3:119011600-119012600	Flanking Active TSS	Fetal Heart	heart
12	chr3:119011600-119012800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr3:119011800-119012600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:119011800-119012600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:119011800-119012600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr3:119011800-119012600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr3:119011800-119012600	Enhancers	Placenta	Placenta
18	chr3:119011800-119012600	Flanking Active TSS	GM12878-XiMat	blood
19	chr3:119011800-119012800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:119011800-119014000	Flanking Bivalent TSS/Enh	Dnd41	blood
21	chr3:119012000-119012600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:119012000-119012600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr3:119012000-119012600	Enhancers	Liver	Liver
24	chr3:119012000-119012600	Enhancers	Brain Substantia Nigra	brain
25	chr3:119012000-119012600	Weak transcription	Lung	lung
26	chr3:119012000-119012600	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr3:119012000-119012800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:119012000-119012800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr3:119012000-119012800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr3:119012000-119012800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:119012200-119012600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:119012200-119012600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:119012200-119012600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:119012200-119012600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr3:119012200-119012600	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr3:119012200-119012600	Flanking Active TSS	A549	lung
37	chr3:119012200-119012800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr3:119012200-119012800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:119012200-119012800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr3:119012200-119012800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr3:119012200-119012800	Flanking Active TSS	HSMMtube	muscle
42	chr3:119012200-119012800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr3:119012200-119012800	Flanking Active TSS	Osteobl	bone
44	chr3:119012200-119013000	Flanking Active TSS	Fetal Thymus	thymus
45	chr3:119012200-119014200	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr3:119012200-119014400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:119012200-119014800	Active TSS	NHDF-Ad	bronchial
48	chr3:119012200-119015000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr3:119012200-119015600	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:119012400-119012600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links