Variant report

Variant	rs558699489
Chromosome Location	chr6:25405721-25405722
allele	C/G
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	ZNF143	chr6:25405020-25405743	GM12878	blood:	n/a	n/a
2	MTA3	chr6:25404914-25405788	GM12878	blood:	n/a	n/a
3	EBF1	chr6:25405051-25405759	GM12878	blood:	n/a	n/a
4	NFIC	chr6:25404897-25406001	GM12878	blood:	n/a	n/a
5	MEF2A	chr6:25404990-25405895	GM12878	blood:	n/a	chr6:25405455-25405464 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405459-25405474 chr6:25405450-25405471 chr6:25405454-25405475 chr6:25405457-25405472 chr6:25405452-25405467 chr6:25405454-25405465 chr6:25405461-25405472 chr6:25405460-25405471 chr6:25405458-25405473 chr6:25405452-25405466 chr6:25405457-25405474 chr6:25405450-25405471 chr6:25405459-25405473 chr6:25405454-25405475 chr6:25405461-25405470 chr6:25405458-25405474
6	MTA3	chr6:25405029-25405830	GM12878	blood:	n/a	n/a
7	SPI1	chr6:25405714-25405885	GM12878	blood:	n/a	chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849
8	SPI1	chr6:25405656-25405960	GM12891	blood:	n/a	chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849
9	PML	chr6:25404914-25405879	GM12878	blood:	n/a	n/a
10	BCLAF1	chr6:25405013-25405950	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405801-25405810
11	RUNX3	chr6:25404863-25406226	GM12878	blood:	n/a	n/a
12	RCOR1	chr6:25405103-25406052	GM12878	blood:	n/a	n/a
13	EP300	chr6:25405031-25405999	GM12878	blood:	n/a	chr6:25405260-25405274 chr6:25405264-25405273 chr6:25405936-25405950
14	EP300	chr6:25405042-25406147	GM12878	blood:	n/a	chr6:25405260-25405274 chr6:25405264-25405273 chr6:25405936-25405950
15	SPI1	chr6:25405657-25406007	GM12878	blood:	n/a	chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849
16	EP300	chr6:25404983-25406098	GM12878	blood:	n/a	chr6:25405260-25405274 chr6:25405264-25405273 chr6:25405936-25405950
17	IKZF1	chr6:25405007-25406188	GM12878	blood:	n/a	chr6:25405768-25405780
18	SPI1	chr6:25405653-25405938	GM12891	blood:	n/a	chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849
19	NFIC	chr6:25404889-25406187	GM12878	blood:	n/a	n/a
20	SPI1	chr6:25404772-25406213	GM12878	blood:	n/a	chr6:25405260-25405269 chr6:25405801-25405810 chr6:25405835-25405848 chr6:25405838-25405847 chr6:25405836-25405849

Variant related genes	Relation type
ENSG00000253017	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1850810	chr6:25405576-25462543	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25402200-25406200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:25402200-25409600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:25403600-25406000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:25403600-25406400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:25403600-25408200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:25403800-25406000	Enhancers	Brain Substantia Nigra	brain
8	chr6:25403800-25406400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25403800-25406400	Weak transcription	Spleen	Spleen
10	chr6:25403800-25410600	Weak transcription	Pancreas	Pancrea
11	chr6:25404200-25406000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr6:25404400-25406400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr6:25404400-25406600	Enhancers	Colonic Mucosa	Colon
14	chr6:25404400-25406600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:25404400-25407400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:25404400-25407600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:25404400-25410800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:25404600-25406000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:25404800-25405800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:25404800-25405800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr6:25404800-25405800	Flanking Active TSS	Fetal Thymus	thymus
22	chr6:25404800-25406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:25404800-25406600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:25405000-25405800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:25405000-25405800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr6:25405000-25405800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:25405000-25406000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr6:25405000-25406000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr6:25405000-25406000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr6:25405000-25406000	Enhancers	Fetal Intestine Small	intestine
31	chr6:25405000-25406000	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr6:25405000-25406200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:25405000-25406200	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr6:25405000-25406200	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr6:25405000-25406200	Enhancers	Fetal Intestine Large	intestine
36	chr6:25405000-25406200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:25405000-25406400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:25405000-25406600	Enhancers	Adipose Nuclei	Adipose
39	chr6:25405200-25405800	Enhancers	H9 Cell Line	embryonic stem cell
40	chr6:25405200-25405800	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:25405200-25405800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr6:25405200-25405800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:25405200-25405800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:25405200-25405800	Weak transcription	Small Intestine	intestine
45	chr6:25405200-25406000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:25405200-25406000	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr6:25405200-25406000	Enhancers	HMEC	breast
48	chr6:25405200-25406200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr6:25405200-25406200	Weak transcription	Lung	lung
50	chr6:25405200-25406400	Weak transcription	Right Atrium	heart

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