Variant report

Variant	rs553339259
Chromosome Location	chr15:41165468-41165469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr15:41163444-41165568	GM12878	blood:	n/a	n/a
2	YY1	chr15:41165177-41166262	GM12878	blood:	n/a	n/a
3	CHD2	chr15:41165022-41165505	GM12878	blood:	n/a	n/a
4	TCF12	chr15:41165435-41166733	ECC-1	luminal epithelium:	n/a	n/a
5	SMARCB1	chr15:41165318-41166665	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:41162820-41166815	Hela-S3	cervix:	n/a	n/a
7	YY1	chr15:41165310-41165623	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:41163392-41166601	GM12878	blood:	n/a	n/a
9	CHD1	chr15:41163921-41165479	GM12878	blood:	n/a	n/a
10	ELF1	chr15:41165073-41166664	GM12878	blood:	n/a	chr15:41165943-41165955 chr15:41166058-41166070 chr15:41166084-41166096
11	PML	chr15:41165241-41166810	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:41162172-41166666	GM12878	blood:	n/a	n/a
13	MAZ	chr15:41165201-41166731	GM12878	blood:	n/a	chr15:41166095-41166104
14	CTBP2	chr15:41165387-41166671	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:41165395-41165670	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:41161854-41166680	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
2	chr15:41164626..41166627-chr15:41240824..41242386,2	MCF-7	breast:
3	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
4	chr15:41097815..41100803-chr15:41163733..41165563,2	K562	blood:
5	chr15:41165369..41165893-chr15:41184005..41184631,2	MCF-7	breast:
6	chr15:41164000..41165836-chr15:41190857..41193283,2	K562	blood:
7	chr15:41147225..41150329-chr15:41164541..41167398,4	K562	blood:
8	chr15:40856363..40858923-chr15:41165345..41167356,2	K562	blood:
9	chr15:41164378..41166011-chr15:41221238..41223138,2	MCF-7	breast:
10	chr15:41066752..41068835-chr15:41164487..41166836,2	K562	blood:
11	chr15:41162876..41167684-chr15:41196844..41200482,5	MCF-7	breast:
12	chr15:41163900..41166288-chr15:41184445..41186416,4	MCF-7	breast:
13	chr15:41104808..41107536-chr15:41164582..41166423,2	MCF-7	breast:
14	chr15:41161907..41163827-chr15:41163924..41166003,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264256	TF binding region
ENSG00000128891	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000128917	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000259405	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
9	esv3343760	chr15:41165085-41167633	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
2	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
3	chr15:41163000-41165800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:41163400-41165600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:41163600-41165800	Flanking Active TSS	GM12878-XiMat	blood
6	chr15:41163600-41166000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:41163800-41165600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr15:41163800-41165600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:41163800-41165600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr15:41163800-41165800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:41163800-41165800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:41163800-41165800	Enhancers	Duodenum Mucosa	Duodenum
13	chr15:41163800-41165800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr15:41163800-41165800	Enhancers	HMEC	breast
15	chr15:41163800-41166200	Enhancers	Fetal Brain Male	brain
16	chr15:41164000-41165600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr15:41164200-41165800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:41164200-41166600	Active TSS	Esophagus	oesophagus
19	chr15:41164400-41165600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr15:41164400-41166000	Enhancers	Gastric	stomach
21	chr15:41164600-41165600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr15:41164800-41165800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:41165000-41165800	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr15:41165000-41166000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:41165000-41166000	Flanking Active TSS	NHEK	skin
26	chr15:41165200-41165600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr15:41165200-41165600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr15:41165200-41165600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr15:41165200-41165600	Bivalent Enhancer	Fetal Intestine Large	intestine
30	chr15:41165200-41165800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr15:41165200-41165800	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:41165200-41165800	Flanking Active TSS	Fetal Brain Female	brain
33	chr15:41165200-41165800	Flanking Bivalent TSS/Enh	Placenta	Placenta
34	chr15:41165200-41166000	Bivalent Enhancer	Fetal Lung	lung
35	chr15:41165200-41166800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:41165200-41166800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr15:41165400-41165600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr15:41165400-41165600	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:41165400-41165600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr15:41165400-41165600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr15:41165400-41165600	Enhancers	Colonic Mucosa	Colon
42	chr15:41165400-41165600	Bivalent/Poised TSS	Fetal Thymus	thymus
43	chr15:41165400-41165600	Flanking Active TSS	A549	lung
44	chr15:41165400-41165600	Enhancers	K562	blood
45	chr15:41165400-41165800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr15:41165400-41165800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
47	chr15:41165400-41165800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr15:41165400-41165800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:41165400-41165800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:41165400-41165800	Enhancers	Fetal Heart	heart

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