Variant report

Variant	rs9904375
Chromosome Location	chr17:20839759-20839760
allele	G/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	JUN	chr17:20838933-20839914	Hela-S3	cervix:	n/a	chr17:20839146-20839155 chr17:20838986-20838996 chr17:20838986-20838996
2	FOS	chr17:20838538-20840654	MCF10A-Er-Src	breast:	n/a	chr17:20839146-20839155 chr17:20838986-20838996 chr17:20840412-20840421 chr17:20840410-20840421 chr17:20839150-20839161 chr17:20838986-20838996
3	STAT3	chr17:20839668-20839967	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr17:20838750-20840680	MCF10A-Er-Src	breast:	n/a	chr17:20839146-20839155 chr17:20838986-20838996 chr17:20840412-20840421 chr17:20840410-20840421 chr17:20839150-20839161 chr17:20838986-20838996
5	MYC	chr17:20839087-20839835	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:20836869..20840041-chr17:20841054..20844534,3	K562	blood:
2	chr17:20839289..20841675-chr17:20882909..20885590,2	MCF-7	breast:
3	chr17:20816615..20818286-chr17:20839545..20841333,2	K562	blood:

Variant related genes	Relation type
ENSG00000264660	TF binding region
ENSG00000233098	TF binding region
ENSG00000266009	Chromatin interaction
ENSG00000264660	Chromatin interaction
ENSG00000265099	Chromatin interaction
ENSG00000233098	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28658139	1.00[EUR][1000 genomes]
rs6587105	1.00[EUR][1000 genomes]
rs73313051	1.00[EUR][1000 genomes]
rs9891613	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9902929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910047	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913944	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1064365	chr17:20801739-20890716	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
6	nsv574597	chr17:20802778-20872331	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv527161	chr17:20814766-20872331	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv457706	chr17:20814766-20872331	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv574598	chr17:20814766-20872331	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20827200-20856200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:20829400-20840600	Weak transcription	Ovary	ovary
3	chr17:20831000-20846800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:20831000-20847200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:20831400-20847000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:20831600-20845800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr17:20832400-20847800	Weak transcription	Gastric	stomach
8	chr17:20834200-20846800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr17:20834600-20847200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr17:20834600-20847800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr17:20835200-20841400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr17:20835600-20840400	Weak transcription	Fetal Stomach	stomach
13	chr17:20835600-20869000	Weak transcription	HepG2	liver
14	chr17:20835800-20840800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:20836800-20841600	Enhancers	Colon Smooth Muscle	Colon
16	chr17:20837000-20840800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr17:20837000-20841000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:20837000-20841800	Enhancers	Hela-S3	cervix
19	chr17:20837200-20840800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr17:20837200-20841400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:20837400-20840800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:20837400-20841200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:20837600-20841400	Enhancers	HMEC	breast
24	chr17:20837800-20840200	Enhancers	NHEK	skin
25	chr17:20838000-20840400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:20838000-20840800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:20838000-20840800	Enhancers	HSMM	muscle
28	chr17:20838000-20841400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr17:20838400-20840400	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr17:20838600-20840600	Enhancers	Adipose Nuclei	Adipose
31	chr17:20838600-20840800	Enhancers	NHLF	lung
32	chr17:20838600-20852400	Weak transcription	K562	blood
33	chr17:20838800-20840400	Enhancers	HSMMtube	muscle
34	chr17:20839200-20840600	Enhancers	Stomach Mucosa	stomach
35	chr17:20839200-20841600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:20839400-20840200	Enhancers	A549	lung
37	chr17:20839400-20840600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:20839400-20841400	Enhancers	NHDF-Ad	bronchial
39	chr17:20839400-20842400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:20839600-20840000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:20839600-20840400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:20839600-20840400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr17:20839600-20840800	Enhancers	Rectal Smooth Muscle	rectum
44	chr17:20839600-20840800	Enhancers	HUVEC	blood vessel
45	chr17:20839600-20841400	Enhancers	NH-A	brain
46	chr17:20839600-20841400	Enhancers	Osteobl	bone
47	chr17:20839600-20841600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:20839600-20844800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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