Variant report

Variant	rs186898552
Chromosome Location	chr3:53168630-53168631
allele	A/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	CTCF	chr3:53168462-53169391	SK-N-SH	brain:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
2	MAZ	chr3:53168584-53169080	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr3:53168628-53169140	HepG2	liver:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
4	CTCF	chr3:53168534-53169190	HCT-116	colon:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
5	EP300	chr3:53168309-53169157	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr3:53168608-53168661	GM19238	blood:	n/a	n/a
7	RAD21	chr3:53168499-53169262	HCT-116	colon:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
8	CTCF	chr3:53168540-53168690	AG04449	skin:	n/a	n/a
9	NFIC	chr3:53168348-53169213	ECC-1	luminal epithelium:	n/a	n/a
10	RAD21	chr3:53168629-53169123	A549	lung:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
11	MAX	chr3:53168477-53169144	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr3:53168601-53169156	H1-hESC	embryonic stem cell:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
13	SMC3	chr3:53168513-53169299	SK-N-SH	brain:	n/a	chr3:53168896-53168910 chr3:53168655-53168665
14	RAD21	chr3:53168593-53169219	ECC-1	luminal epithelium:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
15	RAD21	chr3:53168591-53169249	MCF-7	breast:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
16	RCOR1	chr3:53168485-53169377	IMR90	lung:	n/a	n/a
17	TCF12	chr3:53168341-53169189	ECC-1	luminal epithelium:	n/a	chr3:53168832-53168839 chr3:53168830-53168840
18	RAD21	chr3:53168553-53169259	HCT-116	colon:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
19	CTCF	chr3:53168606-53169125	K562	blood:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
20	MAX	chr3:53168403-53169129	ECC-1	luminal epithelium:	n/a	n/a
21	RAD21	chr3:53168514-53169210	ECC-1	luminal epithelium:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
22	CTCF	chr3:53168629-53169150	MCF-7	breast:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
23	CTCF	chr3:53168448-53169409	HCT-116	colon:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
24	POLR2A	chr3:53168584-53169057	ECC-1	luminal epithelium:	n/a	n/a
25	RAD21	chr3:53168562-53169373	SK-N-SH	brain:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
26	CTCF	chr3:53168511-53169367	A549	lung:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
27	TCF12	chr3:53168467-53169152	ECC-1	luminal epithelium:	n/a	chr3:53168832-53168839 chr3:53168830-53168840
28	RFX5	chr3:53168630-53169234	Hela-S3	cervix:	n/a	n/a
29	CTCF	chr3:53168621-53169209	MCF-7	breast:	n/a	chr3:53168894-53168912 chr3:53168896-53168917 chr3:53168898-53168905 chr3:53168895-53168911 chr3:53168897-53168910
30	RAD21	chr3:53168615-53169235	A549	lung:	n/a	chr3:53168895-53168914 chr3:53168896-53168905 chr3:53168896-53168910
31	NFIC	chr3:53168330-53169155	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53168443..53169334-chr3:53229545..53230512,6	MCF-7	breast:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53168415..53169413-chr3:53219615..53220145,2	MCF-7	breast:
4	chr3:53163343..53166728-chr3:53167224..53170479,4	MCF-7	breast:
5	chr3:53168393..53169379-chr3:53229728..53230708,4	MCF-7	breast:
6	chr3:53168501..53169455-chr3:53194754..53195688,3	MCF-7	breast:
7	chr3:53167017..53169952-chr3:53191720..53194469,2	K562	blood:

Variant related genes	Relation type
RFT1	TF binding region
ENSG00000163932	Chromatin interaction
ENSG00000163933	Chromatin interaction

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	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3381848	chr3:53167712-53172310	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53164800-53170600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:53165000-53169800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53165000-53176200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:53165000-53176400	Weak transcription	Aorta	Aorta
5	chr3:53165200-53169800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:53165400-53169000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:53165400-53173800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:53165400-53176000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:53165600-53168800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:53165600-53168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:53165600-53168800	Weak transcription	Esophagus	oesophagus
12	chr3:53165600-53169200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:53165600-53169600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:53165600-53170800	Weak transcription	Fetal Thymus	thymus
15	chr3:53165600-53173400	Weak transcription	Gastric	stomach
16	chr3:53165600-53174200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:53165600-53174200	Weak transcription	Fetal Heart	heart
18	chr3:53165600-53174200	Weak transcription	Left Ventricle	heart
19	chr3:53165600-53174600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:53165600-53177800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:53165600-53181400	Weak transcription	Spleen	Spleen
22	chr3:53165800-53170600	Weak transcription	GM12878-XiMat	blood
23	chr3:53165800-53175400	Weak transcription	Placenta	Placenta
24	chr3:53166200-53174600	Weak transcription	Primary B cells from cord blood	blood
25	chr3:53166400-53170200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:53166400-53171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:53167200-53174400	Weak transcription	HMEC	breast
28	chr3:53167600-53169200	Enhancers	Liver	Liver
29	chr3:53167600-53170200	Enhancers	Adipose Nuclei	Adipose
30	chr3:53168200-53169200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:53168200-53170000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:53168400-53169200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr3:53168400-53169400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr3:53168400-53169400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr3:53168400-53169400	Enhancers	Hela-S3	cervix
36	chr3:53168400-53169400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr3:53168400-53170000	Enhancers	Duodenum Mucosa	Duodenum
38	chr3:53168400-53170000	Enhancers	Stomach Mucosa	stomach
39	chr3:53168400-53170200	Weak transcription	HepG2	liver
40	chr3:53168400-53170800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:53168600-53168800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:53168600-53169000	Enhancers	Colonic Mucosa	Colon
43	chr3:53168600-53169000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr3:53168600-53169000	Enhancers	Lung	lung
45	chr3:53168600-53169000	Enhancers	Right Atrium	heart
46	chr3:53168600-53169200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:53168600-53169200	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:53168600-53169200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:53168600-53169200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:53168600-53169200	Enhancers	Brain Hippocampus Middle	brain

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