Variant report

Variant	rs569684089
Chromosome Location	chr3:53527993-53527994
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	REST	chr3:53527714-53528699	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr3:53527934-53528162	H1-hESC	embryonic stem cell:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
3	CTCF	chr3:53527900-53528050	HRPEpiC	eye:	n/a	chr3:53527999-53528012
4	E2F6	chr3:53527632-53528771	H1-hESC	embryonic stem cell:	n/a	chr3:53528233-53528242 chr3:53528338-53528348 chr3:53528198-53528207 chr3:53528250-53528259 chr3:53527887-53527896 chr3:53528093-53528103
5	CTCF	chr3:53527930-53528200	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
6	ZBTB7A	chr3:53527742-53528581	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
7	CTCF	chr3:53527911-53528203	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
8	MAX	chr3:53527965-53528914	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr3:53527920-53528222	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53528194-53528204 chr3:53527999-53528012
10	ZBTB7A	chr3:53527826-53528564	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
11	POLR2A	chr3:53527923-53528360	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr3:53527896-53528349	H1-hESC	embryonic stem cell:	n/a	chr3:53528214-53528221
13	MAX	chr3:53527670-53528552	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
14	MAX	chr3:53527931-53528599	ECC-1	luminal epithelium:	n/a	n/a
15	GABPA	chr3:53527938-53528453	H1-hESC	embryonic stem cell:	n/a	chr3:53528198-53528207
16	TAF1	chr3:53527743-53528318	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:53527880-53528262	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
18	SP1	chr3:53527884-53528332	H1-hESC	embryonic stem cell:	n/a	chr3:53528194-53528208 chr3:53527888-53527897 chr3:53527886-53527898 chr3:53527887-53527897 chr3:53528198-53528207 chr3:53527886-53527898 chr3:53528197-53528209 chr3:53527887-53527897 chr3:53528198-53528208 chr3:53527888-53527897 chr3:53528198-53528208 chr3:53528199-53528208 chr3:53528197-53528209 chr3:53527887-53527896 chr3:53528199-53528208
19	POLR2A	chr3:53527966-53528797	MCF-7	breast:	n/a	n/a
20	POLR2A	chr3:53527921-53528865	MCF-7	breast:	n/a	n/a
21	RAD21	chr3:53527746-53528350	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
22	TBP	chr3:53527808-53528315	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr3:53527933-53528466	H1-hESC	embryonic stem cell:	n/a	n/a
24	E2F6	chr3:53527760-53528864	H1-hESC	embryonic stem cell:	n/a	chr3:53528233-53528242 chr3:53528338-53528348 chr3:53528198-53528207 chr3:53528250-53528259 chr3:53527887-53527896 chr3:53528093-53528103
25	POLR2A	chr3:53527829-53528351	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr3:53527920-53528070	MCF-7	breast:	n/a	chr3:53527999-53528012
27	CTCF	chr3:53527961-53527994	LNCaP	prostate:	n/a	n/a
28	CTCF	chr3:53527980-53528130	SK-N-SH_RA	brain:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
29	MAX	chr3:53527740-53528884	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
30	MAX	chr3:53527992-53528892	HepG2	liver:	n/a	n/a
31	ZEB1	chr3:53527645-53528589	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53525897..53528498-chr3:53700129..53702578,2	MCF-7	breast:
2	chr3:53526182..53528875-chr3:53879796..53881358,2	MCF-7	breast:

Variant related genes	Relation type
CACNA1D	TF binding region
ENSG00000016391	Chromatin interaction
ENSG00000157388	Chromatin interaction
ENSG00000056736	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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	esv3442278	chr3:53527437-53530285	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv3444874	chr3:53527737-53529960	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 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	chr3:53527000-53528000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:53527000-53530600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:53527200-53529200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:53527200-53529200	Active TSS	Duodenum Mucosa	Duodenum
5	chr3:53527200-53529200	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr3:53527400-53528000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:53527400-53528400	Enhancers	Stomach Mucosa	stomach
8	chr3:53527400-53529200	Active TSS	Fetal Intestine Large	intestine
9	chr3:53527400-53530200	Active TSS	Brain Hippocampus Middle	brain
10	chr3:53527400-53530400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:53527400-53530400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr3:53527400-53531000	Active TSS	Brain Cingulate Gyrus	brain
13	chr3:53527600-53528000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:53527600-53528000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
15	chr3:53527600-53528000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:53527600-53528000	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr3:53527600-53528000	Active TSS	Ovary	ovary
18	chr3:53527600-53528000	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
19	chr3:53527600-53528000	Bivalent/Poised TSS	NH-A	brain
20	chr3:53527600-53529000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:53527600-53529200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr3:53527600-53529200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
23	chr3:53527600-53529200	Active TSS	Rectal Smooth Muscle	rectum
24	chr3:53527600-53529400	Active TSS	Fetal Brain Female	brain
25	chr3:53527600-53529800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr3:53527600-53530000	Active TSS	Brain Anterior Caudate	brain
27	chr3:53527600-53533000	Enhancers	Fetal Brain Male	brain
28	chr3:53527800-53528000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:53527800-53528000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:53527800-53528000	Enhancers	Liver	Liver
31	chr3:53527800-53528000	Flanking Active TSS	Colonic Mucosa	Colon
32	chr3:53527800-53528000	Flanking Active TSS	Fetal Intestine Small	intestine
33	chr3:53527800-53528000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr3:53527800-53528000	Bivalent Enhancer	Placenta	Placenta
35	chr3:53527800-53528000	Bivalent Enhancer	Left Ventricle	heart
36	chr3:53527800-53528000	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:53527800-53528200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr3:53527800-53528200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr3:53527800-53528400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
40	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
41	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:53527800-53528600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:53527800-53528600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr3:53527800-53528600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:53527800-53529000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:53527800-53529000	Active TSS	HepG2	liver
49	chr3:53527800-53529200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:53527800-53529200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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