Variant report

Variant	rs552869004
Chromosome Location	chr3:53528087-53528088
allele	A/C
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	chr3:53528020-53528170	Caco-2	colon:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
4	CTCF	chr3:53528045-53528158	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
5	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
6	CTCF	chr3:53527930-53528200	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
7	ZBTB7A	chr3:53527742-53528581	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
8	CTCF	chr3:53527911-53528203	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
9	MAX	chr3:53527965-53528914	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr3:53528020-53528170	HUVEC	blood vessel:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
11	POLR2A	chr3:53528007-53528862	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr3:53528000-53528150	HBMEC	blood vessel:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
13	CTCF	chr3:53527920-53528222	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53528194-53528204 chr3:53527999-53528012
14	ZBTB7A	chr3:53527826-53528564	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
15	HA-E2F1	chr3:53528050-53528548	MCF-7	breast:	n/a	chr3:53528233-53528242 chr3:53528338-53528348 chr3:53528198-53528207 chr3:53528250-53528259 chr3:53528093-53528103
16	POLR2A	chr3:53527923-53528360	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr3:53527896-53528349	H1-hESC	embryonic stem cell:	n/a	chr3:53528214-53528221
18	MAX	chr3:53527670-53528552	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
19	CTCF	chr3:53528064-53528153	A549	lung:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
20	MAX	chr3:53527931-53528599	ECC-1	luminal epithelium:	n/a	n/a
21	GABPA	chr3:53527938-53528453	H1-hESC	embryonic stem cell:	n/a	chr3:53528198-53528207
22	JUND	chr3:53528019-53528197	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr3:53528082-53528185	LNCaP	prostate:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
24	TAF1	chr3:53527743-53528318	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr3:53527880-53528262	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
26	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
27	ZEB1	chr3:53528019-53528284	GM12878	blood:	n/a	n/a
28	TCF12	chr3:53528060-53528358	H1-hESC	embryonic stem cell:	n/a	chr3:53528214-53528221
29	POLR2A	chr3:53527966-53528797	MCF-7	breast:	n/a	n/a
30	POLR2A	chr3:53527921-53528865	MCF-7	breast:	n/a	n/a
31	RAD21	chr3:53527746-53528350	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
32	CTCF	chr3:53528000-53528150	A549	lung:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
33	TBP	chr3:53527808-53528315	H1-hESC	embryonic stem cell:	n/a	n/a
34	SIN3A	chr3:53527933-53528466	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr3:53528020-53528170	SK-N-SH_RA	brain:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
36	ZNF143	chr3:53528028-53528563	H1-hESC	embryonic stem cell:	n/a	chr3:53528250-53528260 chr3:53528185-53528203
37	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
38	POLR2A	chr3:53527829-53528351	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr3:53527980-53528130	SK-N-SH_RA	brain:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53527999-53528012
40	MAX	chr3:53527740-53528884	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
41	MAX	chr3:53527992-53528892	HepG2	liver:	n/a	n/a
42	CTCF	chr3:53528040-53528190	HRE	kidney:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
43	CTCF	chr3:53528020-53528170	HRPEpiC	eye:	n/a	chr3:53528088-53528098 chr3:53528084-53528100
44	ZEB1	chr3:53527645-53528589	HepG2	liver:	n/a	n/a
45	POLR2A	chr3:53528067-53528809	A549	lung:	n/a	n/a
46	CTCF	chr3:53528020-53528170	WERI-Rb-1	eye:	n/a	chr3:53528088-53528098 chr3:53528084-53528100

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
ENSG00000056736	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000157388	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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53527000-53530600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:53527200-53529200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:53527200-53529200	Active TSS	Duodenum Mucosa	Duodenum
4	chr3:53527200-53529200	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr3:53527400-53528400	Enhancers	Stomach Mucosa	stomach
6	chr3:53527400-53529200	Active TSS	Fetal Intestine Large	intestine
7	chr3:53527400-53530200	Active TSS	Brain Hippocampus Middle	brain
8	chr3:53527400-53530400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:53527400-53530400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:53527400-53531000	Active TSS	Brain Cingulate Gyrus	brain
11	chr3:53527600-53529000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:53527600-53529200	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:53527600-53529200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
14	chr3:53527600-53529200	Active TSS	Rectal Smooth Muscle	rectum
15	chr3:53527600-53529400	Active TSS	Fetal Brain Female	brain
16	chr3:53527600-53529800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr3:53527600-53530000	Active TSS	Brain Anterior Caudate	brain
18	chr3:53527600-53533000	Enhancers	Fetal Brain Male	brain
19	chr3:53527800-53528200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr3:53527800-53528200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
21	chr3:53527800-53528400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
23	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:53527800-53528600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:53527800-53528600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr3:53527800-53528600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:53527800-53529000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:53527800-53529000	Active TSS	HepG2	liver
31	chr3:53527800-53529200	Active TSS	H9 Cell Line	embryonic stem cell
32	chr3:53527800-53529200	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr3:53527800-53529200	Active TSS	Pancreas	Pancrea
34	chr3:53527800-53529200	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:53527800-53529200	Active TSS	Right Atrium	heart
36	chr3:53527800-53529200	Active TSS	A549	lung
37	chr3:53527800-53530000	Active TSS	Aorta	Aorta
38	chr3:53527800-53530000	Active TSS	Fetal Lung	lung
39	chr3:53527800-53530200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:53527800-53530200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr3:53527800-53530200	Active TSS	Colon Smooth Muscle	Colon
42	chr3:53527800-53530400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:53527800-53530400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr3:53527800-53530400	Active TSS	Fetal Kidney	kidney
45	chr3:53527800-53530600	Active TSS	Brain Angular Gyrus	brain
46	chr3:53527800-53530800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:53528000-53528200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:53528000-53528200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:53528000-53528200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
50	chr3:53528000-53528200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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