Variant report

Variant	rs534895739
Chromosome Location	chr3:53528214-53528215
allele	C/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	REST	chr3:53527714-53528699	H1-neurons	neurons:	n/a	n/a
2	MYC	chr3:53528093-53528548	MCF-7	breast:	n/a	n/a
3	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
4	ZBTB7A	chr3:53527742-53528581	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
5	MAX	chr3:53527965-53528914	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr3:53528007-53528862	ECC-1	luminal epithelium:	n/a	n/a
7	SIN3AK20	chr3:53528182-53528701	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr3:53527920-53528222	MCF-7	breast:	n/a	chr3:53528088-53528098 chr3:53528084-53528100 chr3:53528194-53528204 chr3:53527999-53528012
9	ZBTB7A	chr3:53527826-53528564	ECC-1	luminal epithelium:	n/a	chr3:53528091-53528100
10	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
11	POLR2A	chr3:53528163-53528883	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr3:53527923-53528360	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:53528176-53528557	H1-neurons	neurons:	n/a	n/a
14	YY1	chr3:53528165-53528576	HepG2	liver:	n/a	chr3:53528198-53528207 chr3:53528195-53528209 chr3:53528241-53528255
15	TCF12	chr3:53527896-53528349	H1-hESC	embryonic stem cell:	n/a	chr3:53528214-53528221
16	MAX	chr3:53527670-53528552	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
17	CTCF	chr3:53528160-53528310	GM06990	blood:	n/a	chr3:53528194-53528204
18	MAX	chr3:53527931-53528599	ECC-1	luminal epithelium:	n/a	n/a
19	GABPA	chr3:53527938-53528453	H1-hESC	embryonic stem cell:	n/a	chr3:53528198-53528207
20	TAF1	chr3:53527743-53528318	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr3:53527880-53528262	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
22	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
23	ZEB1	chr3:53528019-53528284	GM12878	blood:	n/a	n/a
24	TCF12	chr3:53528060-53528358	H1-hESC	embryonic stem cell:	n/a	chr3:53528214-53528221
25	POLR2A	chr3:53527966-53528797	MCF-7	breast:	n/a	n/a
26	POLR2A	chr3:53527921-53528865	MCF-7	breast:	n/a	n/a
27	RAD21	chr3:53527746-53528350	H1-hESC	embryonic stem cell:	n/a	chr3:53527996-53528010 chr3:53528089-53528099 chr3:53528195-53528205
28	TBP	chr3:53527808-53528315	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr3:53528182-53528866	A549	lung:	n/a	n/a
30	SIN3A	chr3:53527933-53528466	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZNF143	chr3:53528028-53528563	H1-hESC	embryonic stem cell:	n/a	chr3:53528250-53528260 chr3:53528185-53528203
32	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
33	POLR2A	chr3:53527829-53528351	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:53528094-53528373	ECC-1	luminal epithelium:	n/a	n/a
35	BACH1	chr3:53528166-53528316	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:53527740-53528884	H1-hESC	embryonic stem cell:	n/a	chr3:53527885-53527895 chr3:53527882-53527891
37	MAX	chr3:53527992-53528892	HepG2	liver:	n/a	n/a
38	MYC	chr3:53528102-53528298	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZEB1	chr3:53527645-53528589	HepG2	liver:	n/a	n/a
40	MAX	chr3:53528178-53528869	A549	lung:	n/a	n/a
41	MXI1	chr3:53528161-53528239	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:53528180-53528228	MCF-7	breast:	n/a	n/a
43	POLR2A	chr3:53528067-53528809	A549	lung:	n/a	n/a
44	MXI1	chr3:53528092-53528365	H1-hESC	embryonic stem cell:	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:113 , 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	chr3:53527800-53528400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
21	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:53527800-53528400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:53527800-53528600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:53527800-53528600	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr3:53527800-53528600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:53527800-53529000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:53527800-53529000	Active TSS	HepG2	liver
29	chr3:53527800-53529200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr3:53527800-53529200	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr3:53527800-53529200	Active TSS	Pancreas	Pancrea
32	chr3:53527800-53529200	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:53527800-53529200	Active TSS	Right Atrium	heart
34	chr3:53527800-53529200	Active TSS	A549	lung
35	chr3:53527800-53530000	Active TSS	Aorta	Aorta
36	chr3:53527800-53530000	Active TSS	Fetal Lung	lung
37	chr3:53527800-53530200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:53527800-53530200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr3:53527800-53530200	Active TSS	Colon Smooth Muscle	Colon
40	chr3:53527800-53530400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:53527800-53530400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr3:53527800-53530400	Active TSS	Fetal Kidney	kidney
43	chr3:53527800-53530600	Active TSS	Brain Angular Gyrus	brain
44	chr3:53527800-53530800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:53528000-53528400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr3:53528000-53528400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:53528000-53528400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:53528000-53528400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:53528000-53528400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:53528000-53528400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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