Variant report

Variant	rs537056017
Chromosome Location	chr3:53080733-53080734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:283)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:283 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:53080600-53080750	HCT-116	colon:	n/a	n/a
2	CTCF	chr3:53080620-53080770	AG09309	skin:	n/a	n/a
3	YY1	chr3:53080330-53080878	H1-hESC	embryonic stem cell:	n/a	n/a
4	PML	chr3:53079598-53081008	GM12878	blood:	n/a	n/a
5	TCF12	chr3:53080289-53080995	A549	lung:	n/a	n/a
6	POLR2A	chr3:53079619-53081065	Raji	blood:	n/a	n/a
7	ELF1	chr3:53079606-53081209	GM12878	blood:	n/a	chr3:53080399-53080412
8	MAZ	chr3:53078861-53081185	GM12878	blood:	n/a	n/a
9	RAD21	chr3:53080672-53080825	A549	lung:	n/a	n/a
10	MAX	chr3:53079606-53080905	ECC-1	luminal epithelium:	n/a	n/a
11	CTCF	chr3:53080607-53080888	MCF-7	breast:	n/a	n/a
12	CTCF	chr3:53080660-53080810	AG04450	lung:	n/a	n/a
13	CTCF	chr3:53080465-53081028	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:53080660-53080810	GM12873	blood:	n/a	n/a
15	CTCF	chr3:53080609-53081032	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:53079700-53081059	PBDE	blood:	n/a	n/a
17	CTCF	chr3:53080620-53080770	GM12865	blood:	n/a	n/a
18	MAX	chr3:53080274-53081308	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr3:53079637-53080982	HCT-116	colon:	n/a	n/a
20	CTCF	chr3:53080680-53080830	HUVEC	blood vessel:	n/a	n/a
21	MAX	chr3:53080323-53080784	SK-N-SH	brain:	n/a	n/a
22	CTCF	chr3:53080660-53080810	HFF-Myc	foreskin:	n/a	n/a
23	CTCF	chr3:53080700-53080850	HRE	kidney:	n/a	n/a
24	CTCF	chr3:53080680-53080830	Caco-2	colon:	n/a	n/a
25	SIN3AK20	chr3:53080546-53080877	H1-hESC	embryonic stem cell:	n/a	n/a
26	FOXA2	chr3:53080182-53080796	A549	lung:	n/a	n/a
27	CTCF	chr3:53080640-53080790	GM12869	blood:	n/a	n/a
28	CTCF	chr3:53080680-53080830	HCPEpiC	choroid plexus:	n/a	n/a
29	CTCF	chr3:53080640-53080790	HEK293	kidney:	n/a	n/a
30	CTCF	chr3:53080660-53080810	HMF	breast:	n/a	n/a
31	RAD21	chr3:53080595-53080928	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr3:53079590-53080765	K562	blood:	n/a	n/a
33	POLR2A	chr3:53078724-53081152	GM12892	blood:	n/a	n/a
34	CTCF	chr3:53080700-53080850	GM12872	blood:	n/a	n/a
35	CTCF	chr3:53080680-53080830	HVMF	connective:	n/a	n/a
36	CHD1	chr3:53080449-53080979	GM12878	blood:	n/a	n/a
37	STAT1	chr3:53080509-53080906	GM12878	blood:	n/a	n/a
38	SMC3	chr3:53080646-53080920	GM12878	blood:	n/a	n/a
39	USF1	chr3:53080383-53080739	A549	lung:	n/a	n/a
40	MAX	chr3:53080451-53080873	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:53079632-53081014	GM12878	blood:	n/a	n/a
42	ZNF143	chr3:53079813-53081141	GM12878	blood:	n/a	n/a
43	MXI1	chr3:53080495-53081025	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr3:53080561-53080870	A549	lung:	n/a	n/a
45	CTCF	chr3:53080614-53080853	ProgFib	skin:	n/a	n/a
46	CTCF	chr3:53080660-53080810	AG04449	skin:	n/a	n/a
47	CTCF	chr3:53080660-53080810	NB4	blood:	n/a	n/a
48	ATF2	chr3:53080591-53080904	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr3:53080403-53081499	SK-N-SH	brain:	n/a	n/a
50	SP4	chr3:53080582-53080849	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKCD-2	chr3:53080091-53082182	NONHSAT089977
2	lnc-RFT1-5	chr3:53080476-53080766	NONHSAT089975

No data

Variant related genes	Relation type
SFMBT1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3341503	chr3:53078462-53080760	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3461090	chr3:53078737-53081285	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv590347	chr3:53079048-53088815	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53077800-53080800	Active TSS	Right Atrium	heart
2	chr3:53078000-53081200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:53078200-53080800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:53078200-53080800	Active TSS	Small Intestine	intestine
5	chr3:53078200-53081200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:53078400-53080800	Active TSS	Esophagus	oesophagus
7	chr3:53078400-53081200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:53078400-53081200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:53078400-53081200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:53078600-53080800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:53078600-53080800	Active TSS	Brain Cingulate Gyrus	brain
12	chr3:53078600-53080800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:53078600-53080800	Active TSS	Fetal Intestine Small	intestine
14	chr3:53078600-53080800	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr3:53078600-53080800	Active TSS	HSMMtube	muscle
16	chr3:53078600-53081000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:53078600-53081000	Active TSS	Aorta	Aorta
18	chr3:53078600-53081000	Active TSS	Colon Smooth Muscle	Colon
19	chr3:53078600-53081000	Active TSS	Ovary	ovary
20	chr3:53078600-53081200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:53078600-53081200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:53078600-53081200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:53078600-53081200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:53078600-53081200	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr3:53078600-53081200	Active TSS	HSMM	muscle
26	chr3:53078600-53081400	Active TSS	Fetal Intestine Large	intestine
27	chr3:53078600-53081400	Active TSS	A549	lung
28	chr3:53078600-53081800	Active TSS	Rectal Smooth Muscle	rectum
29	chr3:53078800-53080800	Active TSS	Primary B cells from peripheral blood	blood
30	chr3:53078800-53081000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:53078800-53081000	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr3:53078800-53081000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr3:53078800-53081000	Active TSS	Brain Angular Gyrus	brain
34	chr3:53078800-53081000	Active TSS	Brain Substantia Nigra	brain
35	chr3:53078800-53081000	Active TSS	Lung	lung
36	chr3:53078800-53081200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:53078800-53081200	Active TSS	Brain Anterior Caudate	brain
38	chr3:53079000-53080800	Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:53079000-53080800	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr3:53079000-53081000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:53079000-53081000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:53079000-53081000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:53079000-53081000	Bivalent/Poised TSS	Thymus	Thymus
44	chr3:53079000-53081200	Active TSS	Primary T cells from cord blood	blood
45	chr3:53079000-53081200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:53079000-53081400	Active TSS	Duodenum Mucosa	Duodenum
47	chr3:53079200-53081200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:53079200-53081200	Active TSS	Hela-S3	cervix
49	chr3:53079400-53081000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr3:53079600-53081000	Flanking Active TSS	Primary hematopoietic stem cells	blood

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