Variant report

Variant	rs3806693
Chromosome Location	chr3:53080909-53080910
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:109)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:109 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr3:53079598-53081008	GM12878	blood:	n/a	n/a
2	TCF12	chr3:53080289-53080995	A549	lung:	n/a	n/a
3	POLR2A	chr3:53079619-53081065	Raji	blood:	n/a	n/a
4	ELF1	chr3:53079606-53081209	GM12878	blood:	n/a	chr3:53080399-53080412
5	MAZ	chr3:53078861-53081185	GM12878	blood:	n/a	n/a
6	CTCF	chr3:53080465-53081028	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:53080609-53081032	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:53079700-53081059	PBDE	blood:	n/a	n/a
9	MAX	chr3:53080274-53081308	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:53079637-53080982	HCT-116	colon:	n/a	n/a
11	RAD21	chr3:53080595-53080928	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:53078724-53081152	GM12892	blood:	n/a	n/a
13	CHD1	chr3:53080449-53080979	GM12878	blood:	n/a	n/a
14	SMC3	chr3:53080646-53080920	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:53079632-53081014	GM12878	blood:	n/a	n/a
16	ZNF143	chr3:53079813-53081141	GM12878	blood:	n/a	n/a
17	MXI1	chr3:53080495-53081025	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr3:53080403-53081499	SK-N-SH	brain:	n/a	n/a
19	MAX	chr3:53080071-53081023	A549	lung:	n/a	n/a
20	CTCF	chr3:53080599-53080923	GM10266	blood:	n/a	n/a
21	POLR2A	chr3:53078745-53081057	GM19099	blood:	n/a	n/a
22	CTCF	chr3:53080780-53080930	HAc	cerebellar:	n/a	n/a
23	CTCF	chr3:53080641-53080920	Lung_OC	lung:	n/a	n/a
24	CTCF	chr3:53080599-53080913	H1-hESC	embryonic stem cell:	n/a	n/a
25	RUNX3	chr3:53080611-53081166	GM12878	blood:	n/a	n/a
26	SIN3AK20	chr3:53080320-53080956	MCF-7	breast:	n/a	n/a
27	CHD2	chr3:53080493-53080969	H1-hESC	embryonic stem cell:	n/a	n/a
28	RUNX3	chr3:53080319-53081232	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:53078993-53080976	GM19193	blood:	n/a	n/a
30	CTCF	chr3:53080574-53080934	IMR90	lung:	n/a	n/a
31	POLR2A	chr3:53079836-53081083	GM12878	blood:	n/a	n/a
32	CTCF	chr3:53080307-53081206	A549	lung:	n/a	n/a
33	MYC	chr3:53079925-53081093	MCF-7	breast:	n/a	n/a
34	MAX	chr3:53079496-53081332	A549	lung:	n/a	n/a
35	MAX	chr3:53079846-53080912	GM12878	blood:	n/a	n/a
36	BHLHE40	chr3:53079770-53081260	GM12878	blood:	n/a	n/a
37	RCOR1	chr3:53079805-53081201	GM12878	blood:	n/a	n/a
38	SIN3A	chr3:53079755-53081147	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr3:53080329-53080984	PANC-1	pancreas:	n/a	n/a
40	NFIC	chr3:53080631-53081188	GM12878	blood:	n/a	n/a
41	CTCF	chr3:53080494-53081168	GM12878	blood:	n/a	n/a
42	EBF1	chr3:53080483-53081217	GM12878	blood:	n/a	n/a
43	ATF2	chr3:53080620-53080928	GM12878	blood:	n/a	n/a
44	RAD21	chr3:53080482-53080915	SK-N-SH_RA	brain:	n/a	n/a
45	TCF3	chr3:53079912-53081150	GM12878	blood:	n/a	n/a
46	CTCF	chr3:53080604-53080940	A549	lung:	n/a	n/a
47	TBP	chr3:53080500-53081018	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr3:53079615-53081108	GM12892	blood:	n/a	n/a
49	EGR1	chr3:53080796-53081115	GM12878	blood:	n/a	chr3:53080915-53080929 chr3:53080944-53080958
50	POLR2A	chr3:53079634-53081001	PANC-1	pancreas:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKCD-2	chr3:53080091-53082182	NONHSAT089977

No data

Variant related genes	Relation type
SFMBT1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs13066997	1.00[CHB][hapmap]
rs1986738	1.00[CHB][hapmap]
rs1986739	1.00[CHB][hapmap]
rs2001734	1.00[CHB][hapmap]
rs2246888	1.00[CHB][hapmap]
rs2246889	1.00[CHB][hapmap]
rs2336159	1.00[CHB][hapmap]
rs2336556	1.00[CHB][hapmap]
rs2336557	1.00[CHB][hapmap]
rs2336559	1.00[CHB][hapmap]
rs28696085	1.00[ASN][1000 genomes]
rs28719645	1.00[ASN][1000 genomes]
rs4687675	1.00[CHB][hapmap]
rs55794978	1.00[ASN][1000 genomes]
rs55885034	1.00[ASN][1000 genomes]
rs56835905	1.00[ASN][1000 genomes]
rs57940327	1.00[ASN][1000 genomes]
rs58309671	1.00[ASN][1000 genomes]
rs58840385	1.00[ASN][1000 genomes]
rs59224641	1.00[ASN][1000 genomes]
rs59515578	1.00[ASN][1000 genomes]
rs60648378	1.00[ASN][1000 genomes]
rs60744886	1.00[ASN][1000 genomes]
rs61285888	1.00[ASN][1000 genomes]
rs61437303	1.00[ASN][1000 genomes]
rs61438885	1.00[ASN][1000 genomes]
rs72965345	1.00[ASN][1000 genomes]
rs72965350	1.00[ASN][1000 genomes]
rs72965354	1.00[ASN][1000 genomes]
rs72965361	1.00[ASN][1000 genomes]
rs72965362	1.00[ASN][1000 genomes]
rs72965366	1.00[ASN][1000 genomes]
rs72965381	0.84[ASN][1000 genomes]
rs7628501	1.00[ASN][1000 genomes]
rs7631487	1.00[ASN][1000 genomes]
rs7637212	1.00[CHB][hapmap]
rs9682819	1.00[CHB][hapmap]
rs9819608	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9822686	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9852646	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
6	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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53078000-53081200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:53078200-53081200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:53078400-53081200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:53078400-53081200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:53078400-53081200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:53078600-53081000	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:53078600-53081000	Active TSS	Aorta	Aorta
8	chr3:53078600-53081000	Active TSS	Colon Smooth Muscle	Colon
9	chr3:53078600-53081000	Active TSS	Ovary	ovary
10	chr3:53078600-53081200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:53078600-53081200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:53078600-53081200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:53078600-53081200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:53078600-53081200	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:53078600-53081200	Active TSS	HSMM	muscle
16	chr3:53078600-53081400	Active TSS	Fetal Intestine Large	intestine
17	chr3:53078600-53081400	Active TSS	A549	lung
18	chr3:53078600-53081800	Active TSS	Rectal Smooth Muscle	rectum
19	chr3:53078800-53081000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:53078800-53081000	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr3:53078800-53081000	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr3:53078800-53081000	Active TSS	Brain Angular Gyrus	brain
23	chr3:53078800-53081000	Active TSS	Brain Substantia Nigra	brain
24	chr3:53078800-53081000	Active TSS	Lung	lung
25	chr3:53078800-53081200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:53078800-53081200	Active TSS	Brain Anterior Caudate	brain
27	chr3:53079000-53081000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:53079000-53081000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:53079000-53081000	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr3:53079000-53081000	Bivalent/Poised TSS	Thymus	Thymus
31	chr3:53079000-53081200	Active TSS	Primary T cells from cord blood	blood
32	chr3:53079000-53081200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:53079000-53081400	Active TSS	Duodenum Mucosa	Duodenum
34	chr3:53079200-53081200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:53079200-53081200	Active TSS	Hela-S3	cervix
36	chr3:53079400-53081000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr3:53079600-53081000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr3:53079600-53081000	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr3:53079800-53081200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:53079800-53081200	Bivalent/Poised TSS	Fetal Brain Female	brain
41	chr3:53079800-53081400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
42	chr3:53080200-53081000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:53080200-53081000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:53080200-53081000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:53080200-53081000	Flanking Active TSS	Right Ventricle	heart
46	chr3:53080200-53081200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:53080200-53081200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:53080200-53081200	Flanking Active TSS	Colonic Mucosa	Colon
49	chr3:53080400-53081000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:53080400-53081000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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