Variant report

Variant	rs562193061
Chromosome Location	chr3:53080383-53080384
allele	A/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	YY1	chr3:53080330-53080878	H1-hESC	embryonic stem cell:	n/a	n/a
2	PML	chr3:53079598-53081008	GM12878	blood:	n/a	n/a
3	TCF12	chr3:53080289-53080995	A549	lung:	n/a	n/a
4	POLR2A	chr3:53079619-53081065	Raji	blood:	n/a	n/a
5	ELF1	chr3:53079606-53081209	GM12878	blood:	n/a	chr3:53080399-53080412
6	MAZ	chr3:53078861-53081185	GM12878	blood:	n/a	n/a
7	MAX	chr3:53079606-53080905	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr3:53079683-53080713	A549	lung:	n/a	n/a
9	POLR2A	chr3:53079700-53081059	PBDE	blood:	n/a	n/a
10	MAX	chr3:53080274-53081308	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr3:53079637-53080982	HCT-116	colon:	n/a	n/a
12	MAX	chr3:53080323-53080784	SK-N-SH	brain:	n/a	n/a
13	FOXA2	chr3:53080182-53080796	A549	lung:	n/a	n/a
14	MAX	chr3:53078739-53080587	HepG2	liver:	n/a	n/a
15	TAF1	chr3:53079590-53080694	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr3:53079590-53080765	K562	blood:	n/a	n/a
17	POLR2A	chr3:53078724-53081152	GM12892	blood:	n/a	n/a
18	USF1	chr3:53080353-53080693	GM12878	blood:	n/a	n/a
19	USF1	chr3:53080383-53080739	A549	lung:	n/a	n/a
20	POLR2A	chr3:53079632-53081014	GM12878	blood:	n/a	n/a
21	ZNF143	chr3:53079813-53081141	GM12878	blood:	n/a	n/a
22	PAX5	chr3:53080292-53080511	GM12878	blood:	n/a	n/a
23	ELF1	chr3:53080274-53080567	K562	blood:	n/a	chr3:53080399-53080412
24	CREB1	chr3:53079608-53080444	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:53079628-53080590	ECC-1	luminal epithelium:	n/a	n/a
26	MAX	chr3:53080071-53081023	A549	lung:	n/a	n/a
27	ZBTB7A	chr3:53079944-53080450	K562	blood:	n/a	n/a
28	POLR2A	chr3:53078745-53081057	GM19099	blood:	n/a	n/a
29	HMGN3	chr3:53078698-53080815	K562	blood:	n/a	n/a
30	PAX5	chr3:53080229-53080558	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr3:53080320-53080956	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:53079051-53080741	A549	lung:	n/a	n/a
33	REST	chr3:53079573-53080778	H1-neurons	neurons:	n/a	chr3:53080121-53080134
34	TAF1	chr3:53080331-53080884	H1-hESC	embryonic stem cell:	n/a	n/a
35	RUNX3	chr3:53080319-53081232	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:53079163-53080857	H1-neurons	neurons:	n/a	n/a
37	CTCF	chr3:53080380-53080530	GM12875	blood:	n/a	n/a
38	POLR2A	chr3:53078993-53080976	GM19193	blood:	n/a	n/a
39	E2F6	chr3:53078744-53080891	K562	blood:	n/a	chr3:53080114-53080123 chr3:53078962-53078977 chr3:53080104-53080113
40	POLR2A	chr3:53079352-53080672	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr3:53079836-53081083	GM12878	blood:	n/a	n/a
42	USF1	chr3:53080311-53080738	GM12878	blood:	n/a	n/a
43	CTCF	chr3:53080307-53081206	A549	lung:	n/a	n/a
44	HA-E2F1	chr3:53079166-53080752	Hela-S3	cervix:	n/a	chr3:53080114-53080123 chr3:53080104-53080113
45	PAX5	chr3:53079660-53080735	GM12892	blood:	n/a	chr3:53080110-53080119 chr3:53079725-53079734
46	USF1	chr3:53080338-53080705	A549	lung:	n/a	n/a
47	MYC	chr3:53079925-53081093	MCF-7	breast:	n/a	n/a
48	MAX	chr3:53079496-53081332	A549	lung:	n/a	n/a
49	MAX	chr3:53079846-53080912	GM12878	blood:	n/a	n/a
50	YY1	chr3:53080293-53080618	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:33999620..34000214-chr3:53080089..53080662,2	Hela-S3	cervix:

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

Variant related genes	Relation type
SFMBT1	TF binding region
ENSG00000101019	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv20159	chr3:53078811-53080407	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3461089	chr3:53078962-53080610	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3461091	chr3:53078962-53080610	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	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:122 , 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	chr3:53078400-53080600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr3:53078400-53080600	Active TSS	Placenta	Placenta
8	chr3:53078400-53080600	Active TSS	Pancreas	Pancrea
9	chr3:53078400-53080800	Active TSS	Esophagus	oesophagus
10	chr3:53078400-53081200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr3:53078400-53081200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:53078400-53081200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:53078600-53080400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:53078600-53080400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
15	chr3:53078600-53080400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:53078600-53080400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr3:53078600-53080400	Active TSS	Gastric	stomach
18	chr3:53078600-53080400	Active TSS	Left Ventricle	heart
19	chr3:53078600-53080400	Active TSS	GM12878-XiMat	blood
20	chr3:53078600-53080600	Active TSS	Brain Hippocampus Middle	brain
21	chr3:53078600-53080600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr3:53078600-53080600	Active TSS	Psoas Muscle	Psoas
23	chr3:53078600-53080800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr3:53078600-53080800	Active TSS	Brain Cingulate Gyrus	brain
25	chr3:53078600-53080800	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:53078600-53080800	Active TSS	Fetal Intestine Small	intestine
27	chr3:53078600-53080800	Active TSS	Sigmoid Colon	Sigmoid Colon
28	chr3:53078600-53080800	Active TSS	HSMMtube	muscle
29	chr3:53078600-53081000	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr3:53078600-53081000	Active TSS	Aorta	Aorta
31	chr3:53078600-53081000	Active TSS	Colon Smooth Muscle	Colon
32	chr3:53078600-53081000	Active TSS	Ovary	ovary
33	chr3:53078600-53081200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:53078600-53081200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:53078600-53081200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:53078600-53081200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:53078600-53081200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:53078600-53081200	Active TSS	HSMM	muscle
39	chr3:53078600-53081400	Active TSS	Fetal Intestine Large	intestine
40	chr3:53078600-53081400	Active TSS	A549	lung
41	chr3:53078600-53081800	Active TSS	Rectal Smooth Muscle	rectum
42	chr3:53078800-53080400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:53078800-53080400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr3:53078800-53080400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:53078800-53080400	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr3:53078800-53080400	Active TSS	K562	blood
47	chr3:53078800-53080400	Active TSS	NHLF	lung
48	chr3:53078800-53080600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:53078800-53080600	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:53078800-53080600	Active TSS	NHDF-Ad	bronchial

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