Variant report

Variant	rs539418764
Chromosome Location	chr3:159481611-159481612
allele	A/G
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	CTCF	chr3:159481523-159481626	A549	lung:	n/a	n/a
2	SMARCB1	chr3:159480566-159483718	Hela-S3	cervix:	n/a	chr3:159483592-159483601
3	EP300	chr3:159480674-159482038	A549	lung:	n/a	chr3:159481639-159481652 chr3:159480947-159480956
4	POLR2A	chr3:159480763-159481717	U87	brain:	n/a	n/a
5	POLR2A	chr3:159480562-159484035	PFSK-1	brain:	n/a	n/a
6	CEBPB	chr3:159480064-159482341	Hela-S3	cervix:	n/a	n/a
7	EP300	chr3:159479975-159481767	A549	lung:	n/a	chr3:159481639-159481652 chr3:159480947-159480956
8	MAX	chr3:159480702-159483613	MCF-7	breast:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
9	TAF1	chr3:159480702-159482392	A549	lung:	n/a	n/a
10	ZNF263	chr3:159480693-159484031	HEK293-T-REx	kidney:	n/a	chr3:159481608-159481617 chr3:159482218-159482227 chr3:159482461-159482482 chr3:159483138-159483147
11	ETS1	chr3:159480855-159481736	A549	lung:	n/a	chr3:159481118-159481128 chr3:159481118-159481129 chr3:159481594-159481607 chr3:159481595-159481611 chr3:159481120-159481129
12	POLR2A	chr3:159478872-159485842	IMR90	lung:	n/a	n/a
13	NR3C1	chr3:159480777-159481745	A549	lung:	n/a	n/a
14	YY1	chr3:159481191-159481728	ECC-1	luminal epithelium:	n/a	chr3:159481510-159481524 chr3:159481396-159481410
15	TCF7L2	chr3:159481469-159481667	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr3:159480551-159481771	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:159480747-159483236	MCF-7	breast:	n/a	n/a
18	YY1	chr3:159481052-159481707	HCT-116	colon:	n/a	chr3:159481510-159481524 chr3:159481396-159481410
19	POLR2A	chr3:159480647-159483221	A549	lung:	n/a	n/a
20	MAFK	chr3:159481228-159481654	Hela-S3	cervix:	n/a	n/a
21	SMC3	chr3:159479813-159484045	Hela-S3	cervix:	n/a	chr3:159481356-159481366 chr3:159481836-159481846 chr3:159482090-159482100 chr3:159482126-159482136 chr3:159480742-159480749 chr3:159481981-159481988
22	POLR2A	chr3:159480674-159481714	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr3:159481269-159481673	H1-hESC	embryonic stem cell:	n/a	chr3:159481541-159481550
24	POLR2A	chr3:159480668-159482574	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr3:159481429-159482099	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr3:159480666-159482338	HCT-116	colon:	n/a	n/a
27	JUND	chr3:159481203-159481747	A549	lung:	n/a	chr3:159481541-159481550
28	EGR1	chr3:159481362-159481691	H1-hESC	embryonic stem cell:	n/a	chr3:159481542-159481552 chr3:159481631-159481644
29	MAX	chr3:159480680-159481761	H1-hESC	embryonic stem cell:	n/a	chr3:159481565-159481574
30	RAD21	chr3:159481216-159482033	SK-N-SH_RA	brain:	n/a	chr3:159481305-159481317 chr3:159481836-159481846 chr3:159481412-159481426
31	SIN3AK20	chr3:159481288-159481642	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3AK20	chr3:159481352-159481740	SK-N-SH	brain:	n/a	n/a
33	SRF	chr3:159481266-159481844	ECC-1	luminal epithelium:	n/a	chr3:159481614-159481624
34	ZNF143	chr3:159480705-159481655	Hela-S3	cervix:	n/a	chr3:159481553-159481571 chr3:159481602-159481620 chr3:159481248-159481266
35	HA-E2F1	chr3:159480802-159483168	Hela-S3	cervix:	n/a	chr3:159481831-159481843 chr3:159481261-159481270 chr3:159481372-159481382 chr3:159483006-159483018 chr3:159481542-159481551 chr3:159481378-159481387 chr3:159482172-159482184 chr3:159480946-159480956 chr3:159482085-159482097
36	RAD21	chr3:159481208-159481767	ECC-1	luminal epithelium:	n/a	chr3:159481305-159481317 chr3:159481412-159481426
37	POLR2A	chr3:159480483-159482854	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:159481581-159481632	LNCaP	prostate:	n/a	n/a
39	POLR2A	chr3:159480675-159484005	Hela-S3	cervix:	n/a	n/a
40	MAX	chr3:159480629-159482348	ECC-1	luminal epithelium:	n/a	chr3:159481565-159481574
41	POLR2A	chr3:159480560-159483811	Hela-S3	cervix:	n/a	n/a
42	CREB1	chr3:159480717-159481722	A549	lung:	n/a	n/a
43	POLR2A	chr3:159480579-159482427	HCT-116	colon:	n/a	n/a
44	TEAD4	chr3:159480663-159481736	ECC-1	luminal epithelium:	n/a	n/a
45	NR3C1	chr3:159481342-159481638	A549	lung:	n/a	n/a
46	POLR2A	chr3:159480606-159482497	Hela-S3	cervix:	n/a	n/a
47	MXI1	chr3:159480081-159481644	Hela-S3	cervix:	n/a	n/a
48	SP1	chr3:159480548-159482516	A549	lung:	n/a	chr3:159481886-159481899 chr3:159481542-159481551 chr3:159481606-159481620 chr3:159481892-159481901 chr3:159481902-159481909 chr3:159482087-159482101 chr3:159481834-159481843 chr3:159482175-159482189 chr3:159481892-159481901 chr3:159481538-159481552 chr3:159481609-159481621 chr3:159481891-159481901 chr3:159482086-159482098 chr3:159482088-159482097 chr3:159481891-159481900
49	POLR2A	chr3:159480618-159481756	A549	lung:	n/a	n/a
50	POLR2A	chr3:159479069-159484734	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:2235486..2236448-chr3:159481582..159482538,2	Hela-S3	cervix:
2	chr2:20101237..20102018-chr3:159480945..159481897,2	Hela-S3	cervix:
3	chr18:29671926..29672642-chr3:159481391..159482087,2	Hela-S3	cervix:
4	chr3:159481372..159481986-chr6:26123997..26124942,2	Hela-S3	cervix:
5	chr11:62599099..62599815-chr3:159481032..159481725,2	Hela-S3	cervix:
6	chr11:75272966..75273812-chr3:159481024..159481769,2	HCT-116	colon:

Variant related genes	Relation type
IQCJ-SCHIP1	TF binding region
ENSG00000256690	Chromatin interaction
ENSG00000162236	Chromatin interaction
ENSG00000104886	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000265008	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000149257	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335783	chr3:159480158-159484256	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3426837	chr3:159480283-159483031	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159480000-159483200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr3:159480400-159483400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:159480400-159483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:159480400-159483800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:159480400-159483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:159480400-159484200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:159480600-159482000	Active TSS	Primary hematopoietic stem cells	blood
8	chr3:159480600-159482000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:159480600-159483200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:159480600-159483400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:159480600-159483400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr3:159480600-159483600	Active TSS	Psoas Muscle	Psoas
13	chr3:159480600-159483800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr3:159480600-159483800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:159480600-159483800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:159480600-159484000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:159480600-159485400	Active TSS	Aorta	Aorta
18	chr3:159480800-159481800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:159480800-159482000	Bivalent/Poised TSS	Fetal Thymus	thymus
20	chr3:159480800-159482200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:159480800-159483200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:159480800-159483400	Active TSS	Fetal Intestine Large	intestine
23	chr3:159480800-159483600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:159480800-159483600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:159480800-159483800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:159480800-159483800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:159480800-159483800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:159480800-159483800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:159480800-159483800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:159480800-159483800	Active TSS	Ovary	ovary
31	chr3:159480800-159483800	Active TSS	A549	lung
32	chr3:159480800-159484000	Active TSS	Left Ventricle	heart
33	chr3:159480800-159484600	Active TSS	Colon Smooth Muscle	Colon
34	chr3:159480800-159485000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:159480800-159485000	Active TSS	Fetal Kidney	kidney
36	chr3:159480800-159485200	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:159481000-159481800	Bivalent/Poised TSS	Primary monocytes fromperipheralblood	blood
38	chr3:159481000-159482000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
39	chr3:159481000-159482400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:159481000-159482800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
41	chr3:159481000-159483200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:159481000-159483200	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr3:159481000-159483400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:159481000-159483400	Active TSS	Brain Substantia Nigra	brain
45	chr3:159481000-159483800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:159481000-159483800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:159481000-159483800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:159481000-159483800	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:159481000-159483800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr3:159481000-159483800	Active TSS	Rectal Smooth Muscle	rectum

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