Variant report

Variant	rs539804439
Chromosome Location	chr3:50712318-50712319
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	NRF1	chr3:50712195-50712522	GM12878	blood:	n/a	chr3:50712336-50712345 chr3:50712336-50712350 chr3:50712336-50712347 chr3:50712336-50712347 chr3:50712338-50712347 chr3:50712315-50712326
2	POLR2A	chr3:50712254-50712523	H1-hESC	embryonic stem cell:	n/a	n/a
3	UBTF	chr3:50712225-50712574	K562	blood:	n/a	n/a
4	E2F4	chr3:50712126-50712398	MCF10A-Er-Src	breast:	n/a	chr3:50712337-50712346
5	NRF1	chr3:50712283-50712427	K562	blood:	n/a	chr3:50712336-50712345 chr3:50712336-50712350 chr3:50712336-50712347 chr3:50712336-50712347 chr3:50712338-50712347 chr3:50712315-50712326
6	POLR2A	chr3:50711886-50713116	H1-neurons	neurons:	n/a	n/a
7	SIN3A	chr3:50711967-50712605	H1-hESC	embryonic stem cell:	n/a	chr3:50712252-50712263 chr3:50712167-50712178
8	BHLHE40	chr3:50712228-50712595	HepG2	liver:	n/a	chr3:50712249-50712265 chr3:50712472-50712488
9	TCF7L2	chr3:50712186-50712994	HCT-116	colon:	n/a	n/a
10	MYC	chr3:50712207-50712342	K562	blood:	n/a	n/a
11	E2F6	chr3:50712076-50712617	A549	lung:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
12	EGR1	chr3:50712254-50713285	HCT-116	colon:	n/a	chr3:50712342-50712352 chr3:50712922-50712936 chr3:50712337-50712346 chr3:50712340-50712353 chr3:50712812-50712825 chr3:50712521-50712534 chr3:50712895-50712909 chr3:50712341-50712352 chr3:50712524-50712533
13	HA-E2F1	chr3:50711940-50712494	MCF-7	breast:	n/a	chr3:50712471-50712480 chr3:50712337-50712346
14	POLR2A	chr3:50712095-50712735	HEK293	kidney:	n/a	n/a
15	MAX	chr3:50711562-50713165	H1-hESC	embryonic stem cell:	n/a	chr3:50712815-50712825 chr3:50712930-50712940 chr3:50713023-50713032
16	POLR2A	chr3:50712167-50712612	HCT-116	colon:	n/a	n/a
17	POLR2A	chr3:50712253-50712539	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr3:50712047-50712624	K562	blood:	n/a	n/a
19	MAX	chr3:50711582-50713112	H1-hESC	embryonic stem cell:	n/a	chr3:50712815-50712825 chr3:50712930-50712940 chr3:50713023-50713032
20	E2F6	chr3:50712146-50712847	K562	blood:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
21	POLR2A	chr3:50712274-50712594	Gliobla	brain:	n/a	n/a
22	E2F6	chr3:50711553-50712665	H1-hESC	embryonic stem cell:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
23	MAX	chr3:50712090-50713027	A549	lung:	n/a	chr3:50712815-50712825 chr3:50712930-50712940
24	CCNT2	chr3:50712201-50712753	K562	blood:	n/a	n/a
25	POLR2A	chr3:50712180-50712569	ECC-1	luminal epithelium:	n/a	n/a
26	BACH1	chr3:50711747-50713161	H1-hESC	embryonic stem cell:	n/a	n/a
27	HMGN3	chr3:50712157-50712511	K562	blood:	n/a	n/a
28	CTCF	chr3:50712260-50712410	GM12864	blood:	n/a	n/a
29	FOXA1	chr3:50712172-50712441	HepG2	liver:	n/a	n/a
30	CTBP2	chr3:50711882-50712808	H1-hESC	embryonic stem cell:	n/a	n/a
31	UBTF	chr3:50712264-50712631	K562	blood:	n/a	n/a
32	POLR2A	chr3:50712091-50712652	HCT-116	colon:	n/a	n/a
33	MAX	chr3:50711997-50713076	ECC-1	luminal epithelium:	n/a	chr3:50712815-50712825 chr3:50712930-50712940 chr3:50713023-50713032
34	POLR2A	chr3:50712136-50712638	U87	brain:	n/a	n/a
35	REST	chr3:50711775-50713386	H1-neurons	neurons:	n/a	chr3:50712564-50712577 chr3:50712259-50712272 chr3:50712781-50712791 chr3:50712815-50712828
36	CTCF	chr3:50712287-50713185	SK-N-SH	brain:	n/a	chr3:50712787-50712800 chr3:50712930-50712943 chr3:50712927-50712945 chr3:50712476-50712485 chr3:50712928-50712944 chr3:50712476-50712489
37	MAX	chr3:50712189-50712496	A549	lung:	n/a	n/a
38	TCF7L2	chr3:50712317-50712591	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr3:50712106-50713109	H1-neurons	neurons:	n/a	n/a
40	JUND	chr3:50712142-50712460	A549	lung:	n/a	chr3:50712149-50712163
41	MAX	chr3:50712227-50712662	MCF-7	breast:	n/a	n/a
42	E2F6	chr3:50712021-50713041	H1-hESC	embryonic stem cell:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
43	E2F6	chr3:50712258-50712606	A549	lung:	n/a	chr3:50712579-50712588 chr3:50712471-50712480 chr3:50712337-50712346
44	MYC	chr3:50712230-50713005	MCF-7	breast:	n/a	chr3:50712815-50712825 chr3:50712930-50712940
45	MXI1	chr3:50712302-50712424	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr3:50712091-50712613	HCT-116	colon:	n/a	n/a
47	GABPA	chr3:50712175-50712433	HepG2	liver:	n/a	chr3:50712336-50712345 chr3:50712336-50712350 chr3:50712336-50712347 chr3:50712338-50712347
48	FOXP2	chr3:50712228-50712643	PFSK-1	brain:	n/a	n/a
49	MAX	chr3:50711998-50712649	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr3:50712207-50712689	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
DOCK3	TF binding region
MIR4787	TF binding region

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3398465	chr3:50710948-50713996	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50711400-50714000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:50711400-50714400	Active TSS	Brain Angular Gyrus	brain
3	chr3:50711400-50714400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:50711600-50713800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:50711800-50712400	Enhancers	Spleen	Spleen
6	chr3:50711800-50713000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:50711800-50713000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:50711800-50713000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr3:50711800-50713000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:50711800-50713000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
11	chr3:50711800-50713000	Active TSS	HSMM	muscle
12	chr3:50711800-50713200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:50711800-50713200	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:50711800-50713200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:50711800-50713200	Bivalent/Poised TSS	A549	lung
16	chr3:50711800-50713400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:50711800-50714400	Active TSS	HSMMtube	muscle
18	chr3:50712000-50712400	Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr3:50712000-50712400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr3:50712000-50712400	Bivalent Enhancer	Small Intestine	intestine
21	chr3:50712000-50712400	Flanking Bivalent TSS/Enh	NH-A	brain
22	chr3:50712000-50712600	Active TSS	Esophagus	oesophagus
23	chr3:50712000-50712800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:50712000-50712800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:50712000-50712800	Active TSS	Gastric	stomach
26	chr3:50712000-50712800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
27	chr3:50712000-50712800	Bivalent/Poised TSS	NHEK	skin
28	chr3:50712000-50713000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr3:50712000-50713000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:50712000-50713000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:50712000-50713000	Active TSS	Aorta	Aorta
32	chr3:50712000-50713000	Active TSS	Colon Smooth Muscle	Colon
33	chr3:50712000-50713000	Flanking Active TSS	Pancreas	Pancrea
34	chr3:50712000-50713200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:50712000-50713200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:50712000-50713200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:50712000-50713200	Flanking Bivalent TSS/Enh	Thymus	Thymus
38	chr3:50712000-50713400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:50712000-50713400	Active TSS	Fetal Brain Female	brain
40	chr3:50712000-50713600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr3:50712000-50713600	Active TSS	Brain Substantia Nigra	brain
42	chr3:50712000-50713600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:50712000-50713800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:50712000-50714000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr3:50712000-50714400	Active TSS	Brain Anterior Caudate	brain
46	chr3:50712200-50712400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
47	chr3:50712200-50712400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:50712200-50712400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:50712200-50712400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
50	chr3:50712200-50712400	Enhancers	Lung	lung

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