Variant report

Variant	rs574025760
Chromosome Location	chr2:74229777-74229778
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	ELF1	chr2:74229481-74230476	GM12878	blood:	n/a	chr2:74229529-74229538
2	POLR2A	chr2:74229750-74230041	ECC-1	luminal epithelium:	n/a	n/a
3	TAF1	chr2:74229615-74229964	GM12878	blood:	n/a	n/a
4	THAP1	chr2:74229726-74229958	K562	blood:	n/a	n/a
5	GATA1	chr2:74229631-74230194	PBDE	blood:	n/a	n/a
6	MAX	chr2:74229595-74230533	H1-hESC	embryonic stem cell:	n/a	chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
7	TCF12	chr2:74229627-74229953	GM12878	blood:	n/a	chr2:74229827-74229834
8	YY1	chr2:74229359-74230100	H1-hESC	embryonic stem cell:	n/a	chr2:74230080-74230099 chr2:74229697-74229708 chr2:74229741-74229752 chr2:74229752-74229761 chr2:74229832-74229841 chr2:74229777-74229786 chr2:74229705-74229714 chr2:74229743-74229757 chr2:74229700-74229714 chr2:74229769-74229783
9	RCOR1	chr2:74229558-74230289	K562	blood:	n/a	n/a
10	CTCF	chr2:74229700-74229850	GM12865	blood:	n/a	chr2:74229734-74229747 chr2:74229731-74229740 chr2:74229731-74229744
11	MAX	chr2:74229736-74229942	K562	blood:	n/a	n/a
12	RELA	chr2:74229257-74229785	GM19099	blood:	n/a	n/a
13	ELF1	chr2:74229220-74230300	GM12878	blood:	n/a	chr2:74229529-74229538
14	EGR1	chr2:74229493-74229968	ECC-1	luminal epithelium:	n/a	chr2:74229777-74229792 chr2:74229735-74229748 chr2:74229736-74229750 chr2:74229707-74229717 chr2:74229778-74229791 chr2:74229610-74229620 chr2:74229778-74229788 chr2:74229834-74229844 chr2:74229703-74229716 chr2:74229778-74229791
15	RFX5	chr2:74229776-74229876	HepG2	liver:	n/a	n/a
16	MAZ	chr2:74229385-74231357	K562	blood:	n/a	chr2:74230835-74230844 chr2:74231317-74231327 chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
17	MTA3	chr2:74229153-74229901	GM12878	blood:	n/a	n/a
18	YY1	chr2:74229745-74229932	K562	blood:	n/a	chr2:74229752-74229761 chr2:74229832-74229841 chr2:74229777-74229786 chr2:74229769-74229783
19	POLR2A	chr2:74229532-74230044	GM12878	blood:	n/a	n/a
20	SP1	chr2:74229498-74229955	GM12878	blood:	n/a	chr2:74229775-74229787 chr2:74229707-74229721 chr2:74229775-74229787 chr2:74229708-74229717 chr2:74229706-74229718 chr2:74229806-74229815
21	EGR1	chr2:74229492-74229957	K562	blood:	n/a	chr2:74229777-74229792 chr2:74229735-74229748 chr2:74229736-74229750 chr2:74229707-74229717 chr2:74229778-74229791 chr2:74229610-74229620 chr2:74229778-74229788 chr2:74229834-74229844 chr2:74229703-74229716 chr2:74229778-74229791
22	YY1	chr2:74229436-74229997	H1-hESC	embryonic stem cell:	n/a	chr2:74229697-74229708 chr2:74229741-74229752 chr2:74229752-74229761 chr2:74229832-74229841 chr2:74229777-74229786 chr2:74229705-74229714 chr2:74229743-74229757 chr2:74229700-74229714 chr2:74229769-74229783
23	CTCF	chr2:74229744-74229915	HepG2	liver:	n/a	chr2:74229867-74229880
24	STAT1	chr2:74229250-74229985	GM12878	blood:	n/a	chr2:74229807-74229819
25	MAX	chr2:74229492-74230376	HepG2	liver:	n/a	chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
26	MXI1	chr2:74228178-74230662	IMR90	lung:	n/a	n/a
27	GABPA	chr2:74229527-74229963	H1-hESC	embryonic stem cell:	n/a	n/a
28	NRF1	chr2:74229409-74229836	GM12878	blood:	n/a	n/a
29	ELF1	chr2:74229495-74230006	K562	blood:	n/a	chr2:74229529-74229538
30	GATA2	chr2:74229701-74230318	SH-SY5Y	brain:	n/a	n/a
31	POLR2A	chr2:74229578-74230091	HUVEC	blood vessel:	n/a	n/a
32	NFYB	chr2:74229560-74230034	K562	blood:	n/a	n/a
33	CTCF	chr2:74229381-74229968	GM12878	blood:	n/a	chr2:74229526-74229539 chr2:74229867-74229880 chr2:74229734-74229747 chr2:74229731-74229740 chr2:74229731-74229744
34	CTCF	chr2:74229777-74229955	K562	blood:	n/a	chr2:74229867-74229880
35	POLR2A	chr2:74229740-74229914	A549	lung:	n/a	n/a
36	CTCF	chr2:74229740-74229890	HVMF	connective:	n/a	chr2:74229867-74229880
37	TAF1	chr2:74229593-74230260	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr2:74229757-74230049	MCF-7	breast:	n/a	n/a
39	EGR1	chr2:74229478-74229995	MCF-7	breast:	n/a	chr2:74229777-74229792 chr2:74229490-74229500 chr2:74229489-74229499 chr2:74229735-74229748 chr2:74229736-74229750 chr2:74229707-74229717 chr2:74229778-74229791 chr2:74229610-74229620 chr2:74229778-74229788 chr2:74229834-74229844 chr2:74229703-74229716 chr2:74229778-74229791
40	SIN3A	chr2:74229529-74229989	GM12878	blood:	n/a	chr2:74229826-74229839 chr2:74229682-74229693
41	RCOR1	chr2:74229707-74229919	HepG2	liver:	n/a	n/a
42	EBF1	chr2:74229262-74229826	GM12878	blood:	n/a	n/a
43	CTCF	chr2:74229760-74229910	HPAF	blood vessel:	n/a	chr2:74229867-74229880
44	MYC	chr2:74229577-74229965	MCF-7	breast:	n/a	chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
45	POLR2A	chr2:74229696-74230396	H1-hESC	embryonic stem cell:	n/a	n/a
46	FOS	chr2:74229776-74229865	MCF10A-Er-Src	breast:	n/a	n/a
47	TAF1	chr2:74229689-74229972	PFSK-1	brain:	n/a	n/a
48	GABPA	chr2:74229584-74230409	K562	blood:	n/a	n/a
49	SIN3AK20	chr2:74229391-74229974	K562	blood:	n/a	n/a
50	MYC	chr2:74229674-74229875	MCF-7	breast:	n/a	chr2:74229735-74229745 chr2:74229706-74229716

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:74229775-74229825	SKMC	muscle:	n/a
2	chr2:74229775-74229825	SAEC	small airway:	n/a
3	chr2:74229775-74229825	HEK293	kidney:	embryo
4	chr2:74229775-74229825	SK-N-SH_RA	brain:	n/a
5	chr2:74229775-74229825	BE2_C	brain:	n/a
6	chr2:74229775-74229825	NB4	blood:	n/a
7	chr2:74229775-74229825	HCM	heart:	n/a
8	chr2:74229775-74229825	HEEpiC	esophagus:	n/a
9	chr2:74229775-74229825	AG04449	skin:	fetal
10	chr2:74229775-74229825	NHBE	bronchial:	n/a
11	chr2:74229775-74229825	HCT-116	colon:	n/a
12	chr2:74229775-74229825	LNCaP	prostate:	n/a
13	chr2:74229775-74229825	GM06990	blood:	n/a
14	chr2:74229775-74229825	HRPEpiC	eye:	n/a
15	chr2:74229775-74229825	ovcar-3	ovarian:	n/a
16	chr2:74229775-74229825	HRCEpiC	kidney:	n/a
17	chr2:74229775-74229825	Caco-2	colon:	n/a
18	chr2:74229775-74229825	CMK	blood:	n/a
19	chr2:74229775-74229825	PFSK-1	brain:	n/a
20	chr2:74229775-74229825	PANC-1	pancreas:	n/a
21	chr2:74229775-74229825	HAEpiC	amniotic membrane:	n/a
22	chr2:74229775-74229825	Hela-S3	cervix:	n/a
23	chr2:74229775-74229825	AG10803	skin:	n/a
24	chr2:74229775-74229825	U87	brain:	n/a
25	chr2:74229775-74229825	IMR90	lung:	fetal
26	chr2:74229775-74229825	HCPEpiC	choroid plexus:	n/a
27	chr2:74229775-74229825	HCF	heart:	n/a
28	chr2:74229775-74229825	AoSMC	blood vessel:	n/a
29	chr2:74229775-74229825	HMEC	breast:	n/a
30	chr2:74229775-74229825	SK-N-MC	brain:	n/a
31	chr2:74229775-74229825	NH-A	brain:	n/a
32	chr2:74229775-74229825	HL-60	blood:	n/a
33	chr2:74229775-74229825	A549	lung:	n/a
34	chr2:74229775-74229825	HIPEpiC	eye:	n/a
35	chr2:74229775-74229825	AG04450	lung:	fetal
36	chr2:74229775-74229825	MCF-7	breast:	n/a
37	chr2:74229775-74229825	Jurkat	blood:	n/a
38	chr2:74229775-74229825	K562	blood:	n/a
39	chr2:74229775-74229825	SK-N-SH	brain:	n/a
40	chr2:74229775-74229825	H1-hESC	embryonic stem cell:	embryo
41	chr2:74229775-74229825	HRE	kidney:	n/a
42	chr2:74229775-74229825	HNPCEpiC	eye:	n/a
43	chr2:74229775-74229825	PrEC	prostate:	n/a
44	chr2:74229775-74229825	HPAEpiC	pulmonary alveolar:	n/a
45	chr2:74229775-74229825	RPTEC	kidney:	n/a
46	chr2:74229775-74229825	GM12892	blood:	n/a
47	chr2:74229775-74229825	ECC-1	luminal epithelium:	n/a
48	chr2:74229775-74229825	HUVEC	blood vessel:	n/a
49	chr2:74229775-74229825	GM12878	blood:	n/a
50	chr2:74229775-74229825	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74227509..74230131-chr2:74424857..74427331,4	MCF-7	breast:
2	chr2:74153966..74155499-chr2:74229025..74232283,3	K562	blood:
3	chr2:74054453..74058790-chr2:74226313..74230079,4	MCF-7	breast:
4	chr2:74229598..74231793-chr2:74423826..74425705,2	MCF-7	breast:
5	chr2:74055799..74057566-chr2:74228295..74229864,2	MCF-7	breast:
6	chr2:74153007..74155466-chr2:74228011..74231907,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TET3-3	chr2:74229333-74230678	ucscGeneNc_uc002ske_2

Variant related genes	Relation type
TET3	TF binding region
TET3	CpG island
ENSG00000114956	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011177	chr2:74167343-74239905	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv818048	chr2:74225434-74313080	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3436825	chr2:74228469-74231017	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3394982	chr2:74229169-74232017	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74224000-74230000	Enhancers	Fetal Brain Male	brain
2	chr2:74226200-74232400	Weak transcription	Hela-S3	cervix
3	chr2:74226600-74229800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:74226800-74229800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:74228800-74231000	Weak transcription	Small Intestine	intestine
6	chr2:74228800-74231200	Active TSS	Psoas Muscle	Psoas
7	chr2:74229000-74229800	Active TSS	Colonic Mucosa	Colon
8	chr2:74229200-74229800	Active TSS	Right Atrium	heart
9	chr2:74229200-74230000	Active TSS	Primary T cells from cord blood	blood
10	chr2:74229200-74230000	Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr2:74229200-74230000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:74229200-74230200	Enhancers	Fetal Heart	heart
13	chr2:74229200-74230400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:74229200-74230400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr2:74229200-74230600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:74229200-74230600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr2:74229200-74230800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr2:74229200-74231000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr2:74229200-74231000	Active TSS	Brain Cingulate Gyrus	brain
20	chr2:74229200-74231000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:74229400-74229800	Active TSS	Primary B cells from cord blood	blood
22	chr2:74229400-74229800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:74229400-74229800	Active TSS	Liver	Liver
24	chr2:74229400-74230000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:74229400-74230000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:74229400-74230000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:74229400-74230000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:74229400-74230000	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr2:74229400-74230000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr2:74229400-74230000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:74229400-74230000	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr2:74229400-74230000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:74229400-74230000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr2:74229400-74230000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:74229400-74230000	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:74229400-74230000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:74229400-74230000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:74229400-74230000	Active TSS	Muscle Satellite Cultured Cells	--
39	chr2:74229400-74230000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:74229400-74230000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:74229400-74230000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:74229400-74230000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:74229400-74230000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:74229400-74230000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:74229400-74230000	Active TSS	Adipose Nuclei	Adipose
46	chr2:74229400-74230000	Active TSS	Brain Germinal Matrix	brain
47	chr2:74229400-74230000	Active TSS	Duodenum Mucosa	Duodenum
48	chr2:74229400-74230000	Active TSS	Esophagus	oesophagus
49	chr2:74229400-74230000	Weak transcription	Fetal Kidney	kidney
50	chr2:74229400-74230000	Active TSS	Placenta	Placenta

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