Variant report

Variant	rs553878723
Chromosome Location	chr2:74229489-74229490
allele	-/C
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	chr2:74229480-74229630	HCM	heart:	n/a	chr2:74229526-74229539
2	ELF1	chr2:74229481-74230476	GM12878	blood:	n/a	chr2:74229529-74229538
3	CTCF	chr2:74229400-74229550	HBMEC	blood vessel:	n/a	chr2:74229526-74229539
4	CTCF	chr2:74229420-74229570	GM12873	blood:	n/a	chr2:74229526-74229539
5	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
6	RELA	chr2:74229257-74229785	GM19099	blood:	n/a	n/a
7	ELF1	chr2:74229220-74230300	GM12878	blood:	n/a	chr2:74229529-74229538
8	MAZ	chr2:74229385-74231357	K562	blood:	n/a	chr2:74230835-74230844 chr2:74231317-74231327 chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
9	MTA3	chr2:74229153-74229901	GM12878	blood:	n/a	n/a
10	CTCF	chr2:74229420-74229570	AG10803	skin:	n/a	chr2:74229526-74229539
11	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
12	CTCF	chr2:74229420-74229570	GM12870	blood:	n/a	chr2:74229526-74229539
13	STAT1	chr2:74229250-74229985	GM12878	blood:	n/a	chr2:74229807-74229819
14	CTCF	chr2:74229400-74229550	HMF	breast:	n/a	chr2:74229526-74229539
15	CTCF	chr2:74229460-74229610	HRE	kidney:	n/a	chr2:74229526-74229539
16	MXI1	chr2:74228178-74230662	IMR90	lung:	n/a	n/a
17	CTCF	chr2:74229460-74229610	HA-sp	spinal cord:	n/a	chr2:74229526-74229539
18	NRF1	chr2:74229409-74229836	GM12878	blood:	n/a	n/a
19	CTCF	chr2:74229400-74229550	WI-38	lung:	n/a	chr2:74229526-74229539
20	CTCF	chr2:74229381-74229968	GM12878	blood:	n/a	chr2:74229526-74229539 chr2:74229867-74229880 chr2:74229734-74229747 chr2:74229731-74229740 chr2:74229731-74229744
21	CTCF	chr2:74229480-74229630	GM12871	blood:	n/a	chr2:74229526-74229539
22	CTCF	chr2:74229480-74229630	GM12878	blood:	n/a	chr2:74229526-74229539
23	CTCF	chr2:74229460-74229610	NHDF-neo	bronchial:	n/a	chr2:74229526-74229539
24	RUNX3	chr2:74229446-74229667	GM12878	blood:	n/a	n/a
25	CTCF	chr2:74229360-74229510	GM12864	blood:	n/a	n/a
26	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
27	CTCF	chr2:74229440-74229590	HMF	breast:	n/a	chr2:74229526-74229539
28	CTCF	chr2:74229480-74229630	GM12867	blood:	n/a	chr2:74229526-74229539
29	EBF1	chr2:74229262-74229826	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr2:74229272-74229659	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIN3AK20	chr2:74229391-74229974	K562	blood:	n/a	n/a
32	POLR2A	chr2:74229436-74230610	H1-neurons	neurons:	n/a	n/a
33	CTCF	chr2:74229460-74229610	WERI-Rb-1	eye:	n/a	chr2:74229526-74229539
34	RELA	chr2:74229077-74229897	GM18951	blood:	n/a	n/a
35	POLR2A	chr2:74229471-74230076	PANC-1	pancreas:	n/a	n/a
36	CTCFL	chr2:74229474-74229590	K562	blood:	n/a	n/a
37	ZNF143	chr2:74229360-74229923	GM12878	blood:	n/a	chr2:74229738-74229748
38	CTCF	chr2:74229440-74229590	HUVEC	blood vessel:	n/a	chr2:74229526-74229539
39	ZNF263	chr2:74229104-74230330	HEK293-T-REx	kidney:	n/a	chr2:74229200-74229209 chr2:74229605-74229614
40	TAF1	chr2:74229489-74230526	H1-neurons	neurons:	n/a	n/a
41	YY1	chr2:74229372-74229990	GM12878	blood:	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
42	YY1	chr2:74229389-74229950	GM12891	blood:	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
43	RUNX3	chr2:74229238-74229852	GM12878	blood:	n/a	n/a
44	CTCF	chr2:74229420-74229570	HUVEC	blood vessel:	n/a	chr2:74229526-74229539
45	TBL1XR1	chr2:74229416-74229773	GM12878	blood:	n/a	n/a
46	SIN3AK20	chr2:74229362-74230095	PANC-1	pancreas:	n/a	n/a
47	CTCF	chr2:74229420-74229570	HPAF	blood vessel:	n/a	chr2:74229526-74229539
48	MAZ	chr2:74229216-74230040	GM12878	blood:	n/a	chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
49	CTCF	chr2:74229480-74229630	GM12875	blood:	n/a	chr2:74229526-74229539
50	CTBP2	chr2:74229476-74230346	H1-hESC	embryonic stem cell:	n/a	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	chr2:74156030..74157687-chr2:74228022..74229641,2	K562	blood:
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
ENSG00000114956	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000124356	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:126 , 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	chr2:74226600-74229600	Enhancers	NHEK	skin
4	chr2:74226600-74229800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:74226800-74229600	Enhancers	HMEC	breast
6	chr2:74226800-74229800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:74227000-74229600	Enhancers	Spleen	Spleen
8	chr2:74227200-74229600	Enhancers	Gastric	stomach
9	chr2:74228200-74229600	Weak transcription	HSMMtube	muscle
10	chr2:74228800-74229600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:74228800-74231000	Weak transcription	Small Intestine	intestine
12	chr2:74228800-74231200	Active TSS	Psoas Muscle	Psoas
13	chr2:74229000-74229600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr2:74229000-74229600	Flanking Active TSS	Dnd41	blood
15	chr2:74229000-74229800	Active TSS	Colonic Mucosa	Colon
16	chr2:74229200-74229600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:74229200-74229600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:74229200-74229600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr2:74229200-74229600	Flanking Active TSS	Primary B cells from peripheral blood	blood
20	chr2:74229200-74229600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr2:74229200-74229600	Enhancers	Primary hematopoietic stem cells	blood
22	chr2:74229200-74229600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:74229200-74229600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr2:74229200-74229600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:74229200-74229600	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr2:74229200-74229600	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr2:74229200-74229600	Flanking Active TSS	NH-A	brain
28	chr2:74229200-74229800	Active TSS	Right Atrium	heart
29	chr2:74229200-74230000	Active TSS	Primary T cells from cord blood	blood
30	chr2:74229200-74230000	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:74229200-74230000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:74229200-74230200	Enhancers	Fetal Heart	heart
33	chr2:74229200-74230400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:74229200-74230400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr2:74229200-74230600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr2:74229200-74230600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr2:74229200-74230800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr2:74229200-74231000	Active TSS	H9 Cell Line	embryonic stem cell
39	chr2:74229200-74231000	Active TSS	Brain Cingulate Gyrus	brain
40	chr2:74229200-74231000	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:74229400-74229600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:74229400-74229600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:74229400-74229600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr2:74229400-74229600	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr2:74229400-74229600	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr2:74229400-74229600	Flanking Active TSS	Fetal Thymus	thymus
47	chr2:74229400-74229600	Flanking Active TSS	Pancreas	Pancrea
48	chr2:74229400-74229600	Weak transcription	A549	lung
49	chr2:74229400-74229800	Active TSS	Primary B cells from cord blood	blood
50	chr2:74229400-74229800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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