Variant report

Variant	rs535099162
Chromosome Location	chr2:74229360-74229361
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	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
2	RELA	chr2:74229257-74229785	GM19099	blood:	n/a	n/a
3	ELF1	chr2:74229220-74230300	GM12878	blood:	n/a	chr2:74229529-74229538
4	MTA3	chr2:74229153-74229901	GM12878	blood:	n/a	n/a
5	STAT1	chr2:74229250-74229985	GM12878	blood:	n/a	chr2:74229807-74229819
6	MXI1	chr2:74228178-74230662	IMR90	lung:	n/a	n/a
7	CTCF	chr2:74229360-74229510	GM12864	blood:	n/a	n/a
8	EBF1	chr2:74229262-74229826	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:74228959-74229379	K562	blood:	n/a	n/a
10	SIN3AK20	chr2:74229272-74229659	H1-hESC	embryonic stem cell:	n/a	n/a
11	RELA	chr2:74229077-74229897	GM18951	blood:	n/a	n/a
12	ZNF143	chr2:74229360-74229923	GM12878	blood:	n/a	chr2:74229738-74229748
13	ZNF263	chr2:74229104-74230330	HEK293-T-REx	kidney:	n/a	chr2:74229200-74229209 chr2:74229605-74229614
14	RUNX3	chr2:74229238-74229852	GM12878	blood:	n/a	n/a
15	MAZ	chr2:74229216-74230040	GM12878	blood:	n/a	chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
16	PAX5	chr2:74229352-74229994	GM12892	blood:	n/a	chr2:74229511-74229530 chr2:74229770-74229779 chr2:74229704-74229713 chr2:74229470-74229488
17	MXI1	chr2:74229002-74230685	SK-N-SH	brain:	n/a	n/a
18	YY1	chr2:74229359-74230019	K562	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
19	MAZ	chr2:74228758-74231680	IMR90	lung:	n/a	chr2:74231558-74231567 chr2:74230835-74230844 chr2:74231317-74231327 chr2:74229735-74229745 chr2:74229706-74229716 chr2:74229611-74229621
20	BCL3	chr2:74229324-74230116	GM12878	blood:	n/a	chr2:74229776-74229785 chr2:74229797-74229810 chr2:74229748-74229761 chr2:74229600-74229613
21	CTCF	chr2:74229220-74229370	NHEK	skin:	n/a	n/a
22	SIN3AK20	chr2:74229270-74229573	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr2:74229340-74229570	HRE	kidney:	n/a	chr2:74229526-74229539
24	ZBTB7A	chr2:74229268-74230060	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr2:74229360-74229510	GM12871	blood:	n/a	n/a
26	RELA	chr2:74229281-74229947	GM12891	blood:	n/a	n/a
27	RCOR1	chr2:74229256-74229843	GM12878	blood:	n/a	n/a
28	CTCF	chr2:74229353-74230046	K562	blood:	n/a	chr2:74229526-74229539 chr2:74229867-74229880 chr2:74229734-74229747 chr2:74229731-74229740 chr2:74229731-74229744
29	REST	chr2:74229065-74230761	H1-neurons	neurons:	n/a	chr2:74229782-74229795 chr2:74229689-74229702 chr2:74229689-74229707 chr2:74229644-74229654
30	JUN	chr2:74229246-74229441	H1-hESC	embryonic stem cell:	n/a	n/a
31	SIN3A	chr2:74229264-74230514	H1-hESC	embryonic stem cell:	n/a	chr2:74229826-74229839 chr2:74230418-74230429 chr2:74229682-74229693
32	CTCF	chr2:74229360-74229942	K562	blood:	n/a	chr2:74229526-74229539 chr2:74229867-74229880 chr2:74229734-74229747 chr2:74229731-74229740 chr2:74229731-74229744
33	JUN	chr2:74228917-74231373	K562	blood:	n/a	chr2:74231145-74231157 chr2:74230978-74230987 chr2:74229709-74229718
34	EP300	chr2:74229342-74229542	GM12878	blood:	n/a	n/a
35	EBF1	chr2:74229227-74229903	GM12878	blood:	n/a	n/a
36	RELA	chr2:74229288-74229978	GM19193	blood:	n/a	n/a
37	POLR2A	chr2:74229347-74230687	H1-neurons	neurons:	n/a	n/a
38	STAT5A	chr2:74228911-74229483	GM12878	blood:	n/a	n/a
39	YY1	chr2:74229314-74229976	GM12892	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
40	ZNF384	chr2:74229333-74229373	GM12878	blood:	n/a	n/a
41	MXI1	chr2:74229278-74230240	GM12878	blood:	n/a	n/a
42	NFIC	chr2:74229237-74229487	GM12878	blood:	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	chr2:74227468..74229424-chr2:74305762..74308272,2	K562	blood:
4	chr2:74054453..74058790-chr2:74226313..74230079,4	MCF-7	breast:
5	chr2:74156030..74157687-chr2:74228022..74229641,2	K562	blood:
6	chr2:74055799..74057566-chr2:74228295..74229864,2	MCF-7	breast:
7	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74224000-74229400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:74224000-74230000	Enhancers	Fetal Brain Male	brain
3	chr2:74226000-74229400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:74226000-74229400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:74226200-74229400	Enhancers	A549	lung
6	chr2:74226200-74232400	Weak transcription	Hela-S3	cervix
7	chr2:74226400-74229400	Enhancers	Fetal Intestine Large	intestine
8	chr2:74226400-74229400	Enhancers	Lung	lung
9	chr2:74226600-74229400	Enhancers	Esophagus	oesophagus
10	chr2:74226600-74229600	Enhancers	NHEK	skin
11	chr2:74226600-74229800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:74226800-74229400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:74226800-74229400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:74226800-74229400	Enhancers	Fetal Muscle Trunk	muscle
15	chr2:74226800-74229400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:74226800-74229400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:74226800-74229400	Enhancers	Right Ventricle	heart
18	chr2:74226800-74229600	Enhancers	HMEC	breast
19	chr2:74226800-74229800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:74227000-74229400	Enhancers	Fetal Thymus	thymus
21	chr2:74227000-74229400	Enhancers	NHLF	lung
22	chr2:74227000-74229600	Enhancers	Spleen	Spleen
23	chr2:74227200-74229400	Enhancers	Left Ventricle	heart
24	chr2:74227200-74229400	Enhancers	Pancreas	Pancrea
25	chr2:74227200-74229600	Enhancers	Gastric	stomach
26	chr2:74227400-74229400	Enhancers	NHDF-Ad	bronchial
27	chr2:74227600-74229400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:74227600-74229400	Enhancers	Fetal Stomach	stomach
29	chr2:74227600-74229400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:74228200-74229600	Weak transcription	HSMMtube	muscle
31	chr2:74228400-74229400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr2:74228800-74229400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:74228800-74229400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:74228800-74229400	Enhancers	Liver	Liver
35	chr2:74228800-74229400	Flanking Active TSS	GM12878-XiMat	blood
36	chr2:74228800-74229600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:74228800-74231000	Weak transcription	Small Intestine	intestine
38	chr2:74228800-74231200	Active TSS	Psoas Muscle	Psoas
39	chr2:74229000-74229400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr2:74229000-74229400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr2:74229000-74229400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr2:74229000-74229400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr2:74229000-74229400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr2:74229000-74229400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:74229000-74229400	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr2:74229000-74229400	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr2:74229000-74229400	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr2:74229000-74229400	Flanking Active TSS	Fetal Brain Female	brain
49	chr2:74229000-74229400	Flanking Active TSS	Thymus	Thymus
50	chr2:74229000-74229400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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