Variant report

Variant	rs4322837
Chromosome Location	chr2:113999023-113999024
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	MAX	chr2:113998216-113999609	SK-N-SH	brain:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
2	POLR2A	chr2:113998335-114000919	ECC-1	luminal epithelium:	n/a	n/a
3	SIX5	chr2:113997662-113999126	A549	lung:	n/a	n/a
4	FOXA2	chr2:113998366-113999073	A549	lung:	n/a	n/a
5	SMARCC1	chr2:113997660-113999427	Hela-S3	cervix:	n/a	chr2:113999386-113999395
6	GATA3	chr2:113998285-113999134	A549	lung:	n/a	n/a
7	POLR2A	chr2:113997003-114000128	IMR90	lung:	n/a	n/a
8	FOS	chr2:113997803-113999533	MCF10A-Er-Src	breast:	n/a	chr2:113999384-113999396 chr2:113998584-113998595 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
9	FOSL2	chr2:113997326-113999659	A549	lung:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113998585-113998596 chr2:113999386-113999394
10	E2F6	chr2:113998475-113999603	A549	lung:	n/a	n/a
11	USF1	chr2:113998126-113999212	A549	lung:	n/a	n/a
12	E2F6	chr2:113998194-113999726	A549	lung:	n/a	n/a
13	POLR2A	chr2:113998495-113999803	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr2:113996944-114000866	K562	blood:	n/a	n/a
15	SP1	chr2:113997527-113999233	A549	lung:	n/a	n/a
16	GABPA	chr2:113998062-113999089	A549	lung:	n/a	n/a
17	MAX	chr2:113998374-113999046	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:113997475-113999254	GM12878	blood:	n/a	n/a
19	MAX	chr2:113997698-113999070	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:113997827-113999157	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr2:113998512-113999091	MCF10A-Er-Src	breast:	n/a	n/a
22	MAX	chr2:113996927-113999829	A549	lung:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
23	FOSL1	chr2:113997636-113999713	HCT-116	colon:	n/a	chr2:113999384-113999396 chr2:113999387-113999398 chr2:113999385-113999395 chr2:113999385-113999395 chr2:113999386-113999394
24	CEBPB	chr2:113998388-113999163	MCF-7	breast:	n/a	chr2:113998825-113998836
25	EP300	chr2:113998276-113999029	Hela-S3	cervix:	n/a	n/a
26	NR3C1	chr2:113998393-113999068	A549	lung:	n/a	n/a
27	TCF12	chr2:113998298-113999050	A549	lung:	n/a	n/a
28	TCF12	chr2:113997628-113999335	SK-N-SH	brain:	n/a	n/a
29	STAT3	chr2:113997845-113999093	MCF10A-Er-Src	breast:	n/a	n/a
30	SIN3AK20	chr2:113998245-113999178	MCF-7	breast:	n/a	n/a
31	POLR2A	chr2:113998319-113999234	GM12892	blood:	n/a	n/a
32	NR3C1	chr2:113998209-113999105	A549	lung:	n/a	n/a
33	CEBPB	chr2:113998659-113999062	K562	blood:	n/a	chr2:113998825-113998836
34	ATF3	chr2:113998255-113999144	A549	lung:	n/a	n/a
35	CEBPB	chr2:113998274-113999241	A549	lung:	n/a	chr2:113998825-113998836
36	MXI1	chr2:113997343-113999336	IMR90	lung:	n/a	n/a
37	POLR2A	chr2:113998294-113999102	K562	blood:	n/a	n/a
38	CEBPB	chr2:113998530-113999177	HepG2	liver:	n/a	chr2:113998825-113998836
39	MYC	chr2:113997694-113999664	MCF10A-Er-Src	breast:	n/a	chr2:113999417-113999426 chr2:113999417-113999427 chr2:113999419-113999428 chr2:113999417-113999426 chr2:113999416-113999426 chr2:113999417-113999426 chr2:113999458-113999474 chr2:113999416-113999427
40	CEBPB	chr2:113997382-113999188	IMR90	lung:	n/a	chr2:113998825-113998836
41	JUND	chr2:113997140-113999306	SK-N-SH	brain:	n/a	chr2:113998584-113998595
42	GATA3	chr2:113997609-113999117	SK-N-SH	brain:	n/a	n/a
43	CEBPB	chr2:113997572-113999797	HCT-116	colon:	n/a	chr2:113998825-113998836
44	SIN3AK20	chr2:113997752-113999111	A549	lung:	n/a	n/a
45	ATF3	chr2:113998239-113999189	A549	lung:	n/a	n/a
46	RCOR1	chr2:113998378-113999072	Hela-S3	cervix:	n/a	n/a
47	RAD21	chr2:113997940-113999037	A549	lung:	n/a	n/a
48	NFIC	chr2:113997502-113999532	SK-N-SH	brain:	n/a	n/a
49	TCF12	chr2:113997522-113999698	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr2:113997465-113999660	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
2	chr2:113950220..113951864-chr2:113997428..113999954,2	K562	blood:
3	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:

Variant related genes	Relation type
PAX8	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2289896	0.89[EUR][1000 genomes]
rs3738911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58013292	0.89[EUR][1000 genomes]
rs59641602	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459008	chr2:113972945-114010791	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv582713	chr2:113972945-114010791	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113993400-114000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:113993400-114006600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:113994200-114002000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:113994200-114006600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:113994600-114000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:113994800-114006600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:113995000-114006800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:113995200-114000000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:113995200-114007000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr2:113995600-114000200	Weak transcription	Dnd41	blood
11	chr2:113995600-114008600	Weak transcription	GM12878-XiMat	blood
12	chr2:113996600-114000200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:113997000-113999200	Enhancers	Brain Anterior Caudate	brain
14	chr2:113997000-113999200	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:113997000-113999200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:113997000-113999200	Enhancers	Placenta	Placenta
17	chr2:113997000-113999200	Enhancers	Gastric	stomach
18	chr2:113997000-113999200	Enhancers	Right Atrium	heart
19	chr2:113997000-113999200	Genic enhancers	K562	blood
20	chr2:113997000-113999400	Enhancers	Colonic Mucosa	Colon
21	chr2:113997000-113999400	Enhancers	Spleen	Spleen
22	chr2:113997000-113999600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:113997000-113999600	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:113997000-114000000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:113997000-114000000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:113997000-114000000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr2:113997000-114000600	Enhancers	Esophagus	oesophagus
28	chr2:113997200-113999200	Enhancers	Brain Germinal Matrix	brain
29	chr2:113997200-113999200	Flanking Active TSS	Hela-S3	cervix
30	chr2:113997200-113999600	Enhancers	Stomach Mucosa	stomach
31	chr2:113997400-113999200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:113997400-113999200	Enhancers	Duodenum Mucosa	Duodenum
33	chr2:113997400-113999200	Enhancers	Pancreas	Pancrea
34	chr2:113997400-113999200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr2:113997400-113999400	Enhancers	HUVEC	blood vessel
36	chr2:113997400-113999600	Enhancers	Fetal Stomach	stomach
37	chr2:113997400-113999600	Enhancers	Left Ventricle	heart
38	chr2:113997400-113999800	Enhancers	Right Ventricle	heart
39	chr2:113997400-114000200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr2:113997600-113999600	Enhancers	Ovary	ovary
41	chr2:113997600-113999800	Enhancers	Fetal Intestine Large	intestine
42	chr2:113997600-114001000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:113997800-113999200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:113998000-113999200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:113998000-113999200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:113998000-113999400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:113998000-113999800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:113998000-113999800	Enhancers	Lung	lung
49	chr2:113998200-113999400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr2:113998200-113999600	Enhancers	Brain Inferior Temporal Lobe	brain

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