Variant report

Variant	rs13394820
Chromosome Location	chr2:58290909-58290910
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	STAT3	chr2:58290725-58291112	MCF10A-Er-Src	breast:	n/a	chr2:58290951-58290962
2	EP300	chr2:58290700-58291417	SK-N-SH	brain:	n/a	n/a
3	PBX3	chr2:58290678-58291546	SK-N-SH	brain:	n/a	n/a
4	FOS	chr2:58290782-58291143	MCF10A-Er-Src	breast:	n/a	chr2:58290959-58290970
5	FOS	chr2:58290638-58291176	HUVEC	blood vessel:	n/a	chr2:58290959-58290970
6	CEBPB	chr2:58290722-58291076	IMR90	lung:	n/a	n/a
7	CEBPB	chr2:58290577-58291026	HCT-116	colon:	n/a	n/a
8	STAT3	chr2:58290830-58291143	MCF10A-Er-Src	breast:	n/a	chr2:58290951-58290962
9	CBX3	chr2:58290746-58291227	HCT-116	colon:	n/a	n/a
10	GATA3	chr2:58290582-58291555	SK-N-SH	brain:	n/a	n/a
11	MEF2A	chr2:58290717-58291355	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr2:58290655-58291158	A549	lung:	n/a	n/a
13	TCF12	chr2:58290617-58291338	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr2:58290645-58291109	MCF10A-Er-Src	breast:	n/a	chr2:58290951-58290962
15	FOSL1	chr2:58290780-58291259	HCT-116	colon:	n/a	n/a
16	GATA3	chr2:58290641-58291625	SK-N-SH	brain:	n/a	n/a
17	MEF2A	chr2:58290681-58291359	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr2:58288671-58291267	K562	blood:	n/a	n/a
19	STAT3	chr2:58290827-58291143	MCF10A-Er-Src	breast:	n/a	chr2:58290951-58290962
20	FOS	chr2:58290813-58291132	MCF10A-Er-Src	breast:	n/a	chr2:58290959-58290970
21	JUND	chr2:58290685-58291294	SK-N-SH	brain:	n/a	n/a
22	FOS	chr2:58290791-58291138	MCF10A-Er-Src	breast:	n/a	chr2:58290959-58290970
23	CEBPB	chr2:58290755-58291132	HCT-116	colon:	n/a	n/a
24	JUND	chr2:58290721-58291212	HCT-116	colon:	n/a	n/a
25	EP300	chr2:58290844-58291077	SK-N-SH_RA	brain:	n/a	n/a
26	POLR2A	chr2:58290899-58292068	K562	blood:	n/a	n/a
27	POLR2A	chr2:58290791-58291078	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr2:58290600-58291560	SK-N-SH	brain:	n/a	n/a
29	PBX3	chr2:58290650-58291293	SK-N-SH	brain:	n/a	n/a
30	FOS	chr2:58290793-58291116	MCF10A-Er-Src	breast:	n/a	chr2:58290959-58290970
31	NFIC	chr2:58290683-58291303	SK-N-SH	brain:	n/a	n/a
32	JUND	chr2:58290784-58291184	HCT-116	colon:	n/a	n/a
33	FOSL2	chr2:58290702-58291236	SK-N-SH	brain:	n/a	n/a
34	SP1	chr2:58290769-58291224	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
ENSG00000251738	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165760	0.95[AFR][1000 genomes]
rs10174202	0.98[AFR][1000 genomes]
rs10176681	0.98[AFR][1000 genomes]
rs10178025	0.99[AFR][1000 genomes]
rs10182762	0.92[AFR][1000 genomes]
rs10187411	0.84[AFR][1000 genomes]
rs10203014	0.98[AFR][1000 genomes]
rs1025755	0.90[AFR][1000 genomes]
rs11883874	0.95[AFR][1000 genomes]
rs11891477	0.92[AFR][1000 genomes]
rs11892302	0.93[AFR][1000 genomes]
rs13382369	0.95[AFR][1000 genomes]
rs13405281	0.95[AFR][1000 genomes]
rs13410500	0.95[AFR][1000 genomes]
rs13419989	0.98[AFR][1000 genomes]
rs13431271	0.92[AFR][1000 genomes]
rs2165100	0.98[AFR][1000 genomes]
rs2165103	0.93[AFR][1000 genomes]
rs28521626	1.00[AFR][1000 genomes]
rs4459722	0.92[AFR][1000 genomes]
rs57112138	0.85[AFR][1000 genomes]
rs57597086	0.86[AFR][1000 genomes]
rs58470176	0.95[AFR][1000 genomes]
rs60364084	0.81[AFR][1000 genomes]
rs6718190	0.95[AFR][1000 genomes]
rs72949131	0.84[AFR][1000 genomes]
rs72949137	0.94[AFR][1000 genomes]
rs72949158	0.82[AFR][1000 genomes]
rs72951042	0.91[AFR][1000 genomes]
rs72951048	0.95[AFR][1000 genomes]
rs72951056	0.95[AFR][1000 genomes]
rs73944804	0.92[AFR][1000 genomes]
rs7563312	0.89[AFR][1000 genomes]
rs7569731	0.92[AFR][1000 genomes]
rs7574694	0.98[AFR][1000 genomes]
rs7600213	0.94[AFR][1000 genomes]
rs9973345	0.86[AFR][1000 genomes]
rs9973928	0.93[AFR][1000 genomes]

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	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58274600-58298600	Weak transcription	Spleen	Spleen
2	chr2:58274600-58302400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:58274800-58296400	Weak transcription	Ovary	ovary
4	chr2:58274800-58296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:58274800-58302200	Weak transcription	Aorta	Aorta
6	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:58275000-58291000	Weak transcription	HSMM	muscle
8	chr2:58275000-58297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:58275000-58302600	Weak transcription	Esophagus	oesophagus
10	chr2:58275000-58302800	Weak transcription	Fetal Stomach	stomach
11	chr2:58275000-58305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
13	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
15	chr2:58275400-58291000	Weak transcription	NH-A	brain
16	chr2:58275400-58294400	Weak transcription	Fetal Intestine Small	intestine
17	chr2:58275600-58291000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:58275600-58291000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:58275600-58293800	Weak transcription	Small Intestine	intestine
20	chr2:58275800-58316800	Weak transcription	HMEC	breast
21	chr2:58279000-58319000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:58279400-58315600	Weak transcription	Dnd41	blood
23	chr2:58281000-58297800	Weak transcription	Fetal Lung	lung
24	chr2:58282200-58291400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr2:58282400-58291000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:58282400-58300400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:58282400-58301400	Weak transcription	Lung	lung
28	chr2:58282600-58350400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:58283400-58294400	Strong transcription	Primary B cells from cord blood	blood
30	chr2:58283400-58296600	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:58283600-58298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:58284200-58295400	Weak transcription	Psoas Muscle	Psoas
33	chr2:58284200-58296400	Weak transcription	Left Ventricle	heart
34	chr2:58284200-58303800	Weak transcription	Gastric	stomach
35	chr2:58284200-58317600	Weak transcription	HepG2	liver
36	chr2:58284400-58325000	Weak transcription	NHEK	skin
37	chr2:58284800-58291600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:58285200-58291000	Weak transcription	Right Ventricle	heart
39	chr2:58285200-58317000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:58285800-58293200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:58286000-58296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:58286200-58291000	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr2:58286200-58294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:58286200-58295800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:58286200-58297400	Weak transcription	Adipose Nuclei	Adipose
46	chr2:58286200-58297400	Weak transcription	Fetal Intestine Large	intestine
47	chr2:58286200-58302200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:58286200-58317600	Weak transcription	K562	blood
49	chr2:58286400-58302000	Weak transcription	Hela-S3	cervix
50	chr2:58286400-58317600	Weak transcription	Rectal Mucosa Donor 29	rectum

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