Variant report

Variant	rs3806788
Chromosome Location	chr4:89744825-89744826
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	POLR2A	chr4:89744813-89744995	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF263	chr4:89744152-89744863	K562	blood:	n/a	chr4:89744480-89744501 chr4:89744518-89744539
3	RAD21	chr4:89744160-89745074	Hela-S3	cervix:	n/a	n/a
4	JUN	chr4:89743918-89745319	K562	blood:	n/a	chr4:89744945-89744954 chr4:89744434-89744443
5	POLR2A	chr4:89744014-89745097	K562	blood:	n/a	n/a
6	MAX	chr4:89744128-89745106	NB4	blood:	n/a	n/a
7	JUN	chr4:89744109-89745145	K562	blood:	n/a	chr4:89744945-89744954 chr4:89744434-89744443
8	SIN3A	chr4:89744742-89745045	GM12878	blood:	n/a	n/a
9	CEBPB	chr4:89744049-89745100	IMR90	lung:	n/a	n/a
10	HNF4A	chr4:89744825-89745122	HepG2	liver:	n/a	chr4:89744876-89744888 chr4:89744876-89744888
11	ELK1	chr4:89744463-89744963	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr4:89744240-89745331	GM12878	blood:	n/a	n/a
13	GTF2F1	chr4:89744148-89745099	Hela-S3	cervix:	n/a	n/a
14	FOSL2	chr4:89744694-89745047	A549	lung:	n/a	chr4:89744945-89744954
15	FOXA2	chr4:89744736-89745100	A549	lung:	n/a	chr4:89744908-89744920
16	MBD4	chr4:89744107-89744974	HepG2	liver:	n/a	n/a
17	TBP	chr4:89744145-89745070	K562	blood:	n/a	n/a
18	MAZ	chr4:89744196-89745084	Hela-S3	cervix:	n/a	n/a
19	NFYB	chr4:89744296-89744945	Hela-S3	cervix:	n/a	chr4:89744430-89744445 chr4:89744429-89744441 chr4:89744430-89744445 chr4:89744430-89744444 chr4:89744427-89744442
20	TEAD4	chr4:89744108-89745140	K562	blood:	n/a	n/a
21	MYBL2	chr4:89744071-89744850	HepG2	liver:	n/a	n/a
22	MAX	chr4:89744222-89745112	Hela-S3	cervix:	n/a	n/a
23	BACH1	chr4:89744489-89744872	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr4:89744260-89745120	MCF-7	breast:	n/a	n/a
25	CREB1	chr4:89744734-89745048	H1-hESC	embryonic stem cell:	n/a	chr4:89744943-89744956
26	JUN	chr4:89744753-89745140	HUVEC	blood vessel:	n/a	chr4:89744945-89744954
27	FOS	chr4:89744785-89745121	MCF10A-Er-Src	breast:	n/a	chr4:89744945-89744954
28	E2F4	chr4:89744451-89745046	MCF10A-Er-Src	breast:	n/a	chr4:89744944-89744953 chr4:89744946-89744955
29	ZNF384	chr4:89744366-89745263	GM12878	blood:	n/a	n/a
30	SP1	chr4:89744244-89745165	A549	lung:	n/a	n/a
31	FOS	chr4:89744264-89745114	MCF10A-Er-Src	breast:	n/a	chr4:89744945-89744954 chr4:89744434-89744443
32	MAZ	chr4:89744133-89745109	K562	blood:	n/a	n/a
33	STAT3	chr4:89744806-89745009	MCF10A-Er-Src	breast:	n/a	n/a
34	MAX	chr4:89744194-89745064	A549	lung:	n/a	n/a
35	RXRA	chr4:89744705-89745065	HepG2	liver:	n/a	chr4:89744876-89744890
36	POLR2A	chr4:89744185-89745608	MCF10A-Er-Src	breast:	n/a	n/a
37	ATF2	chr4:89744654-89745116	GM12878	blood:	n/a	n/a
38	NFYB	chr4:89744248-89744921	K562	blood:	n/a	chr4:89744430-89744445 chr4:89744429-89744441 chr4:89744430-89744445 chr4:89744430-89744444 chr4:89744427-89744442
39	ELK1	chr4:89744616-89744952	GM12878	blood:	n/a	n/a
40	ZC3H11A	chr4:89744212-89745028	K562	blood:	n/a	n/a
41	POLR2A	chr4:89743967-89745176	U87	brain:	n/a	n/a
42	HCFC1	chr4:89744182-89745049	K562	blood:	n/a	n/a
43	POLR2A	chr4:89744123-89745026	HUVEC	blood vessel:	n/a	n/a
44	FOXA1	chr4:89744088-89745216	HepG2	liver:	n/a	chr4:89744910-89744925 chr4:89744908-89744920
45	MAFK	chr4:89744172-89745045	K562	blood:	n/a	n/a
46	EP300	chr4:89744737-89745058	GM12878	blood:	n/a	chr4:89744899-89744908 chr4:89744837-89744850 chr4:89744915-89744925
47	FOS	chr4:89744593-89745117	MCF10A-Er-Src	breast:	n/a	chr4:89744945-89744954
48	POLR2A	chr4:89743903-89744939	PFSK-1	brain:	n/a	n/a
49	ZNF263	chr4:89744018-89745117	HEK293-T-REx	kidney:	n/a	chr4:89744480-89744501 chr4:89744518-89744539
50	SIN3AK20	chr4:89744732-89745037	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:89743956..89746323-chr4:89976893..89978969,2	K562	blood:

Variant related genes	Relation type
FAM13A	TF binding region
ENSG00000138640	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2305934	0.82[ASN][1000 genomes]
rs28459962	0.86[ASN][1000 genomes]
rs28542213	0.84[ASN][1000 genomes]
rs62308745	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89740600-89745200	Active TSS	Fetal Intestine Small	intestine
2	chr4:89741000-89745000	Active TSS	Ovary	ovary
3	chr4:89741000-89745200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:89741000-89745200	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:89741200-89745200	Active TSS	Colonic Mucosa	Colon
6	chr4:89741200-89745200	Active TSS	Fetal Intestine Large	intestine
7	chr4:89741200-89745200	Active TSS	Fetal Stomach	stomach
8	chr4:89741400-89745000	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr4:89741400-89745200	Active TSS	Brain Angular Gyrus	brain
10	chr4:89741400-89745200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:89741400-89745400	Active TSS	K562	blood
12	chr4:89741600-89745000	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr4:89741600-89745000	Active TSS	Brain Germinal Matrix	brain
14	chr4:89741600-89745200	Active TSS	Brain Anterior Caudate	brain
15	chr4:89741600-89745200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr4:89741800-89745000	Active TSS	Psoas Muscle	Psoas
17	chr4:89742000-89745200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:89742000-89745200	Active TSS	Aorta	Aorta
19	chr4:89742000-89745200	Active TSS	Brain Substantia Nigra	brain
20	chr4:89742200-89745200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr4:89742200-89745200	Active TSS	Duodenum Mucosa	Duodenum
22	chr4:89742200-89745200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr4:89742400-89745000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:89742400-89745000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:89742400-89745000	Active TSS	Fetal Lung	lung
26	chr4:89742400-89745000	Active TSS	Right Ventricle	heart
27	chr4:89742400-89745000	Active TSS	Hela-S3	cervix
28	chr4:89742400-89745200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:89742400-89745200	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr4:89742400-89745200	Active TSS	Brain Hippocampus Middle	brain
31	chr4:89742400-89745200	Active TSS	Right Atrium	heart
32	chr4:89742400-89745200	Active TSS	A549	lung
33	chr4:89742600-89745400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:89742600-89745400	Active TSS	Fetal Muscle Leg	muscle
35	chr4:89742800-89745000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:89742800-89745000	Active TSS	Colon Smooth Muscle	Colon
37	chr4:89742800-89745200	Active TSS	Thymus	Thymus
38	chr4:89743000-89745000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:89743200-89745200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr4:89743200-89745600	Flanking Active TSS	Dnd41	blood
41	chr4:89743400-89745000	Active TSS	Left Ventricle	heart
42	chr4:89743400-89745000	Active TSS	Stomach Mucosa	stomach
43	chr4:89743400-89745200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:89743400-89745200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr4:89743400-89745200	Active TSS	Brain Cingulate Gyrus	brain
46	chr4:89743400-89745200	Active TSS	NH-A	brain
47	chr4:89743400-89745200	Active TSS	NHDF-Ad	bronchial
48	chr4:89743600-89745200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr4:89743600-89745200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:89743600-89745200	Active TSS	Placenta Amnion	Placenta Amnion

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