Variant report

Variant	rs73828080
Chromosome Location	chr4:79567025-79567026
allele	G/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	CEBPB	chr4:79566928-79567954	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr4:79566984-79567878	A549	lung:	n/a	n/a
3	POLR2A	chr4:79566891-79567931	HUVEC	blood vessel:	n/a	n/a
4	MAFK	chr4:79566918-79567964	Hela-S3	cervix:	n/a	n/a
5	GATA3	chr4:79566962-79568005	SK-N-SH	brain:	n/a	chr4:79567617-79567627
6	POLR2A	chr4:79566911-79567351	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr4:79566847-79567864	Hela-S3	cervix:	n/a	n/a
8	EP300	chr4:79566964-79568012	ECC-1	luminal epithelium:	n/a	chr4:79567616-79567625 chr4:79567615-79567629
9	RFX5	chr4:79565665-79568061	IMR90	lung:	n/a	chr4:79566034-79566049 chr4:79566035-79566049 chr4:79566605-79566614 chr4:79566603-79566617 chr4:79566038-79566047 chr4:79566036-79566044
10	ZNF143	chr4:79566991-79567156	GM12878	blood:	n/a	n/a
11	CTCF	chr4:79566960-79567110	SAEC	small airway:	n/a	n/a
12	POLR2A	chr4:79566875-79567596	HUVEC	blood vessel:	n/a	n/a
13	GATA3	chr4:79566911-79568037	SK-N-SH	brain:	n/a	chr4:79567617-79567627
14	GTF2F1	chr4:79567000-79567894	Hela-S3	cervix:	n/a	n/a
15	NFIC	chr4:79566882-79568082	SK-N-SH	brain:	n/a	n/a
16	MYC	chr4:79566915-79567567	K562	blood:	n/a	n/a
17	CTCF	chr4:79566960-79567110	K562	blood:	n/a	n/a
18	NR3C1	chr4:79566980-79567366	A549	lung:	n/a	n/a
19	TCF12	chr4:79566908-79568011	A549	lung:	n/a	n/a
20	USF1	chr4:79567016-79567696	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr4:79566883-79567749	U87	brain:	n/a	n/a
22	CHD2	chr4:79567007-79567929	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr4:79566911-79567516	SK-N-MC	brain:	n/a	n/a
24	EP300	chr4:79566994-79567937	Hela-S3	cervix:	n/a	chr4:79567616-79567625 chr4:79567615-79567629
25	FOS	chr4:79566991-79567901	MCF10A-Er-Src	breast:	n/a	chr4:79567650-79567657
26	POLR2A	chr4:79566761-79567684	U87	brain:	n/a	n/a
27	JUND	chr4:79566921-79567724	K562	blood:	n/a	chr4:79567650-79567657
28	POLR2A	chr4:79566971-79567303	ECC-1	luminal epithelium:	n/a	n/a
29	MAX	chr4:79566983-79568020	A549	lung:	n/a	n/a
30	TCF12	chr4:79566875-79568119	SK-N-SH	brain:	n/a	n/a
31	ARID3A	chr4:79566867-79567567	K562	blood:	n/a	n/a
32	POLR2A	chr4:79566982-79567706	MCF10A-Er-Src	breast:	n/a	n/a
33	NFYA	chr4:79566951-79567602	Hela-S3	cervix:	n/a	n/a
34	ZNF143	chr4:79566973-79567407	K562	blood:	n/a	n/a
35	FOS	chr4:79566885-79567935	MCF10A-Er-Src	breast:	n/a	chr4:79567650-79567657
36	POLR2A	chr4:79566998-79567810	SK-N-SH	brain:	n/a	n/a
37	EP300	chr4:79566997-79567959	A549	lung:	n/a	chr4:79567616-79567625 chr4:79567615-79567629
38	TBL1XR1	chr4:79567022-79567629	K562	blood:	n/a	n/a
39	MYC	chr4:79567001-79567921	MCF10A-Er-Src	breast:	n/a	n/a
40	RAD21	chr4:79566965-79567353	SK-N-SH_RA	brain:	n/a	n/a
41	TAF1	chr4:79566963-79567729	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr4:79567011-79567913	Hela-S3	cervix:	n/a	n/a
43	SP1	chr4:79566979-79567925	A549	lung:	n/a	n/a
44	STAT3	chr4:79566931-79567910	MCF10A-Er-Src	breast:	n/a	n/a
45	NFIC	chr4:79566986-79568007	SK-N-SH	brain:	n/a	n/a
46	STAT3	chr4:79566956-79567918	MCF10A-Er-Src	breast:	n/a	n/a
47	MAFK	chr4:79566593-79567812	K562	blood:	n/a	n/a
48	MAX	chr4:79566995-79567837	SK-N-SH	brain:	n/a	n/a
49	FOS	chr4:79566642-79567849	HUVEC	blood vessel:	n/a	chr4:79567650-79567657
50	POLR2A	chr4:79566915-79567957	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:79565693..79569294-chr4:79696000..79698136,3	K562	blood:
2	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
3	chr4:79563690..79568625-chr4:79568843..79572048,4	K562	blood:
4	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
5	chr4:79563449..79567560-chr4:79569303..79574487,6	K562	blood:
6	chr4:79564080..79567985-chr4:79696414..79698633,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ANXA3-1	chr4:79567001-79567417	NONHSAT097069

Variant related genes	Relation type
LINC01094	TF binding region
ENSG00000260278	Chromatin interaction
ENSG00000238816	Chromatin interaction
ENSG00000138756	Chromatin interaction
ENSG00000251019	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10452151	1.00[AMR][1000 genomes]
rs55994157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56071306	1.00[AMR][1000 genomes]
rs56098630	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57648305	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57649400	1.00[AMR][1000 genomes]
rs59055207	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59700988	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60681937	1.00[AMR][1000 genomes]
rs60950346	1.00[AMR][1000 genomes]
rs60998921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61075598	1.00[AMR][1000 genomes]
rs61238857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828029	1.00[AMR][1000 genomes]
rs73828034	1.00[AMR][1000 genomes]
rs73828038	1.00[AMR][1000 genomes]
rs73828045	1.00[AMR][1000 genomes]
rs73828046	1.00[AMR][1000 genomes]
rs73828057	1.00[AMR][1000 genomes]
rs73828059	1.00[AMR][1000 genomes]
rs73828064	1.00[AMR][1000 genomes]
rs73828065	1.00[AMR][1000 genomes]
rs73828066	1.00[AMR][1000 genomes]
rs73828067	1.00[AMR][1000 genomes]
rs73828069	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828070	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828073	1.00[AMR][1000 genomes]
rs73828074	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828079	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828092	1.00[AMR][1000 genomes]
rs73828098	1.00[AMR][1000 genomes]
rs73828100	1.00[AMR][1000 genomes]
rs73828102	1.00[AMR][1000 genomes]
rs73830206	1.00[AMR][1000 genomes]
rs73830208	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
3	chr4:79561600-79568000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:79562000-79568000	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:79562800-79567600	Enhancers	Primary hematopoietic stem cells	blood
6	chr4:79563200-79568800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr4:79563400-79567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:79564000-79568000	Enhancers	Fetal Intestine Large	intestine
9	chr4:79564400-79571400	Weak transcription	Fetal Heart	heart
10	chr4:79564400-79577200	Weak transcription	Fetal Thymus	thymus
11	chr4:79564400-79589600	Weak transcription	Lung	lung
12	chr4:79564800-79567200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:79564800-79567600	Enhancers	GM12878-XiMat	blood
14	chr4:79565600-79567200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:79565800-79569000	Weak transcription	Primary T cells from cord blood	blood
16	chr4:79566000-79567800	Enhancers	Fetal Intestine Small	intestine
17	chr4:79566000-79568000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:79566000-79573200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr4:79566200-79569400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:79566400-79567200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:79566400-79567600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:79566400-79567600	Enhancers	Placenta	Placenta
23	chr4:79566400-79567800	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr4:79566400-79568000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:79566400-79568000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:79566400-79568000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr4:79566400-79568000	Flanking Active TSS	HUVEC	blood vessel
28	chr4:79566400-79568000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr4:79566400-79568000	Flanking Active TSS	NHEK	skin
30	chr4:79566400-79569200	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:79566600-79567200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:79566600-79567600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:79566600-79567600	Flanking Active TSS	NHDF-Ad	bronchial
34	chr4:79566600-79567800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:79566600-79567800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:79566600-79567800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:79566600-79567800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr4:79566600-79567800	Enhancers	Psoas Muscle	Psoas
39	chr4:79566600-79567800	Flanking Active TSS	HMEC	breast
40	chr4:79566600-79567800	Flanking Active TSS	NH-A	brain
41	chr4:79566600-79567800	Flanking Active TSS	Osteobl	bone
42	chr4:79566600-79568000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:79566600-79568000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:79566600-79568000	Enhancers	Fetal Muscle Leg	muscle
45	chr4:79566600-79568000	Enhancers	Stomach Mucosa	stomach
46	chr4:79566600-79568000	Flanking Active TSS	A549	lung
47	chr4:79566600-79568000	Flanking Active TSS	Hela-S3	cervix
48	chr4:79566600-79568200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr4:79566600-79568200	Enhancers	Fetal Stomach	stomach
50	chr4:79566800-79567200	Enhancers	Brain Hippocampus Middle	brain

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