Variant report

Variant	rs58498208
Chromosome Location	chr3:46598216-46598217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr3:46598095-46598655	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr3:46598191-46598642	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:46598155-46598642	HUVEC	blood vessel:	n/a	n/a
4	TCF12	chr3:46598093-46598669	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr3:46598208-46598626	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr3:46598200-46598592	MCF10A-Er-Src	breast:	n/a	n/a
7	FOXM1	chr3:46598091-46598646	ECC-1	luminal epithelium:	n/a	n/a
8	RCOR1	chr3:46598171-46598437	Hela-S3	cervix:	n/a	n/a
9	NFIC	chr3:46598196-46598634	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr3:46597988-46598602	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr3:46598198-46598605	U87	brain:	n/a	n/a
12	E2F4	chr3:46598187-46598496	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr3:46598037-46598781	ECC-1	luminal epithelium:	n/a	n/a
14	TCF12	chr3:46598135-46598768	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr3:46598197-46598655	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr3:46598164-46598710	U87	brain:	n/a	n/a
17	TCF12	chr3:46598176-46598612	ECC-1	luminal epithelium:	n/a	n/a
18	RPC155	chr3:46597958-46598482	Hela-S3	cervix:	n/a	n/a
19	JUND	chr3:46598112-46598654	SK-N-SH	brain:	n/a	n/a
20	PBX3	chr3:46598198-46598633	SK-N-SH	brain:	n/a	n/a
21	FOS	chr3:46598175-46598630	MCF10A-Er-Src	breast:	n/a	n/a
22	FOSL2	chr3:46598198-46598601	SK-N-SH	brain:	n/a	n/a
23	RCOR1	chr3:46597440-46598831	IMR90	lung:	n/a	n/a
24	FOS	chr3:46598173-46598599	MCF10A-Er-Src	breast:	n/a	n/a
25	GATA3	chr3:46598116-46598648	SK-N-SH	brain:	n/a	n/a
26	CEBPB	chr3:46598193-46598723	Hela-S3	cervix:	n/a	n/a
27	JUND	chr3:46598088-46598598	SK-N-SH	brain:	n/a	n/a
28	GATA3	chr3:46598115-46598647	SK-N-SH	brain:	n/a	n/a
29	CEBPB	chr3:46598116-46598700	IMR90	lung:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000268324	TF binding region

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4117520	0.81[ASN][1000 genomes]
rs62247858	0.83[ASN][1000 genomes]
rs72622930	0.80[AMR][1000 genomes];0.83[ASN][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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
2	chr3:46578400-46599200	Weak transcription	HSMMtube	muscle
3	chr3:46581200-46599200	Weak transcription	Fetal Heart	heart
4	chr3:46581600-46599400	Weak transcription	Spleen	Spleen
5	chr3:46587200-46598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:46587800-46599600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:46588400-46599600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:46591000-46599400	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:46591000-46599600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:46591200-46599000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:46591400-46598400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:46591400-46598800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:46591400-46599200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:46591400-46599200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46591400-46599200	Weak transcription	Gastric	stomach
16	chr3:46591400-46599200	Weak transcription	Right Ventricle	heart
17	chr3:46591400-46599400	Weak transcription	Lung	lung
18	chr3:46591400-46600200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:46591600-46599800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:46591600-46600000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:46591800-46606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:46592600-46599200	Weak transcription	Thymus	Thymus
23	chr3:46592800-46599200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:46592800-46599200	Weak transcription	Primary T cells from cord blood	blood
25	chr3:46593000-46598800	Weak transcription	NHLF	lung
26	chr3:46593000-46599200	Weak transcription	K562	blood
27	chr3:46593000-46600200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:46593200-46600000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:46593200-46600000	Weak transcription	Ovary	ovary
30	chr3:46595200-46598800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:46595200-46599200	Weak transcription	Psoas Muscle	Psoas
32	chr3:46595200-46599400	Weak transcription	Adipose Nuclei	Adipose
33	chr3:46595200-46599400	Weak transcription	Liver	Liver
34	chr3:46595400-46598400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:46595400-46598600	Weak transcription	Osteobl	bone
36	chr3:46595400-46599200	Weak transcription	Left Ventricle	heart
37	chr3:46595600-46598400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:46597000-46600000	Enhancers	HUVEC	blood vessel
39	chr3:46597400-46599400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:46597600-46599200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr3:46597800-46600000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:46597800-46600000	Enhancers	Hela-S3	cervix
43	chr3:46598000-46598600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:46598000-46598600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:46598000-46598600	Weak transcription	NH-A	brain
46	chr3:46598000-46599000	Weak transcription	Dnd41	blood
47	chr3:46598000-46599600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:46598000-46599800	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links