Variant report

Variant	rs58202935
Chromosome Location	chr5:58335574-58335575
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	FOXA1	chr5:58335202-58335728	HepG2	liver:	n/a	n/a
2	TEAD4	chr5:58335378-58336513	A549	lung:	n/a	n/a
3	PAX5	chr5:58335544-58335855	GM12892	blood:	n/a	n/a
4	MYC	chr5:58333738-58337715	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
5	NR3C1	chr5:58335219-58335721	A549	lung:	n/a	n/a
6	POLR2A	chr5:58334257-58336743	PFSK-1	brain:	n/a	n/a
7	CTBP2	chr5:58334577-58336052	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr5:58335050-58336938	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
9	POLR2A	chr5:58334554-58335885	H1-neurons	neurons:	n/a	n/a
10	SIN3AK20	chr5:58334927-58335732	PFSK-1	brain:	n/a	n/a
11	MYC	chr5:58335113-58335604	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr5:58335148-58335920	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP1	chr5:58335483-58335860	GM12878	blood:	n/a	n/a
14	MAX	chr5:58335169-58335722	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:58335292-58335578	Hela-S3	cervix:	n/a	n/a
16	FOSL2	chr5:58334989-58335646	SK-N-SH	brain:	n/a	n/a
17	MAX	chr5:58334405-58337505	NB4	blood:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
18	POLR2A	chr5:58334850-58335675	Gliobla	brain:	n/a	n/a
19	RAD21	chr5:58335286-58335721	H1-hESC	embryonic stem cell:	n/a	n/a
20	MYC	chr5:58333863-58336853	NB4	blood:	n/a	chr5:58336786-58336799 chr5:58336783-58336802 chr5:58336788-58336798 chr5:58336206-58336221 chr5:58336788-58336797 chr5:58336206-58336216 chr5:58336787-58336798 chr5:58336788-58336798 chr5:58336787-58336798 chr5:58336791-58336799
21	CREB1	chr5:58334850-58335936	A549	lung:	n/a	n/a
22	TCF7L2	chr5:58335390-58335733	MCF-7	breast:	n/a	chr5:58335597-58335611
23	MAX	chr5:58334729-58337074	HepG2	liver:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
24	GATA3	chr5:58334373-58336526	A549	lung:	n/a	n/a
25	MAZ	chr5:58335424-58335769	HepG2	liver:	n/a	n/a
26	EP300	chr5:58335303-58335682	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:58335076-58335676	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr5:58334348-58335954	A549	lung:	n/a	n/a
29	MAZ	chr5:58335102-58335758	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:58334860-58336670	PFSK-1	brain:	n/a	n/a
31	BHLHE40	chr5:58335294-58335644	GM12878	blood:	n/a	n/a
32	TCF7L2	chr5:58335303-58335860	HEK293	kidney:	n/a	chr5:58335597-58335611
33	BHLHE40	chr5:58335361-58335605	A549	lung:	n/a	n/a
34	MAX	chr5:58334700-58335857	SK-N-SH	brain:	n/a	n/a
35	ZNF263	chr5:58334295-58335857	HEK293-T-REx	kidney:	n/a	n/a
36	POLR2A	chr5:58333046-58336833	A549	lung:	n/a	n/a
37	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
38	MXI1	chr5:58334320-58335914	IMR90	lung:	n/a	n/a
39	HDAC2	chr5:58335395-58335706	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr5:58334951-58335660	ECC-1	luminal epithelium:	n/a	n/a
41	CEBPB	chr5:58335158-58335718	A549	lung:	n/a	n/a
42	BCL3	chr5:58335000-58338690	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
43	NR3C1	chr5:58335232-58335800	A549	lung:	n/a	n/a
44	RCOR1	chr5:58335409-58336522	HepG2	liver:	n/a	n/a
45	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
46	FOXA2	chr5:58335274-58336024	A549	lung:	n/a	n/a
47	MXI1	chr5:58334271-58336440	SK-N-SH	brain:	n/a	n/a
48	HEY1	chr5:58334937-58336010	HepG2	liver:	n/a	chr5:58335372-58335387
49	MXI1	chr5:58334805-58336915	HepG2	liver:	n/a	chr5:58336789-58336798
50	TAF1	chr5:58334862-58335755	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB3C-1	chr5:58335035-58336614	NONHSAT101625

Variant related genes	Relation type
ENSG00000247345	TF binding region
PDE4D	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11957770	1.00[EUR][1000 genomes]
rs13360359	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16889175	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2277013	1.00[AMR][1000 genomes]
rs3805555	1.00[AMR][1000 genomes]
rs56658018	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57338410	1.00[AMR][1000 genomes]
rs57454281	1.00[AMR][1000 genomes]
rs57718768	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57835046	0.83[ASN][1000 genomes]
rs58688754	1.00[AMR][1000 genomes]
rs58830206	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59840765	1.00[AMR][1000 genomes]
rs60286676	1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs60527700	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60741550	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60790143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60836618	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60900708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61288498	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6869400	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6883494	0.83[ASN][1000 genomes]
rs73093337	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73093348	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73093351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
2	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:58330600-58336200	Active TSS	Right Atrium	heart
4	chr5:58330800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr5:58331000-58336200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:58331000-58336400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:58331000-58336600	Active TSS	Psoas Muscle	Psoas
8	chr5:58332000-58335800	Active TSS	HSMM	muscle
9	chr5:58333000-58335800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:58333000-58336200	Active TSS	Left Ventricle	heart
11	chr5:58333200-58336000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr5:58333400-58336000	Active TSS	Lung	lung
13	chr5:58333400-58336200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:58333600-58335800	Active TSS	Primary T cells from cord blood	blood
15	chr5:58333600-58335800	Active TSS	Primary T killer memory cells from peripheral blood	blood
16	chr5:58333600-58336000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr5:58333600-58336000	Active TSS	Small Intestine	intestine
18	chr5:58333600-58336400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr5:58333800-58335600	Active TSS	Muscle Satellite Cultured Cells	--
20	chr5:58333800-58335800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr5:58333800-58336000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:58334000-58335600	Bivalent/Poised TSS	HepG2	liver
23	chr5:58334000-58335800	Active TSS	NHLF	lung
24	chr5:58334000-58336000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:58334000-58336000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:58334000-58336000	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr5:58334000-58336000	Active TSS	Gastric	stomach
28	chr5:58334200-58335800	Active TSS	HSMMtube	muscle
29	chr5:58334200-58335800	Active TSS	NHDF-Ad	bronchial
30	chr5:58334200-58336000	Active TSS	Brain Substantia Nigra	brain
31	chr5:58334200-58336200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr5:58334200-58336200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:58334200-58336200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr5:58334400-58335800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr5:58334400-58335800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:58334400-58336000	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr5:58334400-58336000	Active TSS	Fetal Kidney	kidney
38	chr5:58334400-58336000	Active TSS	Thymus	Thymus
39	chr5:58334400-58336200	Active TSS	Aorta	Aorta
40	chr5:58334600-58335600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:58334600-58335600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
42	chr5:58334600-58335800	Active TSS	Primary T cells fromperipheralblood	blood
43	chr5:58334600-58336000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:58334600-58336000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:58334600-58336200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
46	chr5:58334600-58336200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr5:58334800-58335600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:58334800-58335600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:58334800-58335800	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr5:58334800-58335800	Active TSS	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links