Variant report

Variant	rs58384340
Chromosome Location	chr1:225845512-225845513
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	CEBPB	chr1:225845235-225845831	A549	lung:	n/a	n/a
2	KAP1	chr1:225845057-225845767	HEK293	kidney:	n/a	n/a
3	YY1	chr1:225845239-225846118	SK-N-SH	brain:	n/a	chr1:225845481-225845498
4	GATA3	chr1:225845302-225845655	SH-SY5Y	brain:	n/a	chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
5	EP300	chr1:225844906-225845937	ECC-1	luminal epithelium:	n/a	chr1:225845358-225845367 chr1:225845357-225845371
6	TAF1	chr1:225845303-225845639	SK-N-SH	brain:	n/a	n/a
7	SRF	chr1:225845239-225845852	HCT-116	colon:	n/a	chr1:225845486-225845500 chr1:225845486-225845497 chr1:225845483-225845500 chr1:225845827-225845838 chr1:225845482-225845500 chr1:225845487-225845498 chr1:225845483-225845501 chr1:225845482-225845500 chr1:225845485-225845498
8	GATA3	chr1:225844984-225845865	A549	lung:	n/a	chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
9	GATA3	chr1:225845016-225845851	MCF-7	breast:	n/a	chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
10	FOXA1	chr1:225845145-225845585	A549	lung:	n/a	n/a
11	GATA3	chr1:225845127-225845722	MCF-7	breast:	n/a	chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
12	EP300	chr1:225845158-225845705	A549	lung:	n/a	chr1:225845358-225845367 chr1:225845357-225845371
13	MYC	chr1:225845333-225845672	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:225845162-225845830	U87	brain:	n/a	n/a
15	GATA3	chr1:225845056-225846303	SK-N-SH	brain:	n/a	chr1:225846155-225846176 chr1:225846157-225846173 chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
16	STAT3	chr1:225845272-225845663	MCF10A-Er-Src	breast:	n/a	chr1:225845624-225845636
17	GATA3	chr1:225844990-225846449	SK-N-SH	brain:	n/a	chr1:225846155-225846176 chr1:225846157-225846173 chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
18	MYC	chr1:225845249-225845657	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:225845263-225845613	IMR90	lung:	n/a	n/a
20	SMC3	chr1:225845260-225845693	Hela-S3	cervix:	n/a	n/a
21	SRF	chr1:225845122-225845765	ECC-1	luminal epithelium:	n/a	chr1:225845486-225845500 chr1:225845486-225845497 chr1:225845483-225845500 chr1:225845482-225845500 chr1:225845487-225845498 chr1:225845483-225845501 chr1:225845482-225845500 chr1:225845485-225845498
22	STAT3	chr1:225845352-225845748	MCF10A-Er-Src	breast:	n/a	chr1:225845624-225845636
23	CEBPB	chr1:225845339-225845675	A549	lung:	n/a	n/a
24	STAT3	chr1:225845293-225845668	Hela-S3	cervix:	n/a	chr1:225845624-225845636
25	POLR2A	chr1:225845057-225845800	HUVEC	blood vessel:	n/a	n/a
26	MAX	chr1:225845232-225845784	SK-N-SH	brain:	n/a	n/a
27	SRF	chr1:225845378-225845533	K562	blood:	n/a	chr1:225845486-225845500 chr1:225845486-225845497 chr1:225845483-225845500 chr1:225845482-225845500 chr1:225845487-225845498 chr1:225845483-225845501 chr1:225845482-225845500 chr1:225845485-225845498
28	ARID3A	chr1:225845405-225845582	HepG2	liver:	n/a	n/a
29	ELK1	chr1:225845262-225845712	Hela-S3	cervix:	n/a	n/a
30	FOXA1	chr1:225845175-225845664	T-47D	breast:	n/a	n/a
31	RAD21	chr1:225845296-225845651	IMR90	lung:	n/a	n/a
32	FOS	chr1:225845331-225845716	MCF10A-Er-Src	breast:	n/a	chr1:225845360-225845369
33	NFIC	chr1:225845112-225846284	SK-N-SH	brain:	n/a	n/a
34	FOS	chr1:225845254-225845972	MCF10A-Er-Src	breast:	n/a	chr1:225845360-225845369
35	RCOR1	chr1:225845420-225845630	K562	blood:	n/a	n/a
36	POLR2A	chr1:225845289-225845538	ProgFib	skin:	n/a	n/a
37	TEAD4	chr1:225844995-225845676	ECC-1	luminal epithelium:	n/a	n/a
38	TCF12	chr1:225845098-225846193	SK-N-SH	brain:	n/a	n/a
39	RCOR1	chr1:225845288-225845719	Hela-S3	cervix:	n/a	n/a
40	USF2	chr1:225845325-225845603	Hela-S3	cervix:	n/a	n/a
41	TBP	chr1:225845287-225845841	Hela-S3	cervix:	n/a	n/a
42	EP300	chr1:225845273-225845745	Hela-S3	cervix:	n/a	chr1:225845358-225845367 chr1:225845357-225845371
43	FOXA1	chr1:225845137-225845618	T-47D	breast:	n/a	n/a
44	GATA2	chr1:225845286-225845666	SH-SY5Y	brain:	n/a	chr1:225845458-225845465 chr1:225845570-225845579 chr1:225845359-225845369
45	JUND	chr1:225845154-225846173	SK-N-SH	brain:	n/a	chr1:225845360-225845369
46	FOS	chr1:225845327-225845694	Hela-S3	cervix:	n/a	chr1:225845360-225845369
47	BRCA1	chr1:225845174-225845743	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr1:225845162-225845945	U87	brain:	n/a	n/a
49	JUND	chr1:225845424-225845617	HepG2	liver:	n/a	n/a
50	JUND	chr1:225845156-225846195	SK-N-SH	brain:	n/a	chr1:225845360-225845369

No.	Distal block	Cell Line	Cell type
1	chr1:225843047..225846834-chr1:225854050..225856765,3	MCF-7	breast:
2	chr1:225845487..225847211-chr1:225869502..225871326,2	MCF-7	breast:
3	chr1:225844790..225847671-chr1:226111498..226113451,2	MCF-7	breast:

Variant related genes	Relation type
ENAH	TF binding region
ENSG00000143811	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11808089	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57616580	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58221350	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59481688	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60271197	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60588592	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426081	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666276	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687947	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696683	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698989	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702446	1.00[ASN][1000 genomes]
rs73124025	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125705	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125706	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515673	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531033	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555097	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225842000-225846000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:225842000-225865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:225842200-225845800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:225842200-225846000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:225842200-225846000	Enhancers	HMEC	breast
6	chr1:225842200-225846600	Enhancers	Fetal Muscle Leg	muscle
7	chr1:225842200-225847200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:225842400-225845600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:225842800-225846000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:225842800-225846200	Enhancers	HSMM	muscle
11	chr1:225843000-225852400	Weak transcription	Psoas Muscle	Psoas
12	chr1:225843600-225848000	Weak transcription	Brain Substantia Nigra	brain
13	chr1:225843800-225845600	Enhancers	NH-A	brain
14	chr1:225843800-225846200	Enhancers	Hela-S3	cervix
15	chr1:225843800-225846200	Enhancers	HUVEC	blood vessel
16	chr1:225843800-225848000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:225844000-225845600	Enhancers	Fetal Muscle Trunk	muscle
18	chr1:225844000-225854000	Weak transcription	Fetal Lung	lung
19	chr1:225844200-225846600	Enhancers	NHLF	lung
20	chr1:225844600-225846000	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:225844600-225846200	Enhancers	NHEK	skin
22	chr1:225844800-225846200	Enhancers	Rectal Smooth Muscle	rectum
23	chr1:225845000-225845600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:225845000-225845600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:225845000-225845600	Enhancers	Fetal Stomach	stomach
26	chr1:225845000-225845600	Enhancers	Lung	lung
27	chr1:225845000-225845600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:225845000-225846000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:225845000-225846200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:225845200-225845600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:225845200-225845600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:225845200-225845600	Enhancers	Adipose Nuclei	Adipose
33	chr1:225845200-225845600	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr1:225845200-225845600	Enhancers	Placenta	Placenta
35	chr1:225845200-225845600	Enhancers	Ovary	ovary
36	chr1:225845200-225845600	Enhancers	Right Atrium	heart
37	chr1:225845200-225845600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:225845200-225845800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:225845200-225845800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:225845200-225845800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:225845200-225845800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:225845200-225845800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr1:225845200-225845800	Enhancers	Fetal Heart	heart
44	chr1:225845200-225845800	Enhancers	HepG2	liver
45	chr1:225845200-225845800	Enhancers	HSMMtube	muscle
46	chr1:225845200-225846200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:225845200-225846200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:225845200-225846200	Flanking Active TSS	Osteobl	bone
49	chr1:225845400-225845600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:225845400-225845800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links