Variant report

Variant	rs28590546
Chromosome Location	chr9:136996445-136996446
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	TCF12	chr9:136995951-136996566	H1-hESC	embryonic stem cell:	n/a	n/a
2	MYC	chr9:136996270-136996534	MCF-7	breast:	n/a	n/a
3	GTF2F1	chr9:136995913-136996650	Hela-S3	cervix:	n/a	n/a
4	RAD21	chr9:136996023-136996509	H1-hESC	embryonic stem cell:	n/a	chr9:136996424-136996433
5	TEAD4	chr9:136996012-136996632	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr9:136996076-136996512	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr9:136996089-136996706	H1-hESC	embryonic stem cell:	n/a	n/a
8	EP300	chr9:136996120-136996588	T-47D	breast:	n/a	chr9:136996539-136996548 chr9:136996538-136996552
9	GABPA	chr9:136996070-136996509	H1-hESC	embryonic stem cell:	n/a	chr9:136996392-136996406
10	POLR2A	chr9:136995981-136996744	ECC-1	luminal epithelium:	n/a	n/a
11	SP1	chr9:136995980-136996598	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
12	TEAD4	chr9:136996001-136996712	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr9:136996256-136996474	HepG2	liver:	n/a	n/a
14	BRCA1	chr9:136996294-136996598	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr9:136995897-136996780	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr9:136996026-136996558	Hela-S3	cervix:	n/a	chr9:136996424-136996433
17	NR3C1	chr9:136996169-136996724	ECC-1	luminal epithelium:	n/a	chr9:136996428-136996441
18	MAX	chr9:136996094-136996622	H1-hESC	embryonic stem cell:	n/a	n/a
19	BRCA1	chr9:136996163-136996551	Hela-S3	cervix:	n/a	n/a
20	RCOR1	chr9:136996060-136996525	Hela-S3	cervix:	n/a	n/a
21	EBF1	chr9:136996244-136996606	GM12878	blood:	n/a	chr9:136996446-136996455
22	MAX	chr9:136996203-136996542	H1-hESC	embryonic stem cell:	n/a	n/a
23	ELF1	chr9:136996243-136996829	MCF-7	breast:	n/a	n/a
24	TEAD4	chr9:136996083-136996650	MCF-7	breast:	n/a	n/a
25	POLR2A	chr9:136996165-136996481	Hela-S3	cervix:	n/a	n/a
26	USF2	chr9:136996026-136996544	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr9:136996100-136996465	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr9:136996042-136996771	ECC-1	luminal epithelium:	n/a	n/a
29	RFX5	chr9:136995917-136996595	Hela-S3	cervix:	n/a	n/a
30	SMC3	chr9:136996007-136996530	Hela-S3	cervix:	n/a	chr9:136996421-136996435 chr9:136996242-136996249
31	POLR2A	chr9:136996193-136996547	MCF-7	breast:	n/a	n/a
32	CEBPB	chr9:136996059-136996574	Hela-S3	cervix:	n/a	n/a
33	SP1	chr9:136996008-136996534	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
34	POLR2A	chr9:136996140-136996545	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr9:136996019-136996617	HepG2	liver:	n/a	n/a
36	MYC	chr9:136996334-136996486	MCF-7	breast:	n/a	n/a
37	USF2	chr9:136996276-136996484	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAFK	chr9:136996024-136996514	Hela-S3	cervix:	n/a	n/a
39	TEAD4	chr9:136996059-136996595	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr9:136996067-136996558	H1-hESC	embryonic stem cell:	n/a	n/a
41	YY1	chr9:136996205-136996492	H1-hESC	embryonic stem cell:	n/a	n/a
42	TCF12	chr9:136996073-136996499	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr9:136996437-136996617	MCF10A-Er-Src	breast:	n/a	n/a
44	FOXA1	chr9:136996118-136996577	T-47D	breast:	n/a	n/a
45	TBP	chr9:136996097-136996516	H1-hESC	embryonic stem cell:	n/a	n/a
46	ZNF143	chr9:136996236-136996554	Hela-S3	cervix:	n/a	n/a
47	TCF12	chr9:136995899-136996732	ECC-1	luminal epithelium:	n/a	n/a
48	NRF1	chr9:136996247-136996587	H1-hESC	embryonic stem cell:	n/a	chr9:136996392-136996406
49	POLR2A	chr9:136996022-136996566	ECC-1	luminal epithelium:	n/a	n/a
50	MAZ	chr9:136996064-136996641	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:136737938..136739664-chr9:136994862..136997731,2	MCF-7	breast:
2	chr9:136996126..136998065-chr9:137029177..137031559,2	MCF-7	breast:
3	chr9:136992413..136997235-chr9:136998349..137003411,7	K562	blood:

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000273249	Chromatin interaction
ENSG00000221676	Chromatin interaction
ENSG00000196363	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs28523906	0.85[AMR][1000 genomes]
rs28572025	0.85[AMR][1000 genomes]
rs28626222	0.85[AMR][1000 genomes]
rs28637077	0.85[AMR][1000 genomes]
rs28637761	0.85[AMR][1000 genomes]
rs28657551	0.85[AMR][1000 genomes]
rs28726357	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58124205	0.85[AMR][1000 genomes]
rs58734062	0.85[AMR][1000 genomes]
rs73663200	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136991000-136999400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:136992800-136996600	Enhancers	Fetal Muscle Trunk	muscle
3	chr9:136994400-136999400	Weak transcription	Primary B cells from cord blood	blood
4	chr9:136994600-136999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:136994600-136999400	Weak transcription	Spleen	Spleen
6	chr9:136994600-136999800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr9:136995000-136996800	Enhancers	NHEK	skin
8	chr9:136995400-136996600	Weak transcription	Right Atrium	heart
9	chr9:136995800-136996600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:136995800-136996600	Enhancers	Placenta	Placenta
11	chr9:136995800-136996800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:136995800-136996800	Flanking Active TSS	HepG2	liver
13	chr9:136996000-136996600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:136996000-136996600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr9:136996000-136996600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:136996000-136996600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:136996000-136996600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:136996000-136996600	Enhancers	Colonic Mucosa	Colon
19	chr9:136996000-136996600	Enhancers	Fetal Intestine Small	intestine
20	chr9:136996000-136996600	Enhancers	Stomach Mucosa	stomach
21	chr9:136996000-136996800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:136996000-136996800	Enhancers	Fetal Heart	heart
23	chr9:136996000-136996800	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:136996000-136996800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr9:136996000-136996800	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr9:136996000-136996800	Flanking Active TSS	Hela-S3	cervix
27	chr9:136996000-136996800	Enhancers	HMEC	breast
28	chr9:136996000-136996800	Flanking Active TSS	HSMM	muscle
29	chr9:136996000-136996800	Flanking Active TSS	HSMMtube	muscle
30	chr9:136996000-136997000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr9:136996000-136997000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:136996000-136997000	Enhancers	Ovary	ovary
33	chr9:136996000-136997000	Enhancers	Right Ventricle	heart
34	chr9:136996000-136997000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr9:136996000-136997200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr9:136996000-136997200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:136996000-136997400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr9:136996000-136997400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr9:136996000-136997400	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr9:136996000-136997400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr9:136996000-136997600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:136996000-136997800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr9:136996000-136998000	Enhancers	Pancreas	Pancrea
44	chr9:136996200-136996600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:136996200-136996600	Bivalent Enhancer	Brain Germinal Matrix	brain
46	chr9:136996200-136996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:136996200-136996800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr9:136996200-136996800	Enhancers	Esophagus	oesophagus
49	chr9:136996200-136996800	Enhancers	Left Ventricle	heart
50	chr9:136996200-136997000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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