Variant report

Variant	rs28661406
Chromosome Location	chr9:136996291-136996292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

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	RAD21	chr9:136996091-136996432	H1-hESC	embryonic stem cell:	n/a	n/a
7	CHD2	chr9:136996076-136996512	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:136996089-136996706	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr9:136996120-136996588	T-47D	breast:	n/a	chr9:136996539-136996548 chr9:136996538-136996552
10	GABPA	chr9:136996070-136996509	H1-hESC	embryonic stem cell:	n/a	chr9:136996392-136996406
11	POLR2A	chr9:136995981-136996744	ECC-1	luminal epithelium:	n/a	n/a
12	SP1	chr9:136995980-136996598	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
13	TEAD4	chr9:136996001-136996712	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr9:136996256-136996474	HepG2	liver:	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	POLR2A	chr9:136996087-136996434	H1-hESC	embryonic stem cell:	n/a	n/a
18	NR3C1	chr9:136996169-136996724	ECC-1	luminal epithelium:	n/a	chr9:136996428-136996441
19	MAX	chr9:136996094-136996622	H1-hESC	embryonic stem cell:	n/a	n/a
20	BRCA1	chr9:136996163-136996551	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr9:136996060-136996525	Hela-S3	cervix:	n/a	n/a
22	EBF1	chr9:136996244-136996606	GM12878	blood:	n/a	chr9:136996446-136996455
23	MAX	chr9:136996203-136996542	H1-hESC	embryonic stem cell:	n/a	n/a
24	ELF1	chr9:136996243-136996829	MCF-7	breast:	n/a	n/a
25	TEAD4	chr9:136996083-136996650	MCF-7	breast:	n/a	n/a
26	POLR2A	chr9:136996165-136996481	Hela-S3	cervix:	n/a	n/a
27	USF2	chr9:136996026-136996544	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr9:136996100-136996465	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr9:136996042-136996771	ECC-1	luminal epithelium:	n/a	n/a
30	RFX5	chr9:136995917-136996595	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr9:136996007-136996530	Hela-S3	cervix:	n/a	chr9:136996421-136996435 chr9:136996242-136996249
32	POLR2A	chr9:136996193-136996547	MCF-7	breast:	n/a	n/a
33	CEBPB	chr9:136996059-136996574	Hela-S3	cervix:	n/a	n/a
34	SP1	chr9:136996008-136996534	H1-hESC	embryonic stem cell:	n/a	chr9:136996268-136996279
35	POLR2A	chr9:136996140-136996545	Hela-S3	cervix:	n/a	n/a
36	TEAD4	chr9:136996019-136996617	HepG2	liver:	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	FOXA1	chr9:136996118-136996577	T-47D	breast:	n/a	n/a
44	TBP	chr9:136996097-136996516	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZNF143	chr9:136996236-136996554	Hela-S3	cervix:	n/a	n/a
46	TCF12	chr9:136995899-136996732	ECC-1	luminal epithelium:	n/a	n/a
47	NRF1	chr9:136996247-136996587	H1-hESC	embryonic stem cell:	n/a	chr9:136996392-136996406
48	POLR2A	chr9:136996022-136996566	ECC-1	luminal epithelium:	n/a	n/a
49	MAZ	chr9:136996064-136996641	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr9:136996065-136997092	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1128044	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11556390	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28410119	0.87[ASN][1000 genomes]
rs28412218	0.98[ASN][1000 genomes]
rs28415637	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28428662	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28438574	0.96[ASN][1000 genomes]
rs28473092	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28475221	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485659	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28490920	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28508246	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28522840	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28549758	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28567437	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28588875	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28604373	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28610236	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28611335	0.93[ASN][1000 genomes]
rs28635910	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28637447	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28647893	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28648812	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28681320	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695913	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28705801	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34417824	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35401074	0.84[ASN][1000 genomes]
rs35715743	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35949820	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36185416	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55874211	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:68 , 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	chr9:136994400-136996400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:136994400-136999400	Weak transcription	Primary B cells from cord blood	blood
5	chr9:136994600-136999200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:136994600-136999400	Weak transcription	Spleen	Spleen
7	chr9:136994600-136999800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr9:136995000-136996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:136995000-136996800	Enhancers	NHEK	skin
10	chr9:136995200-136996400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:136995400-136996600	Weak transcription	Right Atrium	heart
12	chr9:136995800-136996600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:136995800-136996600	Enhancers	Placenta	Placenta
14	chr9:136995800-136996800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:136995800-136996800	Flanking Active TSS	HepG2	liver
16	chr9:136996000-136996400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:136996000-136996400	Flanking Active TSS	Liver	Liver
18	chr9:136996000-136996400	Enhancers	Brain Cingulate Gyrus	brain
19	chr9:136996000-136996400	Enhancers	Colon Smooth Muscle	Colon
20	chr9:136996000-136996400	Enhancers	Fetal Stomach	stomach
21	chr9:136996000-136996400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr9:136996000-136996400	Flanking Active TSS	A549	lung
23	chr9:136996000-136996400	Bivalent Enhancer	Osteobl	bone
24	chr9:136996000-136996600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:136996000-136996600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:136996000-136996600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:136996000-136996600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:136996000-136996600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr9:136996000-136996600	Enhancers	Colonic Mucosa	Colon
30	chr9:136996000-136996600	Enhancers	Fetal Intestine Small	intestine
31	chr9:136996000-136996600	Enhancers	Stomach Mucosa	stomach
32	chr9:136996000-136996800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:136996000-136996800	Enhancers	Fetal Heart	heart
34	chr9:136996000-136996800	Enhancers	Rectal Smooth Muscle	rectum
35	chr9:136996000-136996800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr9:136996000-136996800	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr9:136996000-136996800	Flanking Active TSS	Hela-S3	cervix
38	chr9:136996000-136996800	Enhancers	HMEC	breast
39	chr9:136996000-136996800	Flanking Active TSS	HSMM	muscle
40	chr9:136996000-136996800	Flanking Active TSS	HSMMtube	muscle
41	chr9:136996000-136997000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr9:136996000-136997000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:136996000-136997000	Enhancers	Ovary	ovary
44	chr9:136996000-136997000	Enhancers	Right Ventricle	heart
45	chr9:136996000-136997000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr9:136996000-136997200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr9:136996000-136997200	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr9:136996000-136997400	Enhancers	H9 Cell Line	embryonic stem cell
49	chr9:136996000-136997400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr9:136996000-136997400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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