Variant report

Variant	rs59069079
Chromosome Location	chr9:97852874-97852875
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	EP300	chr9:97852611-97853195	A549	lung:	n/a	chr9:97852757-97852773 chr9:97852633-97852649 chr9:97852890-97852906
2	CEBPB	chr9:97852557-97853126	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr9:97852568-97853086	ECC-1	luminal epithelium:	n/a	chr9:97852775-97852786
4	BCL3	chr9:97849652-97856909	A549	lung:	n/a	chr9:97849910-97849923 chr9:97856480-97856489 chr9:97852058-97852071
5	POLR2A	chr9:97852683-97853037	K562	blood:	n/a	n/a
6	MAX	chr9:97851150-97853849	A549	lung:	n/a	chr9:97852919-97852929
7	POLR2A	chr9:97852136-97854073	Hela-S3	cervix:	n/a	n/a
8	SIN3AK20	chr9:97852592-97852958	PANC-1	pancreas:	n/a	n/a
9	REST	chr9:97851264-97854236	A549	lung:	n/a	chr9:97853873-97853883 chr9:97852053-97852063 chr9:97852888-97852902 chr9:97853660-97853670 chr9:97852681-97852689 chr9:97852763-97852776 chr9:97853191-97853209 chr9:97852890-97852900
10	ATF3	chr9:97852484-97853318	A549	lung:	n/a	n/a
11	POLR2A	chr9:97850795-97855127	SK-N-SH	brain:	n/a	n/a
12	FOSL2	chr9:97851369-97853944	A549	lung:	n/a	chr9:97853499-97853510
13	TEAD4	chr9:97852349-97853365	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr9:97852184-97855313	ECC-1	luminal epithelium:	n/a	chr9:97854991-97855008 chr9:97852252-97852268 chr9:97854992-97855008
15	POLR2A	chr9:97852177-97854442	HepG2	liver:	n/a	n/a
16	ESR1	chr9:97852588-97853517	ECC-1	luminal epithelium:	n/a	chr9:97853173-97853190
17	POLR2A	chr9:97851010-97853908	PANC-1	pancreas:	n/a	n/a
18	FOSL2	chr9:97851415-97854528	HepG2	liver:	n/a	chr9:97853499-97853510
19	TCF12	chr9:97849698-97856389	A549	lung:	n/a	chr9:97854161-97854171 chr9:97855868-97855877 chr9:97853824-97853834
20	POLR2A	chr9:97852680-97852982	HepG2	liver:	n/a	n/a
21	EP300	chr9:97851976-97853606	SK-N-SH	brain:	n/a	chr9:97852757-97852773 chr9:97852633-97852649 chr9:97852052-97852068 chr9:97852890-97852906
22	CREB1	chr9:97852003-97853102	A549	lung:	n/a	n/a
23	POLR2A	chr9:97850779-97855508	Hela-S3	cervix:	n/a	n/a
24	NR3C1	chr9:97852417-97853005	A549	lung:	n/a	chr9:97852420-97852433
25	PBX3	chr9:97852608-97854173	A549	lung:	n/a	n/a
26	PBX3	chr9:97851400-97852982	A549	lung:	n/a	n/a
27	EP300	chr9:97852368-97853113	A549	lung:	n/a	chr9:97852757-97852773 chr9:97852633-97852649 chr9:97852890-97852906
28	ZBTB7A	chr9:97852265-97855166	ECC-1	luminal epithelium:	n/a	chr9:97852821-97852829
29	HMGN3	chr9:97852643-97852901	K562	blood:	n/a	n/a
30	ELF1	chr9:97852131-97853165	A549	lung:	n/a	chr9:97852711-97852720 chr9:97852606-97852618 chr9:97852707-97852719 chr9:97852750-97852762
31	POLR2A	chr9:97850695-97854293	A549	lung:	n/a	n/a
32	TEAD4	chr9:97852352-97855446	ECC-1	luminal epithelium:	n/a	n/a
33	SRF	chr9:97852515-97853209	ECC-1	luminal epithelium:	n/a	chr9:97852897-97852907
34	POLR2A	chr9:97849710-97856872	A549	lung:	n/a	n/a
35	NR3C1	chr9:97852539-97853087	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr9:97851707-97853426	HepG2	liver:	n/a	n/a
37	NR2F2	chr9:97852585-97853217	MCF-7	breast:	n/a	n/a
38	FOXM1	chr9:97852365-97853440	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr9:97851506-97853059	A549	lung:	n/a	n/a
40	MAX	chr9:97852444-97855345	ECC-1	luminal epithelium:	n/a	chr9:97852919-97852929
41	ESR1	chr9:97852488-97853576	ECC-1	luminal epithelium:	n/a	chr9:97853173-97853190
42	JUND	chr9:97850694-97855193	A549	lung:	n/a	chr9:97851092-97851101 chr9:97854992-97855000 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97854990-97855002 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97853499-97853510 chr9:97851088-97851099
43	EP300	chr9:97852227-97853513	ECC-1	luminal epithelium:	n/a	chr9:97852757-97852773 chr9:97852633-97852649 chr9:97852890-97852906
44	POLR2A	chr9:97851501-97853120	A549	lung:	n/a	n/a
45	ZBTB7A	chr9:97852027-97853110	ECC-1	luminal epithelium:	n/a	chr9:97852821-97852829
46	POLR2A	chr9:97852117-97853556	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr9:97852364-97853030	U87	brain:	n/a	n/a
48	SP1	chr9:97851481-97853257	A549	lung:	n/a	chr9:97852652-97852665 chr9:97852920-97852934
49	ZBTB7A	chr9:97852745-97852977	K562	blood:	n/a	chr9:97852821-97852829
50	NR3C1	chr9:97852505-97853074	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97540701..97545624-chr9:97851316..97856247,6	MCF-7	breast:
2	chr9:97851266..97855469-chr9:97887605..97891480,5	MCF-7	breast:
3	chr9:97850795..97854333-chr9:97877834..97880159,4	MCF-7	breast:
4	chr9:97851403..97855354-chr9:97856847..97861126,5	K562	blood:
5	chr9:97796997..97799888-chr9:97851480..97854262,2	MCF-7	breast:
6	chr9:97846609..97848201-chr9:97850195..97853098,2	K562	blood:
7	chr9:97682387..97688736-chr9:97850073..97858737,16	MCF-7	breast:
8	chr9:97850891..97852903-chr9:97858456..97861126,2	K562	blood:
9	chr9:97813946..97816396-chr9:97851072..97855306,4	MCF-7	breast:
10	chr9:97765811..97769847-chr9:97852030..97854731,4	MCF-7	breast:
11	chr9:97582607..97584454-chr9:97851335..97853316,2	MCF-7	breast:
12	chr9:97439883..97441611-chr9:97852629..97855503,2	MCF-7	breast:
13	chr9:97676581..97686973-chr9:97850461..97860722,21	MCF-7	breast:
14	chr9:97581227..97584378-chr9:97852689..97856383,4	MCF-7	breast:
15	chr9:97547509..97550308-chr9:97851827..97853518,2	MCF-7	breast:
16	chr9:97781116..97783648-chr9:97852617..97854156,2	MCF-7	breast:
17	chr9:97808882..97811165-chr9:97851910..97854865,2	MCF-7	breast:
18	chr9:97543978..97547772-chr9:97852128..97855870,5	MCF-7	breast:
19	chr9:97834760..97837018-chr9:97852814..97855297,3	MCF-7	breast:
20	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
MIR3074	TF binding region
ENSG00000207864	Chromatin interaction
ENSG00000207563	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4647388	1.00[AMR][1000 genomes]
rs9785251	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:97843600-97853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:97844000-97854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:97844400-97854200	Weak transcription	Brain Germinal Matrix	brain
16	chr9:97845800-97854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:97845800-97854400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr9:97846000-97853000	Weak transcription	Fetal Kidney	kidney
19	chr9:97846000-97853200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:97846000-97853800	Weak transcription	GM12878-XiMat	blood
21	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:97846200-97853400	Weak transcription	Small Intestine	intestine
23	chr9:97846200-97853600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
25	chr9:97847000-97853600	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr9:97847200-97853200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:97847200-97854000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr9:97847400-97853600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:97847600-97853800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:97847600-97878400	Weak transcription	Dnd41	blood
31	chr9:97848400-97853400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:97848800-97856800	Weak transcription	HUVEC	blood vessel
33	chr9:97849000-97856400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:97849000-97858400	Enhancers	Brain Cingulate Gyrus	brain
35	chr9:97849200-97854400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr9:97849200-97854600	Weak transcription	Primary T cells from cord blood	blood
37	chr9:97849200-97859200	Weak transcription	Fetal Brain Female	brain
38	chr9:97849200-97863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:97849600-97853000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:97849600-97853800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:97849800-97864600	Enhancers	Psoas Muscle	Psoas
42	chr9:97850000-97853400	Genic enhancers	Right Ventricle	heart
43	chr9:97850000-97853400	Genic enhancers	NHLF	lung
44	chr9:97850000-97856200	Enhancers	NHDF-Ad	bronchial
45	chr9:97850000-97858200	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr9:97850000-97862000	Weak transcription	Hela-S3	cervix
47	chr9:97850200-97854600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:97850200-97855200	Enhancers	Spleen	Spleen
49	chr9:97850200-97855600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:97850800-97857400	Enhancers	Fetal Thymus	thymus

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