Variant report

Variant	rs55708950
Chromosome Location	chr9:97851179-97851180
allele	A/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	POLR2A	chr9:97850981-97851691	HepG2	liver:	n/a	n/a
2	CTCF	chr9:97851140-97851290	HBMEC	blood vessel:	n/a	chr9:97851269-97851278
3	BCL3	chr9:97849652-97856909	A549	lung:	n/a	chr9:97849910-97849923 chr9:97856480-97856489 chr9:97852058-97852071
4	MAX	chr9:97851150-97853849	A549	lung:	n/a	chr9:97852919-97852929
5	POLR2A	chr9:97850795-97855127	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr9:97850781-97851484	A549	lung:	n/a	n/a
7	POLR2A	chr9:97851010-97853908	PANC-1	pancreas:	n/a	n/a
8	TCF12	chr9:97849698-97856389	A549	lung:	n/a	chr9:97854161-97854171 chr9:97855868-97855877 chr9:97853824-97853834
9	POLR2A	chr9:97850779-97855508	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr9:97850706-97851457	A549	lung:	n/a	n/a
11	POLR2A	chr9:97850695-97854293	A549	lung:	n/a	n/a
12	FOSL2	chr9:97850771-97851297	A549	lung:	n/a	chr9:97851092-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851088-97851099
13	POLR2A	chr9:97849710-97856872	A549	lung:	n/a	n/a
14	POLR2A	chr9:97850870-97851312	HepG2	liver:	n/a	n/a
15	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
16	POLR2A	chr9:97850957-97851357	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr9:97851040-97851190	AG09319	gingival:	n/a	chr9:97851135-97851153
18	POLR2A	chr9:97850782-97851959	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:97851005-97851517	A549	lung:	n/a	n/a
20	BCL3	chr9:97850692-97856305	A549	lung:	n/a	chr9:97852058-97852071
21	FOSL2	chr9:97851029-97851413	HepG2	liver:	n/a	chr9:97851092-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851088-97851099
22	EP300	chr9:97850759-97851454	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr9:97850684-97855827	ECC-1	luminal epithelium:	n/a	n/a
24	SIN3AK20	chr9:97851125-97851425	A549	lung:	n/a	n/a
25	POLR2A	chr9:97851055-97855587	ECC-1	luminal epithelium:	n/a	n/a
26	JUND	chr9:97850980-97854866	A549	lung:	n/a	chr9:97851092-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97851091-97851101 chr9:97853499-97853510 chr9:97851088-97851099

No.	Distal block	Cell Line	Cell type
1	chr9:97850795..97854333-chr9:97877834..97880159,4	MCF-7	breast:
2	chr9:97542830..97545595-chr9:97848570..97851188,3	MCF-7	breast:
3	chr9:97848613..97851879-chr9:97854740..97857228,3	K562	blood:
4	chr9:97846609..97848201-chr9:97850195..97853098,2	K562	blood:
5	chr9:97682387..97688736-chr9:97850073..97858737,16	MCF-7	breast:
6	chr9:97629614..97631229-chr9:97851133..97852675,2	MCF-7	breast:
7	chr9:97850891..97852903-chr9:97858456..97861126,2	K562	blood:
8	chr9:97813946..97816396-chr9:97851072..97855306,4	MCF-7	breast:
9	chr9:97676581..97686973-chr9:97850461..97860722,21	MCF-7	breast:
10	chr2:39220003..39220567-chr9:97850457..97851397,2	MCF-7	breast:
11	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

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

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs55838201	0.88[AFR][1000 genomes]
rs57232080	0.94[AFR][1000 genomes]
rs58038897	0.94[AFR][1000 genomes]
rs59149855	0.88[AFR][1000 genomes]
rs59274098	0.82[AFR][1000 genomes]
rs60070508	0.94[AFR][1000 genomes]
rs7032542	0.94[AFR][1000 genomes]
rs7032704	0.94[AFR][1000 genomes]
rs73654506	0.94[AFR][1000 genomes]
rs73654507	0.94[AFR][1000 genomes]
rs73654508	0.94[AFR][1000 genomes]
rs73654509	0.94[AFR][1000 genomes]
rs73654510	0.94[AFR][1000 genomes]
rs73654511	0.94[AFR][1000 genomes]
rs73654512	0.88[AFR][1000 genomes]
rs73654513	0.94[AFR][1000 genomes]
rs73654514	0.94[AFR][1000 genomes]
rs73654515	0.88[AFR][1000 genomes]
rs73654516	0.94[AFR][1000 genomes]
rs73654517	0.81[AFR][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	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
12	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:97842200-97852000	Strong transcription	NHEK	skin
15	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
16	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:97843200-97851600	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr9:97843200-97851800	Genic enhancers	Brain Hippocampus Middle	brain
19	chr9:97843200-97852400	Genic enhancers	Rectal Smooth Muscle	rectum
20	chr9:97843600-97853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:97844000-97854800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr9:97844400-97852200	Strong transcription	Fetal Stomach	stomach
24	chr9:97844400-97854200	Weak transcription	Brain Germinal Matrix	brain
25	chr9:97845000-97852600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:97845800-97854400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:97845800-97854400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr9:97846000-97853000	Weak transcription	Fetal Kidney	kidney
29	chr9:97846000-97853200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr9:97846000-97853800	Weak transcription	GM12878-XiMat	blood
31	chr9:97846000-97861600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:97846200-97851200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:97846200-97853400	Weak transcription	Small Intestine	intestine
34	chr9:97846200-97853600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
36	chr9:97847000-97852600	Genic enhancers	Colon Smooth Muscle	Colon
37	chr9:97847000-97853600	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr9:97847200-97851800	Genic enhancers	Esophagus	oesophagus
39	chr9:97847200-97852800	Genic enhancers	HSMM	muscle
40	chr9:97847200-97853200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:97847200-97854000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr9:97847400-97853600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97847600-97852400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:97847600-97852400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:97847600-97853800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:97847600-97878400	Weak transcription	Dnd41	blood
47	chr9:97847800-97851400	Enhancers	Brain Substantia Nigra	brain
48	chr9:97848400-97851200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr9:97848400-97853400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:97848800-97852800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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