Variant report

Variant	rs55801573
Chromosome Location	chr9:94901388-94901389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:94900456-94901941	HepG2	liver:	n/a	n/a
2	CTCF	chr9:94901326-94901986	A549	lung:	n/a	chr9:94901658-94901667
3	CTCF	chr9:94901280-94901430	SK-N-SH_RA	brain:	n/a	chr9:94901288-94901297 chr9:94901288-94901301
4	MYBL2	chr9:94901342-94901826	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:94900384-94902019	HepG2	liver:	n/a	n/a
6	HEY1	chr9:94901373-94901789	HepG2	liver:	n/a	n/a
7	MAX	chr9:94901385-94901675	K562	blood:	n/a	n/a
8	TEAD4	chr9:94900779-94901843	HepG2	liver:	n/a	n/a
9	MXI1	chr9:94901371-94901755	HepG2	liver:	n/a	n/a
10	CTCF	chr9:94901300-94901450	HVMF	connective:	n/a	n/a
11	MXI1	chr9:94901302-94901862	IMR90	lung:	n/a	n/a
12	SP1	chr9:94900859-94901614	HepG2	liver:	n/a	n/a
13	HEY1	chr9:94900426-94901804	HepG2	liver:	n/a	n/a
14	CTCF	chr9:94901317-94902013	SK-N-SH	brain:	n/a	chr9:94901658-94901667
15	POLR2A	chr9:94901386-94901812	HepG2	liver:	n/a	n/a
16	CTCF	chr9:94901380-94901530	HVMF	connective:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr9:94496317..94496885-chr9:94901207..94901927,2	K562	blood:
3	chr9:94899508..94902437-chr9:95003923..95007845,5	MCF-7	breast:
4	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
5	chr9:94900452..94902204-chr9:94914248..94916401,2	MCF-7	breast:
6	chr9:94899946..94902668-chr9:94908231..94910049,3	K562	blood:

No data

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000198000	Chromatin interaction
ENSG00000225511	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10992240	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992241	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10992244	0.81[EUR][1000 genomes]
rs10992250	1.00[ASN][1000 genomes]
rs10992251	0.81[EUR][1000 genomes]
rs1970119	0.87[ASN][1000 genomes]
rs2398673	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35121804	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35814773	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3858094	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3927571	0.81[EUR][1000 genomes]
rs4391487	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55667598	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56319302	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62564361	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62564363	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62564364	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62568696	0.91[EUR][1000 genomes]
rs62568697	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72748370	1.00[ASN][1000 genomes]
rs7465866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS 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	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94896400-94902400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:94896600-94902400	Weak transcription	Spleen	Spleen
3	chr9:94896600-94902800	Weak transcription	Gastric	stomach
4	chr9:94896800-94902600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:94896800-94902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:94896800-94902800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:94896800-94902800	Weak transcription	Esophagus	oesophagus
8	chr9:94896800-94902800	Weak transcription	Right Atrium	heart
9	chr9:94896800-94902800	Weak transcription	A549	lung
10	chr9:94897200-94901400	Weak transcription	NHLF	lung
11	chr9:94897200-94902400	Weak transcription	Ovary	ovary
12	chr9:94897200-94902800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:94897200-94902800	Weak transcription	HUVEC	blood vessel
14	chr9:94897400-94902400	Weak transcription	Osteobl	bone
15	chr9:94897400-94902800	Weak transcription	NHDF-Ad	bronchial
16	chr9:94897600-94902400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:94897600-94902800	Weak transcription	HMEC	breast
18	chr9:94900000-94901800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:94900000-94903000	Flanking Active TSS	HepG2	liver
20	chr9:94900200-94901400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr9:94900200-94901800	Enhancers	HSMM	muscle
22	chr9:94900200-94902600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:94900200-94902600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:94900200-94903200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:94900400-94902200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:94900400-94902400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:94900400-94902800	Weak transcription	Hela-S3	cervix
28	chr9:94900400-94902800	Weak transcription	K562	blood
29	chr9:94900600-94901600	Enhancers	NH-A	brain
30	chr9:94900600-94902400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr9:94900600-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:94900800-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:94900800-94902600	Weak transcription	Dnd41	blood
34	chr9:94900800-94903000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr9:94900800-94903000	Enhancers	HSMMtube	muscle
36	chr9:94901000-94902200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:94901000-94902200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:94901000-94902200	Weak transcription	Placenta	Placenta
39	chr9:94901000-94902800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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