Variant report

Variant	rs28667175
Chromosome Location	chr9:94900961-94900962
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	CTCF	chr9:94900006-94901137	A549	lung:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
2	CEBPB	chr9:94900895-94901236	HepG2	liver:	n/a	n/a
3	POLR2A	chr9:94900456-94901941	HepG2	liver:	n/a	n/a
4	CTCF	chr9:94900900-94901050	HAc	cerebellar:	n/a	n/a
5	HNF4G	chr9:94900755-94901385	HepG2	liver:	n/a	chr9:94901028-94901041 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901027-94901042 chr9:94901028-94901040 chr9:94901027-94901041
6	RAD21	chr9:94900229-94900982	SK-N-SH	brain:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
7	EP300	chr9:94900747-94901184	HepG2	liver:	n/a	n/a
8	MAX	chr9:94900433-94901112	HepG2	liver:	n/a	chr9:94900481-94900490
9	CEBPB	chr9:94900960-94901140	HepG2	liver:	n/a	n/a
10	RXRA	chr9:94900682-94901237	HepG2	liver:	n/a	chr9:94901024-94901044 chr9:94901028-94901041 chr9:94901028-94901041 chr9:94901026-94901042 chr9:94901028-94901041
11	FOXA1	chr9:94900832-94901262	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:94900860-94901273	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:94900384-94902019	HepG2	liver:	n/a	n/a
14	SMC3	chr9:94900201-94900994	SK-N-SH	brain:	n/a	chr9:94900561-94900575 chr9:94900561-94900568 chr9:94900565-94900575
15	CTCF	chr9:94900170-94901232	SK-N-SH	brain:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
16	CTCF	chr9:94900960-94901110	AG04450	lung:	n/a	n/a
17	YY1	chr9:94900817-94901162	HepG2	liver:	n/a	chr9:94900978-94900987
18	MAZ	chr9:94900945-94901115	HepG2	liver:	n/a	n/a
19	MYBL2	chr9:94900771-94901322	HepG2	liver:	n/a	n/a
20	CTCF	chr9:94900900-94901050	HCPEpiC	choroid plexus:	n/a	n/a
21	RCOR1	chr9:94900561-94901104	HepG2	liver:	n/a	n/a
22	CTCF	chr9:94900920-94901070	HPF	lung:	n/a	n/a
23	TEAD4	chr9:94900779-94901843	HepG2	liver:	n/a	n/a
24	EP300	chr9:94900820-94901070	HepG2	liver:	n/a	n/a
25	USF1	chr9:94900724-94901063	HepG2	liver:	n/a	n/a
26	CTCF	chr9:94900880-94901030	HCFaa	heart:	n/a	n/a
27	HNF4A	chr9:94900814-94901209	HepG2	liver:	n/a	chr9:94901026-94901041 chr9:94901028-94901041 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901027-94901042 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901105-94901120
28	BHLHE40	chr9:94900446-94901149	HepG2	liver:	n/a	n/a
29	HNF4G	chr9:94900795-94901227	HepG2	liver:	n/a	chr9:94901028-94901041 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901027-94901042 chr9:94901028-94901040 chr9:94901027-94901041
30	FOXA1	chr9:94900806-94901265	HepG2	liver:	n/a	n/a
31	FOXA1	chr9:94900771-94901314	HepG2	liver:	n/a	n/a
32	RAD21	chr9:94900364-94900963	HCT-116	colon:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
33	HNF4A	chr9:94900852-94901244	HepG2	liver:	n/a	chr9:94901026-94901041 chr9:94901028-94901041 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901027-94901042 chr9:94901028-94901040 chr9:94901027-94901041 chr9:94901105-94901120
34	MYC	chr9:94900529-94901305	HepG2	liver:	n/a	n/a
35	CTCF	chr9:94900960-94901110	SAEC	small airway:	n/a	n/a
36	TBP	chr9:94900893-94901149	HepG2	liver:	n/a	n/a
37	YY1	chr9:94900399-94901179	HepG2	liver:	n/a	chr9:94900978-94900987 chr9:94900651-94900662
38	FOXA1	chr9:94900714-94901206	HepG2	liver:	n/a	n/a
39	RXRA	chr9:94900842-94901217	HepG2	liver:	n/a	chr9:94901024-94901044 chr9:94901028-94901041 chr9:94901028-94901041 chr9:94901026-94901042 chr9:94901028-94901041
40	MAX	chr9:94900386-94901070	HepG2	liver:	n/a	chr9:94900481-94900490
41	HDAC2	chr9:94900786-94901219	HepG2	liver:	n/a	n/a
42	MAZ	chr9:94900028-94901177	IMR90	lung:	n/a	chr9:94900481-94900490
43	CTCF	chr9:94900960-94901110	GM12864	blood:	n/a	n/a
44	RAD21	chr9:94900349-94901008	HCT-116	colon:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
45	CTCF	chr9:94900840-94900990	GM12874	blood:	n/a	n/a
46	SP1	chr9:94900859-94901614	HepG2	liver:	n/a	n/a
47	POLR2A	chr9:94900739-94901347	HepG2	liver:	n/a	n/a
48	FOXA2	chr9:94900820-94901211	HepG2	liver:	n/a	n/a
49	HEY1	chr9:94900426-94901804	HepG2	liver:	n/a	n/a
50	ARID3A	chr9:94900919-94901145	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:94900132..94901096-chr9:95004214..95005474,7	MCF-7	breast:
2	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
3	chr9:94899508..94902437-chr9:95003923..95007845,5	MCF-7	breast:
4	chr9:94897363..94901349-chr9:95056061..95059787,4	K562	blood:
5	chr9:94898446..94901351-chr9:94903571..94905297,4	K562	blood:
6	chr9:94899081..94901349-chr9:95056061..95058658,2	K562	blood:
7	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
8	chr9:94900452..94902204-chr9:94914248..94916401,2	MCF-7	breast:
9	chr9:94899946..94902668-chr9:94908231..94910049,3	K562	blood:

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

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10119866	0.86[ASN][1000 genomes]
rs10992243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339442	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339869	0.86[ASN][1000 genomes]
rs12349856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28789204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57310547	0.86[ASN][1000 genomes]
rs57904627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59671839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60568227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479406	1.00[EUR][1000 genomes]
rs6479407	1.00[EUR][1000 genomes]
rs73514437	1.00[EUR][1000 genomes]
rs7861776	1.00[EUR][1000 genomes]
rs7865975	1.00[EUR][1000 genomes]
rs7866872	1.00[EUR][1000 genomes]
rs7869291	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870092	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:42 , 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	chr9:94899800-94901000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr9:94900000-94901800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:94900000-94903000	Flanking Active TSS	HepG2	liver
21	chr9:94900200-94901000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr9:94900200-94901000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:94900200-94901400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:94900200-94901800	Enhancers	HSMM	muscle
25	chr9:94900200-94902600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:94900200-94902600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:94900200-94903200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:94900400-94901000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:94900400-94902200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:94900400-94902400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:94900400-94902800	Weak transcription	Hela-S3	cervix
32	chr9:94900400-94902800	Weak transcription	K562	blood
33	chr9:94900600-94901000	Enhancers	Placenta	Placenta
34	chr9:94900600-94901600	Enhancers	NH-A	brain
35	chr9:94900600-94902400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr9:94900600-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:94900800-94901000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr9:94900800-94901000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:94900800-94902600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:94900800-94902600	Weak transcription	Dnd41	blood
41	chr9:94900800-94903000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:94900800-94903000	Enhancers	HSMMtube	muscle

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