Variant report

Variant	rs2069419
Chromosome Location	chr9:22009337-22009338
allele	A/C/G/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	MXI1	chr9:22008381-22010136	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr9:22009200-22009350	GM12869	blood:	n/a	n/a
3	RCOR1	chr9:22008736-22009453	GM12878	blood:	n/a	n/a
4	CTCF	chr9:22009280-22009415	Lung_OC	lung:	n/a	n/a
5	POLR2A	chr9:22009310-22009700	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:22009035-22009737	SK-N-MC	brain:	n/a	n/a
7	USF1	chr9:22009264-22009567	HepG2	liver:	n/a	n/a
8	CREB1	chr9:22008536-22009696	HepG2	liver:	n/a	n/a
9	MAX	chr9:22008537-22009878	Hela-S3	cervix:	n/a	n/a
10	JUND	chr9:22009270-22009449	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:22009028-22009478	HUVEC	blood vessel:	n/a	n/a
12	ZNF143	chr9:22008573-22009620	GM12878	blood:	n/a	n/a
13	TEAD4	chr9:22008406-22009861	ECC-1	luminal epithelium:	n/a	n/a
14	RCOR1	chr9:22008578-22009761	Hela-S3	cervix:	n/a	n/a
15	TAF1	chr9:22009017-22009521	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr9:22008556-22009778	IMR90	lung:	n/a	chr9:22009587-22009600 chr9:22009173-22009183
17	SIN3AK20	chr9:22009067-22009502	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr9:22009082-22009411	PFSK-1	brain:	n/a	n/a
19	SMC3	chr9:22008102-22009872	SK-N-SH	brain:	n/a	chr9:22009174-22009184
20	POLR2A	chr9:22008868-22009727	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr9:22008853-22009777	HepG2	liver:	n/a	n/a
22	SP4	chr9:22008987-22009585	H1-hESC	embryonic stem cell:	n/a	chr9:22009373-22009389 chr9:22009371-22009387
23	MAX	chr9:22008586-22009686	SK-N-SH	brain:	n/a	n/a
24	REST	chr9:22009153-22009712	HepG2	liver:	n/a	chr9:22009381-22009399
25	HA-E2F1	chr9:22008553-22009724	MCF-7	breast:	n/a	chr9:22009431-22009443 chr9:22009463-22009472
26	RAD21	chr9:22008301-22009843	Hela-S3	cervix:	n/a	chr9:22009565-22009577
27	CTCF	chr9:22008394-22009907	HCT-116	colon:	n/a	chr9:22009587-22009600 chr9:22009173-22009183
28	TEAD4	chr9:22008495-22009713	H1-hESC	embryonic stem cell:	n/a	n/a
29	ZKSCAN1	chr9:22008340-22009701	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr9:22008859-22009753	HUVEC	blood vessel:	n/a	n/a
31	CTCF	chr9:22009240-22009390	GM06990	blood:	n/a	n/a
32	MAZ	chr9:22008557-22009467	GM12878	blood:	n/a	n/a
33	MYC	chr9:22008718-22009507	H1-hESC	embryonic stem cell:	n/a	n/a
34	RCOR1	chr9:22009175-22009619	HepG2	liver:	n/a	n/a
35	POLR2A	chr9:22009048-22009705	HCT-116	colon:	n/a	n/a
36	MAX	chr9:22008582-22009607	H1-hESC	embryonic stem cell:	n/a	n/a
37	MXI1	chr9:22009200-22009693	GM12878	blood:	n/a	n/a
38	USF2	chr9:22008665-22009639	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAZ	chr9:22008505-22009682	Hela-S3	cervix:	n/a	n/a
40	PML	chr9:22009108-22009456	MCF-7	breast:	n/a	n/a
41	CTBP2	chr9:22008576-22009656	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr9:22008564-22009718	ECC-1	luminal epithelium:	n/a	n/a
43	USF1	chr9:22009242-22009508	GM12878	blood:	n/a	n/a
44	SIN3AK20	chr9:22009041-22009490	SK-N-SH	brain:	n/a	n/a
45	MAX	chr9:22008727-22009619	GM12878	blood:	n/a	n/a
46	CREB1	chr9:22008561-22009708	H1-hESC	embryonic stem cell:	n/a	n/a
47	SMC3	chr9:22008471-22009881	Hela-S3	cervix:	n/a	chr9:22009174-22009184
48	POLR2A	chr9:22009078-22009750	HL-60	blood:	n/a	n/a
49	BRCA1	chr9:22008562-22009823	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr9:22008581-22009766	SK-N-SH_RA	brain:	n/a	chr9:22009565-22009577

No.	Distal block	Cell Line	Cell type
1	chr9:22005608..22009530-chr9:22211237..22215024,4	MCF-7	breast:
2	chr9:21992827..21995558-chr9:22007456..22010608,5	MCF-7	breast:
3	chr9:21800247..21802715-chr9:22007122..22010872,3	MCF-7	breast:
4	chr11:62622316..62623099-chr9:22008957..22009804,2	Hela-S3	cervix:
5	chr9:22007147..22011040-chr9:22011810..22014340,4	MCF-7	breast:
6	chr9:22007424..22010079-chr9:22214224..22216298,2	MCF-7	breast:

Variant related genes	Relation type
UBA52P6	TF binding region
CDKN2B	TF binding region
ENSG00000240498	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000215221	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000236921	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3731207	1.00[AMR][1000 genomes]
rs3731225	1.00[AMR][1000 genomes]
rs55796448	1.00[AMR][1000 genomes]
rs7027610	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73649993	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv1821117	chr9:21933029-22012229	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1018514	chr9:21944275-22075326	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv892746	chr9:21953137-22028801	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv892747	chr9:21984661-22068646	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv892748	chr9:22005647-22011642	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv613760	chr9:22006269-22009960	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv973479	chr9:22006327-22010710	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22005600-22009400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:22005800-22009800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr9:22006200-22009600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:22006400-22009400	Active TSS	Rectal Mucosa Donor 31	rectum
5	chr9:22006400-22009400	Active TSS	HMEC	breast
6	chr9:22006400-22010000	Active TSS	Muscle Satellite Cultured Cells	--
7	chr9:22006400-22010000	Active TSS	HSMMtube	muscle
8	chr9:22006600-22009400	Active TSS	Duodenum Mucosa	Duodenum
9	chr9:22006600-22009400	Active TSS	Hela-S3	cervix
10	chr9:22006600-22009400	Active TSS	NHEK	skin
11	chr9:22006600-22009600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:22006600-22009600	Active TSS	NHLF	lung
13	chr9:22006600-22010000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:22006800-22010000	Active TSS	NH-A	brain
15	chr9:22007200-22009400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr9:22007400-22009600	Active TSS	NHDF-Ad	bronchial
17	chr9:22007400-22010000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr9:22007600-22009600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:22007800-22009800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr9:22007800-22009800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr9:22008000-22009400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:22008000-22009600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr9:22008000-22009600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr9:22008000-22009600	Active TSS	HSMM	muscle
25	chr9:22008000-22009800	Active TSS	Colonic Mucosa	Colon
26	chr9:22008000-22009800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr9:22008200-22009600	Active TSS	Brain Angular Gyrus	brain
28	chr9:22008200-22009600	Active TSS	Placenta Amnion	Placenta Amnion
29	chr9:22008200-22009600	Active TSS	Rectal Smooth Muscle	rectum
30	chr9:22008200-22009800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:22008200-22009800	Active TSS	Placenta	Placenta
32	chr9:22008200-22009800	Active TSS	Right Atrium	heart
33	chr9:22008200-22010000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr9:22008200-22010000	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr9:22008400-22009400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
36	chr9:22008400-22009600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:22008400-22009600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
38	chr9:22008400-22009600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
39	chr9:22008400-22009600	Bivalent/Poised TSS	Fetal Kidney	kidney
40	chr9:22008400-22009600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr9:22008400-22009600	Active TSS	HepG2	liver
42	chr9:22008400-22009600	Active TSS	Osteobl	bone
43	chr9:22008400-22009800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:22008400-22009800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:22008400-22009800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr9:22008400-22009800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
47	chr9:22008400-22009800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
48	chr9:22008400-22009800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
49	chr9:22008400-22009800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:22008400-22009800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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