Variant report

Variant	rs2069420
Chromosome Location	chr9:22008504-22008505
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	MXI1	chr9:22008381-22010136	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr9:22008406-22009861	ECC-1	luminal epithelium:	n/a	n/a
3	SMC3	chr9:22008102-22009872	SK-N-SH	brain:	n/a	chr9:22009174-22009184
4	RAD21	chr9:22008301-22009843	Hela-S3	cervix:	n/a	chr9:22009565-22009577
5	CTCF	chr9:22008394-22009907	HCT-116	colon:	n/a	chr9:22009587-22009600 chr9:22009173-22009183
6	TEAD4	chr9:22008495-22009713	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZKSCAN1	chr9:22008340-22009701	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr9:22008471-22009881	Hela-S3	cervix:	n/a	chr9:22009174-22009184
9	CTCF	chr9:22008487-22009519	HCT-116	colon:	n/a	chr9:22009173-22009183
10	GTF2F1	chr9:22008495-22009800	Hela-S3	cervix:	n/a	n/a
11	RAD21	chr9:22008356-22009808	IMR90	lung:	n/a	chr9:22009565-22009577
12	POLR2A	chr9:22008497-22009615	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr9:22008485-22009723	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr9:22008503-22009514	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr9:22008477-22008973	GM12878	blood:	n/a	n/a
16	TCF12	chr9:22008473-22009625	ECC-1	luminal epithelium:	n/a	chr9:22009494-22009502
17	RFX5	chr9:22008437-22009841	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr9:22008469-22008740	SH-SY5Y	brain:	n/a	n/a
19	MAZ	chr9:22008407-22009820	IMR90	lung:	n/a	n/a
20	GATA3	chr9:22008460-22008965	T-47D	breast:	n/a	n/a
21	SMC3	chr9:22008440-22009685	GM12878	blood:	n/a	chr9:22009174-22009184
22	CHD1	chr9:22007880-22009989	IMR90	lung:	n/a	n/a
23	CTCF	chr9:22008399-22009975	SK-N-SH	brain:	n/a	chr9:22009587-22009600 chr9:22009173-22009183
24	POLR2A	chr9:22007801-22009751	H1-neurons	neurons:	n/a	n/a
25	CTCF	chr9:22008500-22008650	NHEK	skin:	n/a	n/a
26	GATA1	chr9:22008169-22009792	PBDE	blood:	n/a	chr9:22008455-22008464
27	RAD21	chr9:22008327-22009895	HCT-116	colon:	n/a	chr9:22009565-22009577
28	EP300	chr9:22008471-22009830	ECC-1	luminal epithelium:	n/a	chr9:22008512-22008526
29	RAD21	chr9:22008478-22009805	ECC-1	luminal epithelium:	n/a	chr9:22009565-22009577
30	NRF1	chr9:22008436-22009770	SK-N-SH	brain:	n/a	chr9:22009464-22009473 chr9:22009462-22009473
31	RAD21	chr9:22008494-22008944	HepG2	liver:	n/a	n/a
32	GATA2	chr9:22008496-22008958	HUVEC	blood vessel:	n/a	n/a
33	TCF12	chr9:22008483-22009745	ECC-1	luminal epithelium:	n/a	chr9:22009494-22009502
34	MXI1	chr9:22008281-22009909	IMR90	lung:	n/a	n/a
35	POLR2A	chr9:22008458-22009745	Hela-S3	cervix:	n/a	n/a
36	MAX	chr9:22008447-22009691	ECC-1	luminal epithelium:	n/a	n/a
37	RAD21	chr9:22008394-22009931	HCT-116	colon:	n/a	chr9:22009565-22009577
38	GATA3	chr9:22008403-22008923	T-47D	breast:	n/a	chr9:22008455-22008464
39	POLR2A	chr9:22008234-22009689	IMR90	lung:	n/a	n/a
40	FOXM1	chr9:22008343-22009078	GM12878	blood:	n/a	n/a
41	NFIC	chr9:22008493-22009604	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr9:22007993-22009814	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr9:22007891-22009895	H1-neurons	neurons:	n/a	n/a
44	CHD1	chr9:22008491-22008543	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr9:22007656-22009795	Hela-S3	cervix:	n/a	n/a
46	CUX1	chr9:22008101-22008684	GM12878	blood:	n/a	n/a
47	TBP	chr9:22008260-22009740	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:22008067-22009853	Hela-S3	cervix:	n/a	n/a
49	GATA2	chr9:22008497-22009582	SH-SY5Y	brain:	n/a	n/a

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	chr7:73588443..73589078-chr9:22008320..22009302,2	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
ENSG00000215221	Chromatin interaction
ENSG00000266446	Chromatin interaction
ENSG00000236921	Chromatin interaction
ENSG00000099810	Chromatin interaction
ENSG00000264545	Chromatin interaction
ENSG00000106682	Chromatin interaction
ENSG00000147889	Chromatin interaction
ENSG00000240498	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16935753	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2151279	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217990	1.00[EUR][1000 genomes]
rs3217994	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3217999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218003	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3218023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731205	1.00[EUR][1000 genomes]
rs56235436	0.83[AMR][1000 genomes]
rs60693449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61564778	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73650003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652816	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652824	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652825	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652841	0.83[AMR][1000 genomes]
rs73652842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652843	1.00[EUR][1000 genomes]
rs73652845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652846	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652847	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652848	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73652849	1.00[AMR][1000 genomes];1.00[EUR][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:107 , 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	chr9:22006200-22008600	Weak transcription	Gastric	stomach
4	chr9:22006200-22008600	Weak transcription	Lung	lung
5	chr9:22006200-22008800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:22006200-22009600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:22006400-22008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:22006400-22008600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:22006400-22008600	Weak transcription	Pancreas	Pancrea
10	chr9:22006400-22009400	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr9:22006400-22009400	Active TSS	HMEC	breast
12	chr9:22006400-22010000	Active TSS	Muscle Satellite Cultured Cells	--
13	chr9:22006400-22010000	Active TSS	HSMMtube	muscle
14	chr9:22006600-22009400	Active TSS	Duodenum Mucosa	Duodenum
15	chr9:22006600-22009400	Active TSS	Hela-S3	cervix
16	chr9:22006600-22009400	Active TSS	NHEK	skin
17	chr9:22006600-22009600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:22006600-22009600	Active TSS	NHLF	lung
19	chr9:22006600-22010000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:22006800-22010000	Active TSS	NH-A	brain
21	chr9:22007200-22009400	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:22007400-22008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:22007400-22008600	Weak transcription	Esophagus	oesophagus
24	chr9:22007400-22008600	Genic enhancers	Dnd41	blood
25	chr9:22007400-22009600	Active TSS	NHDF-Ad	bronchial
26	chr9:22007400-22010000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:22007600-22009600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr9:22007800-22009800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr9:22007800-22009800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
30	chr9:22008000-22008600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr9:22008000-22008600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
32	chr9:22008000-22008600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr9:22008000-22008600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr9:22008000-22008600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:22008000-22008600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr9:22008000-22008600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr9:22008000-22009400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:22008000-22009600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr9:22008000-22009600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
40	chr9:22008000-22009600	Active TSS	HSMM	muscle
41	chr9:22008000-22009800	Active TSS	Colonic Mucosa	Colon
42	chr9:22008000-22009800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
43	chr9:22008200-22008600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
44	chr9:22008200-22008800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
45	chr9:22008200-22009000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:22008200-22009000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr9:22008200-22009000	Bivalent Enhancer	Fetal Heart	heart
48	chr9:22008200-22009600	Active TSS	Brain Angular Gyrus	brain
49	chr9:22008200-22009600	Active TSS	Placenta Amnion	Placenta Amnion
50	chr9:22008200-22009600	Active TSS	Rectal Smooth Muscle	rectum

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