Variant report

Variant	rs2188127
Chromosome Location	chr9:21965232-21965233
allele	C/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	EP300	chr9:21965105-21965324	GM12878	blood:	n/a	chr9:21965118-21965134
2	TCF12	chr9:21964709-21966048	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr9:21964963-21965391	ECC-1	luminal epithelium:	n/a	n/a
4	RELA	chr9:21965092-21965708	GM12892	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
5	NFIC	chr9:21964653-21966052	ECC-1	luminal epithelium:	n/a	n/a
6	RELA	chr9:21965091-21965495	GM15510	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
7	SMC3	chr9:21965139-21966042	SK-N-SH	brain:	n/a	n/a
8	STAT5A	chr9:21965098-21965481	GM12878	blood:	n/a	n/a
9	RELA	chr9:21965072-21966038	GM18505	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
10	MAX	chr9:21964853-21965907	ECC-1	luminal epithelium:	n/a	chr9:21964946-21964957 chr9:21964942-21964961 chr9:21965814-21965824 chr9:21965026-21965035
11	ATF2	chr9:21965042-21965442	GM12878	blood:	n/a	n/a
12	RUNX3	chr9:21965057-21965860	GM12878	blood:	n/a	chr9:21965445-21965462
13	POLR2A	chr9:21964929-21971504	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr9:21964918-21965933	HL-60	blood:	n/a	n/a
15	YY1	chr9:21965219-21965483	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr9:21965114-21965577	GM12878	blood:	n/a	n/a
17	SP1	chr9:21965135-21965401	GM12878	blood:	n/a	chr9:21965287-21965296 chr9:21965286-21965295 chr9:21965286-21965300
18	RELA	chr9:21965004-21965847	GM19193	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
19	POLR2A	chr9:21964927-21965275	ECC-1	luminal epithelium:	n/a	n/a
20	BACH1	chr9:21965034-21966311	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr9:21964896-21966610	SK-N-MC	brain:	n/a	n/a
22	TAF1	chr9:21964921-21965270	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr9:21965200-21965350	AG04450	lung:	n/a	n/a
24	POLR2A	chr9:21964857-21965905	ECC-1	luminal epithelium:	n/a	n/a
25	RUNX3	chr9:21965023-21965862	GM12878	blood:	n/a	chr9:21965445-21965462
26	RELA	chr9:21965028-21965834	GM18951	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
27	BHLHE40	chr9:21964937-21965362	GM12878	blood:	n/a	chr9:21965119-21965135
28	MAX	chr9:21964844-21965457	ECC-1	luminal epithelium:	n/a	chr9:21964946-21964957 chr9:21964942-21964961 chr9:21965026-21965035
29	HDAC2	chr9:21964972-21965367	H1-hESC	embryonic stem cell:	n/a	n/a
30	RELA	chr9:21964930-21966348	GM12891	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
31	CTBP2	chr9:21964975-21966544	H1-hESC	embryonic stem cell:	n/a	n/a
32	EP300	chr9:21964829-21965384	ECC-1	luminal epithelium:	n/a	chr9:21965118-21965134
33	MTA3	chr9:21964998-21966053	GM12878	blood:	n/a	n/a
34	NFIC	chr9:21964717-21965918	ECC-1	luminal epithelium:	n/a	n/a
35	SP1	chr9:21965067-21965438	GM12878	blood:	n/a	chr9:21965287-21965296 chr9:21965286-21965295 chr9:21965286-21965300
36	SUZ12	chr9:21964942-21966524	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr9:21965100-21965250	AG04449	skin:	n/a	n/a
38	RELA	chr9:21965057-21965798	GM10847	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
39	CTCF	chr9:21964955-21966087	SK-N-SH	brain:	n/a	n/a
40	RELA	chr9:21965080-21965776	GM12878	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289
41	USF1	chr9:21964864-21965396	ECC-1	luminal epithelium:	n/a	chr9:21965119-21965135
42	SUZ12	chr9:21964929-21971601	NT2-D1	testis:	n/a	n/a
43	RFX5	chr9:21965160-21965347	HepG2	liver:	n/a	n/a
44	RELA	chr9:21965053-21965802	GM19099	blood:	n/a	chr9:21965280-21965289 chr9:21965280-21965289

Variant related genes	Relation type
C9orf53	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13297747	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2518719	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3731198	0.81[EUR][1000 genomes]
rs3731217	0.81[EUR][1000 genomes]
rs3731222	0.81[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	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	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	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
5	esv3365660	chr9:21944001-21969383	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21962000-21966200	Weak transcription	Hela-S3	cervix
2	chr9:21963600-21966200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
3	chr9:21964400-21969000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr9:21964600-21966400	Bivalent Enhancer	Fetal Thymus	thymus
5	chr9:21964800-21965400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr9:21964800-21965600	Bivalent Enhancer	Lung	lung
7	chr9:21964800-21965800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr9:21964800-21965800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr9:21964800-21965800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr9:21964800-21965800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:21964800-21965800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr9:21964800-21966000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr9:21964800-21966000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:21964800-21966400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr9:21965000-21965400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
16	chr9:21965000-21965400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:21965000-21965400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:21965000-21965400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:21965000-21965400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
20	chr9:21965000-21965400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
21	chr9:21965000-21965400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:21965000-21965400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:21965000-21965400	Bivalent Enhancer	Brain Angular Gyrus	brain
24	chr9:21965000-21965400	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
25	chr9:21965000-21965400	Flanking Active TSS	Gastric	stomach
26	chr9:21965000-21965400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
27	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:21965000-21965600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
33	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
35	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:21965000-21965600	Bivalent Enhancer	Fetal Brain Male	brain
37	chr9:21965000-21965600	Flanking Active TSS	Pancreas	Pancrea
38	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
39	chr9:21965000-21965600	Enhancers	Spleen	Spleen
40	chr9:21965000-21965600	Flanking Bivalent TSS/Enh	NHLF	lung
41	chr9:21965000-21965600	Flanking Active TSS	Osteobl	bone
42	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:21965000-21965800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
46	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr9:21965000-21965800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood

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