Variant report

Variant	rs12996578
Chromosome Location	chr2:30477220-30477221
allele	C/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	PML	chr2:30476652-30477408	K562	blood:	n/a	n/a
2	IRF1	chr2:30475715-30477360	K562	blood:	n/a	chr2:30476614-30476628 chr2:30476614-30476627 chr2:30476611-30476625 chr2:30476614-30476626 chr2:30476615-30476625 chr2:30476612-30476626 chr2:30476614-30476626 chr2:30476615-30476629 chr2:30476609-30476626 chr2:30476614-30476625 chr2:30476613-30476627
3	CCNT2	chr2:30475777-30477399	K562	blood:	n/a	n/a
4	CEBPD	chr2:30476650-30477349	K562	blood:	n/a	n/a
5	CEBPD	chr2:30476654-30477426	K562	blood:	n/a	n/a
6	PML	chr2:30476585-30477233	K562	blood:	n/a	n/a
7	MYC	chr2:30475648-30477561	K562	blood:	n/a	chr2:30475974-30475985
8	NR2F2	chr2:30476682-30477333	K562	blood:	n/a	n/a
9	MXI1	chr2:30475565-30477348	IMR90	lung:	n/a	n/a
10	JUN	chr2:30475558-30478014	K562	blood:	n/a	chr2:30475991-30476002
11	POLR2A	chr2:30475616-30477288	PBDE	blood:	n/a	n/a
12	POLR2A	chr2:30476701-30477315	K562	blood:	n/a	n/a
13	POLR2A	chr2:30477023-30477346	SK-N-MC	brain:	n/a	n/a
14	TEAD4	chr2:30475600-30477422	K562	blood:	n/a	n/a
15	POLR2A	chr2:30477217-30477236	K562	blood:	n/a	n/a
16	JUND	chr2:30476766-30477291	K562	blood:	n/a	n/a
17	IRF1	chr2:30476636-30477406	K562	blood:	n/a	n/a
18	GATA2	chr2:30476780-30477433	K562	blood:	n/a	n/a
19	TAL1	chr2:30475796-30477437	K562	blood:	n/a	n/a
20	ATF1	chr2:30476777-30477253	K562	blood:	n/a	n/a
21	RCOR1	chr2:30476716-30477292	K562	blood:	n/a	n/a
22	ZNF274	chr2:30475631-30477310	K562	blood:	n/a	n/a
23	EP300	chr2:30475628-30477686	K562	blood:	n/a	n/a
24	POLR2A	chr2:30475522-30479423	A549	lung:	n/a	n/a
25	POLR2A	chr2:30475619-30477342	K562	blood:	n/a	n/a
26	TBL1XR1	chr2:30475713-30477260	K562	blood:	n/a	n/a
27	GATA1	chr2:30475558-30477534	K562	blood:	n/a	chr2:30476141-30476148 chr2:30476277-30476293 chr2:30476279-30476286 chr2:30476134-30476155 chr2:30476141-30476148 chr2:30476141-30476148 chr2:30475991-30476000
28	GATA1	chr2:30476838-30477249	PBDEFetal	blood:	n/a	n/a
29	POLR2A	chr2:30476727-30477252	K562	blood:	n/a	n/a
30	STAT5A	chr2:30476633-30477408	K562	blood:	n/a	n/a
31	KAP1	chr2:30475664-30477261	K562	blood:	n/a	n/a
32	CEBPB	chr2:30476618-30477223	K562	blood:	n/a	n/a
33	MYC	chr2:30476663-30477298	K562	blood:	n/a	n/a
34	NR2F2	chr2:30475461-30477445	K562	blood:	n/a	n/a
35	SMARCA4	chr2:30475820-30477396	K562	blood:	n/a	n/a
36	EP300	chr2:30475752-30477392	K562	blood:	n/a	n/a
37	TEAD4	chr2:30476607-30477423	K562	blood:	n/a	n/a
38	ZNF143	chr2:30475861-30477260	K562	blood:	n/a	n/a
39	GATA2	chr2:30476737-30477362	K562	blood:	n/a	n/a
40	TBL1XR1	chr2:30475692-30477354	K562	blood:	n/a	n/a
41	POLR2A	chr2:30477119-30482747	SK-N-MC	brain:	n/a	n/a
42	TRIM28	chr2:30476669-30477289	K562	blood:	n/a	n/a
43	GATA1	chr2:30475641-30477410	PBDE	blood:	n/a	chr2:30476141-30476148 chr2:30476277-30476293 chr2:30476279-30476286 chr2:30476134-30476155 chr2:30476141-30476148 chr2:30476141-30476148 chr2:30475991-30476000
44	STAT5A	chr2:30476687-30477221	K562	blood:	n/a	n/a
45	CUX1	chr2:30475708-30477292	K562	blood:	n/a	chr2:30476313-30476324
46	ARID3A	chr2:30475870-30477402	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:30474584..30477299-chr2:30489169..30490893,2	K562	blood:
2	chr2:30452787..30458792-chr2:30474216..30479125,11	K562	blood:
3	chr2:30412652..30418181-chr2:30474392..30478394,5	K562	blood:
4	chr2:30470010..30473545-chr2:30474573..30477601,4	K562	blood:
5	chr2:30470929..30473564-chr2:30474573..30477601,4	K562	blood:
6	chr2:30475603..30478549-chr2:30478723..30480577,2	K562	blood:
7	chr2:30451092..30457677-chr2:30474497..30480716,15	K562	blood:
8	chr2:30476110..30477763-chr2:30668991..30671262,2	K562	blood:
9	chr2:30459999..30464804-chr2:30474137..30477672,6	K562	blood:
10	chr2:30475438..30481096-chr2:30481124..30485591,9	K562	blood:
11	chr2:30475984..30481096-chr2:30481124..30486276,10	K562	blood:
12	chr2:30476489..30478735-chr2:30510499..30512254,2	K562	blood:

Variant related genes	Relation type
ENSG00000256261	TF binding region
ENSG00000256261	Chromatin interaction
ENSG00000213626	Chromatin interaction
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1001202	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1001203	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185575	1.00[YRI][hapmap]
rs11127261	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127262	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675079	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679132	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679137	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11681350	1.00[ASN][1000 genomes]
rs11687193	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11688651	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690392	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690435	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690629	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690883	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11694534	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694679	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714304	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027149	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030064	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030740	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs13422834	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34097147	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35163883	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952114	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62141090	1.00[ASN][1000 genomes]
rs62141122	1.00[ASN][1000 genomes]
rs6736034	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs829585	1.00[ASN][1000 genomes]
rs906864	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9967840	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457800-30481000	Weak transcription	Gastric	stomach
2	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:30465400-30480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
5	chr2:30467600-30479600	Weak transcription	Fetal Brain Female	brain
6	chr2:30470400-30478000	Enhancers	Left Ventricle	heart
7	chr2:30470400-30479600	Genic enhancers	Fetal Thymus	thymus
8	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:30471200-30479600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:30471400-30479400	Enhancers	Placenta	Placenta
12	chr2:30471800-30481600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:30472200-30478800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:30472200-30480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:30472400-30478200	Enhancers	Right Atrium	heart
16	chr2:30472600-30480000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:30472600-30483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:30473000-30479600	Enhancers	Fetal Heart	heart
19	chr2:30473200-30480000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:30473400-30477600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:30473400-30480800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:30473400-30480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:30474200-30478000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:30474200-30479400	Enhancers	Fetal Intestine Large	intestine
25	chr2:30474200-30480800	Enhancers	Pancreas	Pancrea
26	chr2:30474400-30477800	Enhancers	Right Ventricle	heart
27	chr2:30474400-30481400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:30474600-30477600	Enhancers	Fetal Intestine Small	intestine
29	chr2:30474600-30477600	Enhancers	Small Intestine	intestine
30	chr2:30474800-30478000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr2:30475200-30478200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:30475400-30477400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:30475600-30477400	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr2:30475600-30477400	Flanking Active TSS	K562	blood
35	chr2:30475600-30478600	Enhancers	Fetal Muscle Leg	muscle
36	chr2:30475800-30477600	Weak transcription	Aorta	Aorta
37	chr2:30476000-30477800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:30476000-30479000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:30476000-30480200	Weak transcription	GM12878-XiMat	blood
40	chr2:30476200-30477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:30476200-30477600	Weak transcription	Lung	lung
42	chr2:30476200-30477600	Enhancers	Thymus	Thymus
43	chr2:30476200-30478000	Enhancers	HSMMtube	muscle
44	chr2:30476200-30478200	Enhancers	Stomach Smooth Muscle	stomach
45	chr2:30476200-30478400	Weak transcription	Psoas Muscle	Psoas
46	chr2:30476200-30479400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:30476200-30479400	Genic enhancers	HSMM	muscle
48	chr2:30476200-30479600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr2:30476200-30479800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:30476200-30480000	Genic enhancers	Primary T cells fromperipheralblood	blood

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