Variant report

Variant	rs13409562
Chromosome Location	chr2:30476497-30476498
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	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
2	CCNT2	chr2:30475777-30477399	K562	blood:	n/a	n/a
3	CBX3	chr2:30475625-30476513	K562	blood:	n/a	n/a
4	TCF12	chr2:30475393-30476662	A549	lung:	n/a	chr2:30476354-30476363
5	REST	chr2:30475603-30476819	A549	lung:	n/a	chr2:30475777-30475790
6	MYC	chr2:30475648-30477561	K562	blood:	n/a	chr2:30475974-30475985
7	POLR2A	chr2:30475781-30477145	K562	blood:	n/a	n/a
8	HCFC1	chr2:30475814-30476856	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	TEAD4	chr2:30475600-30477422	K562	blood:	n/a	n/a
13	ZMIZ1	chr2:30475614-30476579	K562	blood:	n/a	n/a
14	POLR2A	chr2:30475462-30477109	SK-N-MC	brain:	n/a	n/a
15	MAFK	chr2:30475809-30477061	K562	blood:	n/a	chr2:30476623-30476640 chr2:30476097-30476108 chr2:30476095-30476109
16	TAL1	chr2:30475796-30477437	K562	blood:	n/a	n/a
17	ZNF274	chr2:30475631-30477310	K562	blood:	n/a	n/a
18	EP300	chr2:30475628-30477686	K562	blood:	n/a	n/a
19	POLR2A	chr2:30475522-30479423	A549	lung:	n/a	n/a
20	POLR2A	chr2:30475619-30477342	K562	blood:	n/a	n/a
21	GATA3	chr2:30475380-30476518	A549	lung:	n/a	chr2:30476141-30476148 chr2:30476277-30476293 chr2:30476279-30476286 chr2:30476134-30476155 chr2:30476141-30476148 chr2:30476141-30476148 chr2:30475991-30476000
22	TBL1XR1	chr2:30475713-30477260	K562	blood:	n/a	n/a
23	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
24	KAP1	chr2:30475664-30477261	K562	blood:	n/a	n/a
25	MAFF	chr2:30475815-30476625	K562	blood:	n/a	n/a
26	POLR2A	chr2:30475585-30476535	K562	blood:	n/a	n/a
27	NR2F2	chr2:30475461-30477445	K562	blood:	n/a	n/a
28	SMARCA4	chr2:30475820-30477396	K562	blood:	n/a	n/a
29	GATA3	chr2:30475734-30476522	SK-N-SH	brain:	n/a	chr2:30476141-30476148 chr2:30476277-30476293 chr2:30476279-30476286 chr2:30476134-30476155 chr2:30476141-30476148 chr2:30476141-30476148 chr2:30475991-30476000
30	EP300	chr2:30475752-30477392	K562	blood:	n/a	n/a
31	BACH1	chr2:30475845-30476983	K562	blood:	n/a	n/a
32	EP300	chr2:30475516-30476548	A549	lung:	n/a	n/a
33	ZNF143	chr2:30475861-30477260	K562	blood:	n/a	n/a
34	JUND	chr2:30475743-30476502	K562	blood:	n/a	chr2:30475991-30476002
35	TBL1XR1	chr2:30475692-30477354	K562	blood:	n/a	n/a
36	FOXA2	chr2:30475803-30476620	A549	lung:	n/a	chr2:30476362-30476374 chr2:30476358-30476370 chr2:30475810-30475822
37	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
38	KAP1	chr2:30475685-30476578	HEK293	kidney:	n/a	n/a
39	NR2F2	chr2:30475637-30476579	K562	blood:	n/a	n/a
40	CUX1	chr2:30475708-30477292	K562	blood:	n/a	chr2:30476313-30476324
41	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
ENSG00000172954	Chromatin interaction
ENSG00000256261	Chromatin interaction
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10185575	1.00[AMR][1000 genomes]
rs10206966	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12714304	1.00[YRI][hapmap]
rs13388013	1.00[AMR][1000 genomes]
rs13408775	1.00[AMR][1000 genomes]
rs13424193	1.00[AMR][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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457000-30476600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:30457800-30481000	Weak transcription	Gastric	stomach
3	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:30465400-30480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:30466000-30477000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
7	chr2:30467600-30479600	Weak transcription	Fetal Brain Female	brain
8	chr2:30470400-30478000	Enhancers	Left Ventricle	heart
9	chr2:30470400-30479600	Genic enhancers	Fetal Thymus	thymus
10	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:30471200-30479600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:30471400-30479400	Enhancers	Placenta	Placenta
14	chr2:30471800-30481600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:30472200-30478800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:30472200-30480400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:30472400-30478200	Enhancers	Right Atrium	heart
18	chr2:30472600-30480000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:30472600-30483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:30473000-30479600	Enhancers	Fetal Heart	heart
21	chr2:30473200-30480000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:30473400-30477600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:30473400-30480800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:30473400-30480800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:30473600-30477200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:30474000-30476800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr2:30474000-30477200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:30474200-30477000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:30474200-30477200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:30474200-30478000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:30474200-30479400	Enhancers	Fetal Intestine Large	intestine
32	chr2:30474200-30480800	Enhancers	Pancreas	Pancrea
33	chr2:30474400-30476800	Enhancers	NHLF	lung
34	chr2:30474400-30477800	Enhancers	Right Ventricle	heart
35	chr2:30474400-30481400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:30474600-30477000	Enhancers	NH-A	brain
37	chr2:30474600-30477600	Enhancers	Fetal Intestine Small	intestine
38	chr2:30474600-30477600	Enhancers	Small Intestine	intestine
39	chr2:30474800-30476800	Enhancers	Rectal Smooth Muscle	rectum
40	chr2:30474800-30477000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:30474800-30477000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr2:30474800-30477000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:30474800-30477200	Enhancers	Stomach Mucosa	stomach
44	chr2:30474800-30478000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:30475000-30476800	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr2:30475000-30477200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr2:30475200-30476800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr2:30475200-30477000	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:30475200-30477000	Enhancers	NHDF-Ad	bronchial
50	chr2:30475200-30478200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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