Variant report

Variant	rs13288485
Chromosome Location	chr9:136398612-136398613
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	RAD21	chr9:136398054-136398742	MCF-7	breast:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
2	JUN	chr9:136398048-136398635	K562	blood:	n/a	n/a
3	RAD21	chr9:136398166-136398615	H1-hESC	embryonic stem cell:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
4	MAX	chr9:136398060-136398643	MCF-7	breast:	n/a	n/a
5	RAD21	chr9:136397887-136398790	HCT-116	colon:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136397926-136397939 chr9:136398364-136398376
6	CTCF	chr9:136398206-136398612	HepG2	liver:	n/a	n/a
7	CTCF	chr9:136397766-136398950	SK-N-SH	brain:	n/a	chr9:136397961-136397969
8	CTCF	chr9:136397936-136398797	HCT-116	colon:	n/a	chr9:136397961-136397969
9	RAD21	chr9:136398118-136398661	ECC-1	luminal epithelium:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
10	CTCF	chr9:136398147-136398631	K562	blood:	n/a	n/a
11	RAD21	chr9:136398166-136398624	A549	lung:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
12	RAD21	chr9:136398044-136398680	ECC-1	luminal epithelium:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
13	CTCF	chr9:136398580-136398730	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr9:136398074-136398698	MCF-7	breast:	n/a	n/a
15	CTCF	chr9:136398049-136398699	HCT-116	colon:	n/a	n/a
16	RAD21	chr9:136398068-136398712	A549	lung:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
17	RAD21	chr9:136398099-136398717	MCF-7	breast:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
18	RAD21	chr9:136397937-136398782	HCT-116	colon:	n/a	chr9:136398364-136398374 chr9:136398362-136398375 chr9:136398364-136398376
19	RAD21	chr9:136397945-136401922	SK-N-SH	brain:	n/a	chr9:136398364-136398374 chr9:136399822-136399835 chr9:136399556-136399570 chr9:136398362-136398375 chr9:136398364-136398376
20	SMC3	chr9:136398102-136401007	SK-N-SH	brain:	n/a	chr9:136398360-136398374 chr9:136400504-136400514 chr9:136400129-136400143 chr9:136398364-136398374 chr9:136398728-136398735
21	CTCF	chr9:136398139-136398687	MCF-7	breast:	n/a	n/a
22	STAT5A	chr9:136398277-136398777	GM12878	blood:	n/a	n/a
23	CTCF	chr9:136397953-136398737	A549	lung:	n/a	chr9:136397961-136397969

No.	Distal block	Cell Line	Cell type
1	chr9:136397949..136398752-chr9:136594528..136595564,4	MCF-7	breast:
2	chr9:136397976..136398826-chr9:136528405..136529390,2	MCF-7	breast:
3	chr6:138026186..138027074-chr9:136397930..136398654,2	MCF-7	breast:
4	chr9:136397453..136398861-chr9:136590869..136592101,16	MCF-7	breast:
5	chr9:136391559..136394179-chr9:136396681..136398640,3	MCF-7	breast:
6	chr9:136397889..136398896-chr9:136591136..136592105,6	MCF-7	breast:
7	chr9:136397639..136398833-chr9:136580643..136581791,10	MCF-7	breast:
8	chr9:136397959..136398834-chr9:136591115..136592093,4	K562	blood:
9	chr9:136398236..136398863-chr9:136573868..136574473,2	MCF-7	breast:
10	chr9:136397924..136398838-chr9:136580700..136581803,6	MCF-7	breast:
11	chr9:136397854..136398745-chr9:136593068..136593594,3	K562	blood:

Variant related genes	Relation type
ADAMTSL2	TF binding region
TMEM8C	TF binding region
ENSG00000187616	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12345442	1.00[CEU][hapmap]
rs12345624	1.00[CEU][hapmap]
rs35984966	0.96[EUR][1000 genomes]
rs66938753	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7024668	1.00[CEU][hapmap]
rs7027605	1.00[CEU][hapmap]
rs73661429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894059	chr9:136123840-136486929	Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv894077	chr9:136166346-136515297	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv894078	chr9:136194595-136484292	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv933226	chr9:136224559-136407071	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv894083	chr9:136281753-136452144	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv894084	chr9:136281753-136458311	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv894085	chr9:136281753-136478442	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv894092	chr9:136311679-136452144	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv894093	chr9:136311679-136458311	Genic enhancers Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv894094	chr9:136311679-136528721	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
14	nsv894097	chr9:136333356-136407208	Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv894098	chr9:136335824-136452144	Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
16	nsv894099	chr9:136337168-136459543	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
17	nsv894100	chr9:136371224-136547602	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv894101	chr9:136378650-136458311	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv894102	chr9:136388223-136496708	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv894103	chr9:136397195-136442192	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv615637	chr9:136397834-136404516	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136392200-136398800	Weak transcription	Gastric	stomach
2	chr9:136393600-136399400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr9:136394200-136399200	Weak transcription	Left Ventricle	heart
4	chr9:136394200-136399200	Weak transcription	Pancreas	Pancrea
5	chr9:136394400-136399200	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr9:136394600-136399200	Weak transcription	Fetal Heart	heart
7	chr9:136395000-136399000	Weak transcription	Fetal Brain Female	brain
8	chr9:136395400-136398800	Weak transcription	Right Ventricle	heart
9	chr9:136397600-136398800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:136397600-136398800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
11	chr9:136397600-136399200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr9:136397600-136399200	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:136397600-136399200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr9:136397600-136399200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr9:136397600-136399200	Enhancers	Brain Substantia Nigra	brain
16	chr9:136397600-136399200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
17	chr9:136397800-136398800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr9:136397800-136399200	Enhancers	Liver	Liver
19	chr9:136397800-136399200	Enhancers	Brain Hippocampus Middle	brain
20	chr9:136397800-136399600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr9:136397800-136399600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr9:136397800-136400400	Enhancers	HSMM	muscle
23	chr9:136398000-136399000	Enhancers	Stomach Smooth Muscle	stomach
24	chr9:136398000-136399200	Enhancers	Brain Germinal Matrix	brain
25	chr9:136398000-136399200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr9:136398000-136399200	Enhancers	Right Atrium	heart
27	chr9:136398000-136399400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:136398000-136399400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:136398000-136399600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr9:136398000-136399800	Enhancers	Brain Angular Gyrus	brain
31	chr9:136398000-136400000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:136398000-136400200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
33	chr9:136398000-136400200	Bivalent Enhancer	Placenta	Placenta
34	chr9:136398000-136400200	Enhancers	HSMMtube	muscle
35	chr9:136398200-136398800	Enhancers	Brain Anterior Caudate	brain
36	chr9:136398200-136398800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
37	chr9:136398200-136399200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:136398200-136399200	Enhancers	Brain Cingulate Gyrus	brain
39	chr9:136398200-136399400	Bivalent Enhancer	Thymus	Thymus
40	chr9:136398200-136399600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr9:136398200-136399800	Enhancers	Fetal Lung	lung
42	chr9:136398200-136402000	Enhancers	Fetal Brain Male	brain
43	chr9:136398400-136398800	Weak transcription	Lung	lung
44	chr9:136398400-136399000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:136398400-136399000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr9:136398400-136399200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:136398400-136399200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
48	chr9:136398400-136399400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
49	chr9:136398400-136399400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
50	chr9:136398400-136399400	Enhancers	Colon Smooth Muscle	Colon

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