Variant report

Variant	rs374296258
Chromosome Location	chr9:6568370-6568371
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	CTCF	chr9:6568238-6568454	Pancreas_OC	pancreas:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
2	CTCF	chr9:6568129-6568482	K562	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
3	STAT3	chr9:6568151-6568443	MCF10A-Er-Src	breast:	n/a	n/a
4	RAD21	chr9:6568008-6568563	A549	lung:	n/a	chr9:6568318-6568337
5	CTCF	chr9:6568214-6568371	H1-hESC	embryonic stem cell:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
6	CTCF	chr9:6568220-6568370	HRPEpiC	eye:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
7	CTCF	chr9:6568161-6568403	SK-N-SH_RA	brain:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
8	CTCF	chr9:6568280-6568430	AG09319	gingival:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
9	CTCF	chr9:6568260-6568410	NHDF-neo	bronchial:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
10	CTCF	chr9:6568240-6568390	HPAF	blood vessel:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
11	CTCF	chr9:6568300-6568450	HCPEpiC	choroid plexus:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
12	CTCF	chr9:6568240-6568390	Hela-S3	cervix:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
13	CTCF	chr9:6568340-6568490	HVMF	connective:	n/a	n/a
14	CTCF	chr9:6568232-6568414	Medullo	brain:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
15	SMC3	chr9:6568151-6568406	K562	blood:	n/a	n/a
16	CTCF	chr9:6568257-6568396	SK-N-SH_RA	brain:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
17	CTCF	chr9:6568227-6568426	Hela-S3	cervix:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
18	E2F4	chr9:6568269-6568472	MCF10A-Er-Src	breast:	n/a	chr9:6568269-6568278
19	CTCF	chr9:6568231-6568429	LNCaP	prostate:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
20	RAD21	chr9:6568207-6568472	HepG2	liver:	n/a	chr9:6568318-6568337
21	CTCF	chr9:6568230-6568429	GM12878	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
22	CTCF	chr9:6568220-6568370	RPTEC	kidney:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
23	TAL1	chr9:6568230-6568514	K562	blood:	n/a	chr9:6568361-6568379
24	CTCF	chr9:6568240-6568390	WI-38	lung:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
25	CTCF	chr9:6568220-6568370	K562	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
26	CTCF	chr9:6568220-6568370	HFF-Myc	foreskin:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
27	CTCF	chr9:6568213-6568411	Lung_OC	lung:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
28	SMC3	chr9:6566409-6568638	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr9:6568220-6568370	HCPEpiC	choroid plexus:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
30	CTCF	chr9:6568280-6568430	HVMF	connective:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
31	CTCF	chr9:6568240-6568390	HMF	breast:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
32	CTCF	chr9:6568273-6568402	Kidney_OC	kidney:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
33	CTCF	chr9:6568260-6568410	HMF	breast:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
34	CTCF	chr9:6568220-6568370	BE2_C	brain:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
35	CTCF	chr9:6568240-6568390	GM12867	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
36	CTCF	chr9:6568260-6568410	SAEC	small airway:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
37	CTCF	chr9:6568240-6568390	GM12801	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
38	CTCF	chr9:6568280-6568430	HMEC	breast:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
39	RAD21	chr9:6568083-6568597	ECC-1	luminal epithelium:	n/a	chr9:6568318-6568337
40	CTCF	chr9:6568240-6568390	RPTEC	kidney:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
41	CTCF	chr9:6568240-6568390	AoAF	blood vessel:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
42	CTCF	chr9:6568280-6568430	BJ	skin:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
43	CTCF	chr9:6568083-6568508	MCF-7	breast:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
44	CTCF	chr9:6568300-6568450	HCFaa	heart:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
45	CTCF	chr9:6568240-6568390	GM12871	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
46	SMC3	chr9:6568171-6568481	HepG2	liver:	n/a	n/a
47	RAD21	chr9:6568074-6568531	ECC-1	luminal epithelium:	n/a	chr9:6568318-6568337
48	RAD21	chr9:6568084-6568481	HepG2	liver:	n/a	chr9:6568318-6568337
49	CTCF	chr9:6568220-6568370	GM12865	blood:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338
50	CTCF	chr9:6568220-6568370	Caco-2	colon:	n/a	chr9:6568321-6568337 chr9:6568315-6568336 chr9:6568320-6568338

No.	Distal block	Cell Line	Cell type
1	chr9:6411889..6413422-chr9:6565833..6568598,2	K562	blood:
2	chr9:6354058..6354828-chr9:6567905..6568745,4	MCF-7	breast:
3	chr9:6354258..6354771-chr9:6567896..6568668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237158	TF binding region
GLDC	TF binding region
ENSG00000252110	TF binding region
ENSG00000147854	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv934176	chr9:6517535-6644738	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv892163	chr9:6523056-6632061	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025627	chr9:6523056-6648098	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
15	nsv613206	chr9:6525753-6686738	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
16	esv3324686	chr9:6528411-6728310	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
17	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
18	nsv1018308	chr9:6544766-6869653	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
19	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
20	nsv1018870	chr9:6548393-6708345	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	nsv892164	chr9:6555079-6664282	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv931094	chr9:6558442-6672439	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
24	nsv1016600	chr9:6566610-6695986	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
25	nsv1033539	chr9:6566610-7022554	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
26	nsv613207	chr9:6567841-6676953	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	nsv466111	chr9:6567841-7017391	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
28	nsv613208	chr9:6567841-7017391	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6532000-6570400	Strong transcription	Liver	Liver
2	chr9:6554600-6568600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:6558600-6586600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:6558800-6580800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:6559200-6583400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:6560200-6569400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:6560200-6572200	Weak transcription	GM12878-XiMat	blood
8	chr9:6561200-6591000	Weak transcription	Placenta	Placenta
9	chr9:6563400-6583000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:6565400-6575200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:6565400-6586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:6565600-6569400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:6565600-6577000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:6566400-6575400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr9:6566600-6579800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:6566800-6572800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:6567000-6575400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:6567000-6581000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr9:6567200-6568400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr9:6567200-6569200	Enhancers	HMEC	breast
21	chr9:6567400-6568400	Enhancers	Brain Anterior Caudate	brain
22	chr9:6567400-6576800	Weak transcription	HepG2	liver
23	chr9:6567400-6579800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:6567600-6568400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:6567600-6568600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:6567600-6568600	Enhancers	Osteobl	bone
27	chr9:6567600-6569000	Enhancers	Hela-S3	cervix
28	chr9:6567600-6571400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:6567600-6599600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr9:6567800-6568400	Enhancers	NH-A	brain
31	chr9:6567800-6568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:6567800-6568600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:6567800-6568600	Enhancers	A549	lung
34	chr9:6567800-6568600	Enhancers	HUVEC	blood vessel
35	chr9:6567800-6568600	Enhancers	NHLF	lung
36	chr9:6567800-6569200	Enhancers	NHEK	skin
37	chr9:6568000-6568400	Enhancers	NHDF-Ad	bronchial
38	chr9:6568200-6568400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr9:6568200-6568600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr9:6568200-6569000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:6568200-6569600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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