Variant report

Variant	rs561884293
Chromosome Location	chr3:121265671-121265672
allele	-/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	CEBPB	chr3:121264767-121265991	A549	lung:	n/a	chr3:121265493-121265506 chr3:121265176-121265189 chr3:121265495-121265506
2	RAD21	chr3:121265429-121265970	ECC-1	luminal epithelium:	n/a	chr3:121265702-121265721 chr3:121265706-121265715
3	CTCF	chr3:121264809-121265939	GM12878	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
4	SIX5	chr3:121264551-121266074	A549	lung:	n/a	n/a
5	CTCF	chr3:121265640-121265790	HCFaa	heart:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
6	MXI1	chr3:121263658-121266103	IMR90	lung:	n/a	n/a
7	CTCF	chr3:121265580-121265730	GM12878	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
8	CTCF	chr3:121265580-121265730	HL-60	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
9	CTCF	chr3:121265600-121265750	GM12874	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
10	CTCF	chr3:121265640-121265790	NB4	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
11	CTCF	chr3:121265660-121265810	GM06990	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
12	MAFK	chr3:121264673-121265901	K562	blood:	n/a	n/a
13	TBP	chr3:121264658-121265786	Hela-S3	cervix:	n/a	n/a
14	ARID3A	chr3:121265453-121265941	HepG2	liver:	n/a	n/a
15	MAZ	chr3:121265541-121265909	K562	blood:	n/a	n/a
16	KAP1	chr3:121264240-121265888	HEK293	kidney:	n/a	n/a
17	CTCF	chr3:121265580-121265730	BE2_C	brain:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
18	ZNF143	chr3:121265552-121265924	K562	blood:	n/a	n/a
19	CTCF	chr3:121265621-121265782	GM13977	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
20	CTCF	chr3:121265490-121265895	A549	lung:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
21	CTCF	chr3:121265660-121265810	HEEpiC	esophagus:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
22	CTCF	chr3:121265657-121265725	GM20000	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
23	FOXA1	chr3:121265520-121265947	HepG2	liver:	n/a	n/a
24	CTCF	chr3:121265541-121265923	H1-hESC	embryonic stem cell:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
25	CTCF	chr3:121265620-121265770	HBMEC	blood vessel:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
26	POLR2A	chr3:121264378-121265762	GM18951	blood:	n/a	n/a
27	CTCF	chr3:121265640-121265790	BJ	skin:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
28	CTCF	chr3:121265640-121265790	SK-N-SH_RA	brain:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
29	CEBPB	chr3:121265352-121265933	HepG2	liver:	n/a	chr3:121265493-121265506 chr3:121265495-121265506
30	REST	chr3:121264530-121265672	H1-neurons	neurons:	n/a	n/a
31	RAD21	chr3:121264782-121265968	IMR90	lung:	n/a	chr3:121265702-121265721 chr3:121265706-121265715
32	TEAD4	chr3:121265460-121265966	HepG2	liver:	n/a	n/a
33	CEBPB	chr3:121264621-121266051	GM12878	blood:	n/a	chr3:121265493-121265506 chr3:121265176-121265189 chr3:121265495-121265506
34	RFX5	chr3:121265543-121265912	Hela-S3	cervix:	n/a	n/a
35	FOS	chr3:121265471-121265791	MCF10A-Er-Src	breast:	n/a	chr3:121265650-121265659
36	CTCF	chr3:121265640-121265790	HMF	breast:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
37	CTCF	chr3:121265626-121265829	A549	lung:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
38	CTCF	chr3:121265660-121265810	HVMF	connective:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
39	CTCF	chr3:121265638-121265819	HepG2	liver:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
40	CTCF	chr3:121265640-121265790	GM12871	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
41	YY1	chr3:121265613-121265896	SK-N-SH_RA	brain:	n/a	n/a
42	HDAC2	chr3:121265592-121265869	HepG2	liver:	n/a	chr3:121265598-121265612 chr3:121265601-121265615 chr3:121265597-121265611 chr3:121265599-121265613
43	RAD21	chr3:121265550-121265924	K562	blood:	n/a	chr3:121265702-121265721 chr3:121265706-121265715
44	SIN3AK20	chr3:121263953-121265775	MCF-7	breast:	n/a	n/a
45	CEBPB	chr3:121264666-121266054	MCF-7	breast:	n/a	chr3:121265493-121265506 chr3:121265176-121265189 chr3:121265495-121265506
46	CTCF	chr3:121265585-121265827	K562	blood:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
47	ZNF143	chr3:121264634-121265874	GM12878	blood:	n/a	n/a
48	CTCF	chr3:121265620-121265770	MCF-7	breast:	n/a	chr3:121265701-121265719 chr3:121265703-121265724 chr3:121265702-121265718
49	CEBPB	chr3:121265292-121265994	K562	blood:	n/a	chr3:121265493-121265506 chr3:121265495-121265506
50	HCFC1	chr3:121264036-121266047	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:121264864..121267091-chr3:122101354..122103102,2	MCF-7	breast:
2	chr3:121263813..121266298-chr3:122398939..122401596,2	K562	blood:
3	chr3:121265150..121267222-chr3:121267374..121269393,2	K562	blood:
4	chr3:121264298..121266034-chr3:122100794..122102974,2	MCF-7	breast:
5	chr3:121265303..121265930-chr3:121811130..121811872,2	MCF-7	breast:
6	chr3:121264839..121267237-chr3:122281910..122284575,2	MCF-7	breast:

Variant related genes	Relation type
POLQ	TF binding region
ENSG00000114023	Chromatin interaction
ENSG00000160124	Chromatin interaction
ENSG00000138496	Chromatin interaction
ENSG00000173193	Chromatin interaction
ENSG00000163840	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998555	chr3:120700604-121348015	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv591400	chr3:121070299-121339354	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv877381	chr3:121192350-121343500	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1007522	chr3:121200563-121374051	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv999349	chr3:121253990-121360206	Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3445327	chr3:121260311-121288302	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	esv2757006	chr3:121264886-121323465	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv2759172	chr3:121264886-121323465	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121263200-121265800	Active TSS	NHLF	lung
2	chr3:121263400-121265800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:121263400-121265800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:121263400-121265800	Active TSS	K562	blood
5	chr3:121263600-121265800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:121263600-121265800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:121263600-121265800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:121263600-121265800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:121263600-121265800	Active TSS	Brain Germinal Matrix	brain
10	chr3:121263600-121265800	Active TSS	NH-A	brain
11	chr3:121263800-121265800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:121263800-121265800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr3:121263800-121265800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:121263800-121265800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:121263800-121265800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:121263800-121265800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:121263800-121265800	Active TSS	Fetal Brain Female	brain
18	chr3:121263800-121265800	Active TSS	Fetal Intestine Small	intestine
19	chr3:121263800-121265800	Active TSS	Hela-S3	cervix
20	chr3:121263800-121265800	Active TSS	NHDF-Ad	bronchial
21	chr3:121263800-121266000	Active TSS	Fetal Kidney	kidney
22	chr3:121263800-121266000	Active TSS	A549	lung
23	chr3:121264000-121265800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:121264000-121265800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr3:121264000-121265800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr3:121264000-121265800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:121264000-121265800	Active TSS	Fetal Intestine Large	intestine
28	chr3:121264000-121265800	Active TSS	Thymus	Thymus
29	chr3:121264000-121265800	Active TSS	HSMMtube	muscle
30	chr3:121264200-121265800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:121264200-121265800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:121264200-121265800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:121264200-121265800	Active TSS	Brain Substantia Nigra	brain
34	chr3:121264200-121265800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:121264200-121265800	Active TSS	Psoas Muscle	Psoas
36	chr3:121264200-121266000	Flanking Active TSS	Liver	Liver
37	chr3:121264400-121265800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:121264400-121265800	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr3:121264400-121265800	Active TSS	Fetal Stomach	stomach
40	chr3:121264400-121265800	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:121264400-121265800	Active TSS	Right Atrium	heart
42	chr3:121264600-121265800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr3:121264600-121265800	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr3:121264600-121265800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr3:121264600-121265800	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr3:121264600-121265800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:121264600-121265800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr3:121264600-121265800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:121264600-121265800	Active TSS	Brain Angular Gyrus	brain
50	chr3:121264600-121265800	Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links