Variant report

Variant	rs562211480
Chromosome Location	chr1:154158862-154158863
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	chr1:154158629-154158864	MCF-7	breast:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
2	CTCF	chr1:154158800-154158950	A549	lung:	n/a	n/a
3	CTCF	chr1:154158484-154158881	A549	lung:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
4	CTCF	chr1:154158720-154158870	MCF-7	breast:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
5	ZNF384	chr1:154158622-154158882	K562	blood:	n/a	n/a
6	MYC	chr1:154158602-154158930	K562	blood:	n/a	chr1:154158894-154158903
7	CTCF	chr1:154158607-154158906	Medullo	brain:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
8	CTCF	chr1:154158619-154158888	MCF-7	breast:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
9	CTCF	chr1:154158440-154159216	SK-N-SH	brain:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
10	FOS	chr1:154158683-154159038	MCF10A-Er-Src	breast:	n/a	chr1:154158892-154158903 chr1:154158894-154158902
11	RAD21	chr1:154158411-154159063	HCT-116	colon:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
12	RAD21	chr1:154158566-154158933	GM12878	blood:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
13	CTCF	chr1:154158631-154158864	GM19240	blood:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
14	RAD21	chr1:154158514-154158972	HepG2	liver:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
15	RAD21	chr1:154158622-154158885	HepG2	liver:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
16	CTCF	chr1:154158565-154158917	IMR90	lung:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
17	CTCF	chr1:154158606-154158892	HUVEC	blood vessel:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
18	GATA3	chr1:154158530-154159513	T-47D	breast:	n/a	chr1:154158800-154158808 chr1:154158892-154158901 chr1:154158550-154158571
19	CTCF	chr1:154158546-154158946	GM12878	blood:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
20	RAD21	chr1:154158593-154158930	K562	blood:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
21	SMC3	chr1:154158593-154158918	K562	blood:	n/a	chr1:154158742-154158752 chr1:154158738-154158752
22	MAZ	chr1:154158590-154158982	K562	blood:	n/a	chr1:154158894-154158903
23	CTCF	chr1:154158740-154158890	BE2_C	brain:	n/a	n/a
24	CTCF	chr1:154158630-154158873	GM19239	blood:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
25	CTCF	chr1:154158347-154159114	A549	lung:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
26	CTCF	chr1:154158720-154158870	NHDF-neo	bronchial:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
27	CTCF	chr1:154158780-154158930	HFF-Myc	foreskin:	n/a	n/a
28	GATA2	chr1:154158692-154158974	SH-SY5Y	brain:	n/a	chr1:154158800-154158808 chr1:154158892-154158901
29	ZNF143	chr1:154158568-154158918	GM12878	blood:	n/a	n/a
30	RAD21	chr1:154158517-154159013	ECC-1	luminal epithelium:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
31	CTCF	chr1:154158760-154158910	HFF-Myc	foreskin:	n/a	n/a
32	RAD21	chr1:154158501-154158933	A549	lung:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
33	CTCF	chr1:154158760-154158910	WI-38	lung:	n/a	n/a
34	GATA3	chr1:154158756-154159284	MCF-7	breast:	n/a	chr1:154158800-154158808 chr1:154158892-154158901
35	SMC3	chr1:154158568-154158979	Hela-S3	cervix:	n/a	chr1:154158742-154158752 chr1:154158738-154158752
36	RAD21	chr1:154158546-154159060	MCF-7	breast:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
37	RAD21	chr1:154158495-154158901	SK-N-SH_RA	brain:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
38	CTCF	chr1:154158589-154158955	HepG2	liver:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
39	RAD21	chr1:154158403-154159098	SK-N-SH	brain:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
40	RAD21	chr1:154158496-154159131	MCF-7	breast:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
41	CTCF	chr1:154158760-154158910	HCM	heart:	n/a	n/a
42	RAD21	chr1:154158419-154159048	HCT-116	colon:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754
43	TEAD4	chr1:154158522-154159020	K562	blood:	n/a	n/a
44	CEBPD	chr1:154158708-154159966	K562	blood:	n/a	n/a
45	HCFC1	chr1:154158660-154158888	K562	blood:	n/a	n/a
46	CTCF	chr1:154158588-154158903	T-47D	breast:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
47	RCOR1	chr1:154158685-154158896	K562	blood:	n/a	n/a
48	BHLHE40	chr1:154158700-154158934	K562	blood:	n/a	n/a
49	CTCF	chr1:154158456-154158933	K562	blood:	n/a	chr1:154158738-154158759 chr1:154158736-154158754 chr1:154158739-154158752
50	RAD21	chr1:154158528-154158966	H1-hESC	embryonic stem cell:	n/a	chr1:154158740-154158753 chr1:154158742-154158752 chr1:154158737-154158756 chr1:154158742-154158754

No.	Distal block	Cell Line	Cell type
1	chr1:154157284..154158987-chr1:154175294..154177755,2	K562	blood:
2	chr1:154158462..154159551-chr1:154244419..154245220,5	MCF-7	breast:
3	chr1:154158286..154159217-chr1:154244364..154245091,5	MCF-7	breast:
4	chr1:154158680..154159404-chr8:91334673..91335355,2	MCF-7	breast:
5	chr1:154158539..154161524-chr1:154242189..154245561,3	MCF-7	breast:
6	chr1:154153141..154174161-chr1:154187746..154196033,47	MCF-7	breast:
7	chr1:154158527..154159393-chr1:154171168..154172306,5	MCF-7	breast:
8	chr1:154145134..154153289-chr1:154153487..154160631,22	K562	blood:
9	chr1:154158467..154161316-chr1:154169815..154172829,3	MCF-7	breast:
10	chr1:154129855..154131682-chr1:154158722..154160655,2	K562	blood:
11	chr1:153963252..153965177-chr1:154158511..154161067,3	MCF-7	breast:
12	chr1:154158424..154161181-chr1:154245114..154247197,2	MCF-7	breast:
13	chr1:154158281..154159315-chr1:154244452..154245349,6	K562	blood:
14	chr1:154156233..154161758-chr1:154162933..154167291,6	K562	blood:
15	chr1:154157441..154159782-chr1:154297521..154299444,2	MCF-7	breast:
16	chr1:154158325..154158864-chr1:154325830..154326669,2	MCF-7	breast:
17	chr1:153938202..153942686-chr1:154154566..154158952,5	MCF-7	breast:
18	chr1:154158329..154159389-chr1:154307310..154308142,3	MCF-7	breast:
19	chr1:154158378..154160175-chr1:154161458..154162989,2	K562	blood:
20	chr1:154158089..154161877-chr1:154191453..154195317,5	K562	blood:
21	chr1:154155278..154160143-chr1:154165338..154167782,4	K562	blood:
22	chr1:154149113..154161877-chr1:154185436..154196776,24	K562	blood:
23	chr1:154157620..154160474-chr1:154243122..154244827,3	MCF-7	breast:
24	chr1:154154597..154158912-chr1:154243474..154246502,4	K562	blood:
25	chr1:154158245..154159342-chr1:154307445..154308150,3	K562	blood:
26	chr1:154158282..154159260-chr1:154244542..154245527,2	MCF-7	breast:

Variant related genes	Relation type
TPM3	TF binding region
ENSG00000143515	Chromatin interaction
ENSG00000215938	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143575	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143569	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS 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 miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	esv3453084	chr1:154156328-154161626	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
8	esv3453085	chr1:154156328-154161626	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
9	esv12863	chr1:154158242-154161302	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154156200-154163000	Weak transcription	Psoas Muscle	Psoas
2	chr1:154156400-154159000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:154156400-154159000	Weak transcription	A549	lung
4	chr1:154156400-154159400	Weak transcription	Small Intestine	intestine
5	chr1:154156400-154159600	Weak transcription	GM12878-XiMat	blood
6	chr1:154156400-154163200	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:154156400-154164200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:154156600-154164200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:154156800-154164200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:154157200-154164400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:154158000-154159600	Enhancers	Hela-S3	cervix
12	chr1:154158200-154159000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr1:154158200-154159000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:154158200-154159000	Enhancers	HSMMtube	muscle
15	chr1:154158200-154159600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:154158200-154159800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:154158400-154159400	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:154158400-154159400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:154158400-154159600	Enhancers	HSMM	muscle
20	chr1:154158400-154159800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:154158400-154159800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:154158400-154159800	Enhancers	Fetal Intestine Small	intestine
23	chr1:154158400-154160200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:154158400-154160200	Enhancers	HepG2	liver
25	chr1:154158400-154160400	Enhancers	Stomach Mucosa	stomach
26	chr1:154158400-154160600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr1:154158600-154159000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:154158600-154159000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:154158600-154159400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:154158600-154160600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:154158800-154159000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:154158800-154159000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:154158800-154159000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:154158800-154159000	Enhancers	Fetal Kidney	kidney
35	chr1:154158800-154159000	Enhancers	Pancreas	Pancrea
36	chr1:154158800-154159200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:154158800-154159200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:154158800-154159400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:154158800-154159600	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:154158800-154159800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:154158800-154159800	Enhancers	Fetal Intestine Large	intestine
42	chr1:154158800-154160000	Flanking Active TSS	K562	blood
43	chr1:154158800-154160800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links