Variant report

Variant	rs549034947
Chromosome Location	chr12:56118536-56118537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:291)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:291 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:56118457-56118711	GM19239	blood:	n/a	n/a
2	CTCF	chr12:56118500-56118650	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr12:56118480-56118630	WI-38	lung:	n/a	n/a
4	POLR2A	chr12:56116371-56118897	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:56118242-56118740	HCT-116	colon:	n/a	n/a
6	POLR2A	chr12:56116320-56119253	ProgFib	skin:	n/a	n/a
7	CTCF	chr12:56118464-56118717	Pancreas_OC	pancreas:	n/a	n/a
8	CTCF	chr12:56118293-56118841	K562	blood:	n/a	n/a
9	CTCF	chr12:56118520-56118670	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:56117999-56118767	HUVEC	blood vessel:	n/a	n/a
11	BCL3	chr12:56117805-56118681	A549	lung:	n/a	n/a
12	CTCF	chr12:56118500-56118650	HEK293	kidney:	n/a	n/a
13	CTCF	chr12:56118395-56118753	K562	blood:	n/a	n/a
14	RFX5	chr12:56118486-56118734	Hela-S3	cervix:	n/a	n/a
15	PML	chr12:56117788-56118988	K562	blood:	n/a	n/a
16	POLR2A	chr12:56118407-56118658	GM12878	blood:	n/a	n/a
17	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
18	CTCF	chr12:56118461-56118690	GM10248	blood:	n/a	n/a
19	CTCF	chr12:56118460-56118610	GM12868	blood:	n/a	n/a
20	PML	chr12:56117944-56118934	GM12878	blood:	n/a	n/a
21	CTCF	chr12:56118500-56118650	GM12864	blood:	n/a	n/a
22	POLR2A	chr12:56117447-56118801	GM12891	blood:	n/a	n/a
23	CTCF	chr12:56118500-56118650	HCT-116	colon:	n/a	n/a
24	POLR2A	chr12:56116248-56119994	A549	lung:	n/a	n/a
25	POLR2A	chr12:56117422-56118720	Hela-S3	cervix:	n/a	n/a
26	YY1	chr12:56118430-56118712	GM12892	blood:	n/a	n/a
27	CTCF	chr12:56118204-56118996	HCT-116	colon:	n/a	n/a
28	CTCF	chr12:56118500-56118650	HBMEC	blood vessel:	n/a	n/a
29	ZNF143	chr12:56118430-56118759	Hela-S3	cervix:	n/a	chr12:56118650-56118659
30	CTCF	chr12:56118460-56118699	MCF-7	breast:	n/a	n/a
31	SMC3	chr12:56118119-56119205	SK-N-SH	brain:	n/a	n/a
32	RAD21	chr12:56118402-56118765	IMR90	lung:	n/a	n/a
33	CTCF	chr12:56118460-56118610	HA-sp	spinal cord:	n/a	n/a
34	USF2	chr12:56118481-56118701	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr12:56118459-56118733	H1-hESC	embryonic stem cell:	n/a	n/a
36	SMC3	chr12:56118413-56118768	K562	blood:	n/a	n/a
37	POLR2A	chr12:56117328-56118733	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr12:56118304-56118791	MCF-7	breast:	n/a	n/a
39	CTCF	chr12:56118460-56118610	GM12869	blood:	n/a	n/a
40	CTCF	chr12:56118440-56118590	GM12868	blood:	n/a	n/a
41	CTCF	chr12:56118405-56118762	IMR90	lung:	n/a	n/a
42	CTCF	chr12:56118458-56118703	A549	lung:	n/a	n/a
43	RAD21	chr12:56118282-56118895	A549	lung:	n/a	n/a
44	CTCF	chr12:56118500-56118650	HL-60	blood:	n/a	n/a
45	SPI1	chr12:56118384-56118870	HL-60	blood:	n/a	n/a
46	YY1	chr12:56118389-56118727	GM12878	blood:	n/a	n/a
47	CTCF	chr12:56118500-56118650	AG09319	gingival:	n/a	n/a
48	CTCF	chr12:56118500-56118650	AG04450	lung:	n/a	n/a
49	MXI1	chr12:56118415-56118612	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr12:56118386-56118755	SK-N-SH_RA	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56118524-56118574	HCF	heart:	n/a
2	chr12:56118524-56118574	BJ	skin:	n/a
3	chr12:56118524-56118574	SKMC	muscle:	n/a
4	chr12:56118524-56118574	MCF-7	breast:	n/a
5	chr12:56118524-56118574	Caco-2	colon:	n/a
6	chr12:56118524-56118574	RPTEC	kidney:	n/a
7	chr12:56118524-56118574	SK-N-MC	brain:	n/a
8	chr12:56118524-56118574	PFSK-1	brain:	n/a
9	chr12:56118524-56118574	H1-hESC	embryonic stem cell:	embryo
10	chr12:56118524-56118574	AG04449	skin:	fetal
11	chr12:56118524-56118574	GM12891	blood:	n/a
12	chr12:56118524-56118574	AG09319	gingival:	n/a
13	chr12:56118524-56118574	PrEC	prostate:	n/a
14	chr12:56118524-56118574	HNPCEpiC	eye:	n/a
15	chr12:56118524-56118574	U87	brain:	n/a
16	chr12:56118524-56118574	NHBE	bronchial:	n/a
17	chr12:56118524-56118574	HRPEpiC	eye:	n/a
18	chr12:56118524-56118574	ECC-1	luminal epithelium:	n/a
19	chr12:56118524-56118574	HPAEpiC	pulmonary alveolar:	n/a
20	chr12:56118524-56118574	LNCaP	prostate:	n/a
21	chr12:56118524-56118574	AoSMC	blood vessel:	n/a
22	chr12:56118524-56118574	HCM	heart:	n/a
23	chr12:56118524-56118574	HEEpiC	esophagus:	n/a
24	chr12:56118524-56118574	HL-60	blood:	n/a
25	chr12:56118524-56118574	HCT-116	colon:	n/a
26	chr12:56118524-56118574	T-47D	breast:	n/a
27	chr12:56118524-56118574	IMR90	lung:	fetal
28	chr12:56118524-56118574	HCPEpiC	choroid plexus:	n/a
29	chr12:56118524-56118574	SK-N-SH_RA	brain:	n/a
30	chr12:56118524-56118574	HepG2	liver:	n/a
31	chr12:56118524-56118574	HMEC	breast:	n/a
32	chr12:56118524-56118574	HAEpiC	amniotic membrane:	n/a
33	chr12:56118524-56118574	BE2_C	brain:	n/a
34	chr12:56118524-56118574	MCF10A-Er-Src	breast:	n/a
35	chr12:56118524-56118574	Jurkat	blood:	n/a
36	chr12:56118524-56118574	NHDF-neo	bronchial:	n/a
37	chr12:56118524-56118574	HRCEpiC	kidney:	n/a
38	chr12:56118524-56118574	SAEC	small airway:	n/a
39	chr12:56118524-56118574	NB4	blood:	n/a
40	chr12:56118524-56118574	AG04450	lung:	fetal
41	chr12:56118524-56118574	NT2-D1	testis:	n/a
42	chr12:56118524-56118574	GM12878	blood:	n/a
43	chr12:56118524-56118574	Hela-S3	cervix:	n/a
44	chr12:56118524-56118574	PANC-1	pancreas:	n/a
45	chr12:56118524-56118574	CMK	blood:	n/a
46	chr12:56118524-56118574	GM06990	blood:	n/a
47	chr12:56118524-56118574	HUVEC	blood vessel:	n/a
48	chr12:56118524-56118574	SK-N-SH	brain:	n/a
49	chr12:56118524-56118574	NH-A	brain:	n/a
50	chr12:56118524-56118574	GM12892	blood:	n/a

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56118429..56118954-chr12:56190727..56191514,2	K562	blood:
2	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
3	chr12:56110479..56111014-chr12:56118069..56118640,2	K562	blood:
4	chr12:56118075..56119434-chr12:56130540..56132004,12	MCF-7	breast:
5	chr12:56037529..56040108-chr12:56117252..56119317,2	K562	blood:
6	chr12:56088490..56090282-chr12:56117395..56118988,2	MCF-7	breast:
7	chr12:56118355..56119078-chr12:56130717..56131614,5	K562	blood:
8	chr12:56075054..56077566-chr12:56115620..56119645,3	MCF-7	breast:
9	chr12:56118190..56119080-chr12:56130780..56131563,6	MCF-7	breast:
10	chr12:56117825..56119634-chr17:57178406..57181247,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258056	TF binding region
ENSG00000258056	CpG island
ENSG00000170439	Chromatin interaction
ENSG00000135424	Chromatin interaction
ENSG00000135414	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv559005	chr12:56117570-56120934	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56111200-56120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:56112600-56118800	Weak transcription	Small Intestine	intestine
3	chr12:56112800-56120800	Weak transcription	Fetal Brain Male	brain
4	chr12:56112800-56121000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:56113200-56118600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:56113200-56120000	Strong transcription	Brain Germinal Matrix	brain
7	chr12:56113200-56120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:56114200-56118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr12:56114400-56118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:56114400-56121000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:56115000-56118600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:56115000-56118600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr12:56115000-56120400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:56115400-56118600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:56115400-56120400	Genic enhancers	Fetal Intestine Large	intestine
16	chr12:56115400-56120400	Strong transcription	Fetal Stomach	stomach
17	chr12:56115400-56120600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:56115400-56121000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:56115400-56121200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:56115600-56120400	Strong transcription	Lung	lung
21	chr12:56115600-56120600	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr12:56115600-56120800	Genic enhancers	Fetal Muscle Leg	muscle
23	chr12:56116000-56120600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:56116200-56118600	Strong transcription	NHEK	skin
25	chr12:56116200-56120400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:56116400-56120400	Genic enhancers	Fetal Intestine Small	intestine
27	chr12:56116600-56118600	Strong transcription	Brain Anterior Caudate	brain
28	chr12:56116600-56119400	Genic enhancers	Right Ventricle	heart
29	chr12:56116600-56119600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:56116600-56120200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:56116600-56120400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:56116600-56120400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:56116600-56120400	Genic enhancers	Adipose Nuclei	Adipose
34	chr12:56116600-56120400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr12:56116600-56120600	Genic enhancers	Rectal Mucosa Donor 29	rectum
36	chr12:56116600-56120800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr12:56116600-56121800	Transcr. at gene 5' and 3'	HSMM	muscle
38	chr12:56116600-56122200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:56116800-56118600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:56116800-56118600	Strong transcription	Fetal Brain Female	brain
41	chr12:56116800-56119000	Genic enhancers	NHDF-Ad	bronchial
42	chr12:56116800-56119000	Genic enhancers	Osteobl	bone
43	chr12:56116800-56119200	Genic enhancers	Fetal Thymus	thymus
44	chr12:56116800-56119600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:56116800-56119600	Genic enhancers	Colonic Mucosa	Colon
46	chr12:56116800-56120400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56116800-56120600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:56116800-56120600	Genic enhancers	A549	lung
49	chr12:56116800-56120800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:56116800-56120800	Strong transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links