Variant report

Variant	rs554817253
Chromosome Location	chr12:58147914-58147915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr12:58147642-58147977	K562	blood:	n/a	n/a
2	POLR2A	chr12:58147697-58147952	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:58147339-58147964	HepG2	liver:	n/a	n/a
4	NRF1	chr12:58147820-58148990	SK-N-SH	brain:	n/a	n/a
5	TBL1XR1	chr12:58147454-58148074	K562	blood:	n/a	n/a
6	MAFK	chr12:58147711-58147930	K562	blood:	n/a	n/a
7	TAL1	chr12:58147576-58147959	K562	blood:	n/a	chr12:58147658-58147667

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58147888-58147938	T-47D	breast:	n/a
2	chr12:58147888-58147938	ovcar-3	ovarian:	n/a
3	chr12:58147888-58147938	HepG2	liver:	n/a
4	chr12:58147888-58147938	BJ	skin:	n/a
5	chr12:58147888-58147938	RPTEC	kidney:	n/a
6	chr12:58147888-58147938	HCT-116	colon:	n/a
7	chr12:58147888-58147938	Jurkat	blood:	n/a
8	chr12:58147888-58147938	SK-N-MC	brain:	n/a
9	chr12:58147888-58147938	SK-N-SH	brain:	n/a
10	chr12:58147888-58147938	AoSMC	blood vessel:	n/a
11	chr12:58147888-58147938	BE2_C	brain:	n/a
12	chr12:58147888-58147938	PFSK-1	brain:	n/a
13	chr12:58147888-58147938	MCF-7	breast:	n/a
14	chr12:58147888-58147938	NHDF-neo	bronchial:	n/a
15	chr12:58147888-58147938	AG04450	lung:	fetal
16	chr12:58147888-58147938	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:58147888-58147938	AG09309	skin:	n/a
18	chr12:58147888-58147938	K562	blood:	n/a
19	chr12:58147888-58147938	PANC-1	pancreas:	n/a
20	chr12:58147888-58147938	Caco-2	colon:	n/a
21	chr12:58147888-58147938	HCPEpiC	choroid plexus:	n/a
22	chr12:58147888-58147938	GM12891	blood:	n/a
23	chr12:58147888-58147938	HRCEpiC	kidney:	n/a
24	chr12:58147888-58147938	ProgFib	skin:	n/a
25	chr12:58147888-58147938	Hela-S3	cervix:	n/a
26	chr12:58147888-58147938	HRPEpiC	eye:	n/a
27	chr12:58147888-58147938	HL-60	blood:	n/a
28	chr12:58147888-58147938	NH-A	brain:	n/a
29	chr12:58147888-58147938	NB4	blood:	n/a
30	chr12:58147888-58147938	AG09319	gingival:	n/a
31	chr12:58147888-58147938	SAEC	small airway:	n/a
32	chr12:58147888-58147938	SK-N-SH_RA	brain:	n/a
33	chr12:58147888-58147938	GM06990	blood:	n/a
34	chr12:58147888-58147938	HNPCEpiC	eye:	n/a
35	chr12:58147888-58147938	ECC-1	luminal epithelium:	n/a
36	chr12:58147888-58147938	HEK293	kidney:	embryo
37	chr12:58147888-58147938	LNCaP	prostate:	n/a
38	chr12:58147888-58147938	HAEpiC	amniotic membrane:	n/a
39	chr12:58147888-58147938	PrEC	prostate:	n/a
40	chr12:58147888-58147938	A549	lung:	n/a
41	chr12:58147888-58147938	HIPEpiC	eye:	n/a
42	chr12:58147888-58147938	IMR90	lung:	fetal
43	chr12:58147888-58147938	GM12892	blood:	n/a
44	chr12:58147888-58147938	AG10803	skin:	n/a
45	chr12:58147888-58147938	HCF	heart:	n/a
46	chr12:58147888-58147938	NT2-D1	testis:	n/a
47	chr12:58147888-58147938	CMK	blood:	n/a
48	chr12:58147888-58147938	SKMC	muscle:	n/a
49	chr12:58147888-58147938	HMEC	breast:	n/a
50	chr12:58147888-58147938	HUVEC	blood vessel:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58003234..58004876-chr12:58145695..58148256,2	K562	blood:
2	chr12:57914860..57917603-chr12:58144909..58148802,3	K562	blood:
3	chr12:58146971..58149952-chr17:56735164..56736689,2	MCF-7	breast:
4	chr12:57912818..57918945-chr12:58145879..58149998,6	MCF-7	breast:
5	chr12:58144944..58148202-chr12:58236897..58241575,4	MCF-7	breast:
6	chr12:58146595..58149356-chr12:58175469..58178051,2	K562	blood:
7	chr12:58147914..58149817-chr12:124454309..124457254,2	MCF-7	breast:
8	chr12:58144058..58148099-chr12:58238749..58241436,3	K562	blood:
9	chr12:57909291..57914221-chr12:58144639..58148673,6	K562	blood:

No data

Variant related genes	Relation type
MARCH9	TF binding region
CDK4	TF binding region
CDK4	CpG island
MARCH9	CpG island
ENSG00000240771	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000119242	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000270061	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000179195	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription 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 miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	esv3374332	chr12:58147710-58151058	Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58146200-58148000	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr12:58146200-58148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:58146200-58148200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:58146200-58148200	Weak transcription	Lung	lung
5	chr12:58146200-58148400	Weak transcription	Small Intestine	intestine
6	chr12:58146200-58148600	Weak transcription	Aorta	Aorta
7	chr12:58146400-58148200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:58146400-58148800	Flanking Active TSS	K562	blood
9	chr12:58146600-58148200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr12:58146600-58148200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:58146600-58148200	Weak transcription	Esophagus	oesophagus
12	chr12:58146600-58148200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:58146600-58148200	Weak transcription	Gastric	stomach
14	chr12:58146600-58148200	Weak transcription	Left Ventricle	heart
15	chr12:58146600-58148200	Weak transcription	Spleen	Spleen
16	chr12:58146600-58148400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:58146600-58148400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:58146800-58148000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:58146800-58148000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr12:58146800-58148000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:58146800-58148000	Enhancers	Primary T cells from cord blood	blood
22	chr12:58146800-58148000	Enhancers	Hela-S3	cervix
23	chr12:58146800-58148200	Enhancers	Primary B cells from cord blood	blood
24	chr12:58146800-58148200	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:58146800-58148200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:58146800-58148200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:58146800-58148200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:58146800-58148200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr12:58146800-58148200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr12:58146800-58148200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:58146800-58148200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:58146800-58148200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:58146800-58148200	Weak transcription	Brain Substantia Nigra	brain
34	chr12:58146800-58148200	Weak transcription	Colonic Mucosa	Colon
35	chr12:58146800-58148200	Enhancers	Fetal Intestine Large	intestine
36	chr12:58146800-58148200	Enhancers	Fetal Stomach	stomach
37	chr12:58146800-58148200	Enhancers	Fetal Thymus	thymus
38	chr12:58146800-58148200	Weak transcription	Psoas Muscle	Psoas
39	chr12:58146800-58148200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr12:58146800-58148200	Weak transcription	Right Atrium	heart
41	chr12:58146800-58148200	Enhancers	Thymus	Thymus
42	chr12:58146800-58148200	Enhancers	HMEC	breast
43	chr12:58146800-58148400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:58146800-58148400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:58146800-58148400	Weak transcription	Ovary	ovary
46	chr12:58147000-58148000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:58147000-58148000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:58147000-58148000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:58147000-58148000	Weak transcription	Liver	Liver
50	chr12:58147000-58148000	Weak transcription	Brain Angular Gyrus	brain

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