Variant report

Variant	rs566746200
Chromosome Location	chr12:58133412-58133413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:58133328-58133528	K562	blood:	n/a	n/a
2	RFX5	chr12:58132334-58133513	SK-N-SH	brain:	n/a	chr12:58133399-58133413 chr12:58133395-58133412 chr12:58133396-58133411 chr12:58133401-58133410 chr12:58133396-58133411 chr12:58133396-58133411

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:58133411-58133461	HMEC	breast:	n/a
2	chr12:58133411-58133461	U87	brain:	n/a
3	chr12:58133411-58133461	ProgFib	skin:	n/a
4	chr12:58133411-58133461	SK-N-SH	brain:	n/a
5	chr12:58133411-58133461	NHDF-neo	bronchial:	n/a
6	chr12:58133411-58133461	AG10803	skin:	n/a
7	chr12:58133411-58133461	BE2_C	brain:	n/a
8	chr12:58133411-58133461	A549	lung:	n/a
9	chr12:58133411-58133461	SK-N-SH_RA	brain:	n/a
10	chr12:58133411-58133461	HIPEpiC	eye:	n/a
11	chr12:58133411-58133461	K562	blood:	n/a
12	chr12:58133411-58133461	HCM	heart:	n/a
13	chr12:58133411-58133461	RPTEC	kidney:	n/a
14	chr12:58133411-58133461	HPAEpiC	pulmonary alveolar:	n/a
15	chr12:58133411-58133461	GM06990	blood:	n/a
16	chr12:58133411-58133461	GM19239	blood:	n/a
17	chr12:58133411-58133461	MCF-7	breast:	n/a
18	chr12:58133411-58133461	PrEC	prostate:	n/a
19	chr12:58133411-58133461	CMK	blood:	n/a
20	chr12:58133411-58133461	HRCEpiC	kidney:	n/a
21	chr12:58133411-58133461	HUVEC	blood vessel:	n/a
22	chr12:58133411-58133461	AG09319	gingival:	n/a
23	chr12:58133411-58133461	Jurkat	blood:	n/a
24	chr12:58133411-58133461	BJ	skin:	n/a
25	chr12:58133411-58133461	ovcar-3	ovarian:	n/a
26	chr12:58133411-58133461	SKMC	muscle:	n/a
27	chr12:58133411-58133461	HNPCEpiC	eye:	n/a
28	chr12:58133411-58133461	AoSMC	blood vessel:	n/a
29	chr12:58133411-58133461	GM12878	blood:	n/a
30	chr12:58133411-58133461	Hepatocyte	liver:	n/a
31	chr12:58133411-58133461	MCF10A-Er-Src	breast:	n/a
32	chr12:58133411-58133461	HCF	heart:	n/a
33	chr12:58133411-58133461	AG04449	skin:	fetal
34	chr12:58133411-58133461	PANC-1	pancreas:	n/a
35	chr12:58133411-58133461	HepG2	liver:	n/a
36	chr12:58133411-58133461	AG04450	lung:	fetal
37	chr12:58133411-58133461	IMR90	lung:	fetal
38	chr12:58133411-58133461	GM12891	blood:	n/a
39	chr12:58133411-58133461	HEK293	kidney:	embryo
40	chr12:58133411-58133461	HL-60	blood:	n/a
41	chr12:58133411-58133461	ECC-1	luminal epithelium:	n/a
42	chr12:58133411-58133461	HAEpiC	amniotic membrane:	n/a
43	chr12:58133411-58133461	HCT-116	colon:	n/a
44	chr12:58133411-58133461	SK-N-MC	brain:	n/a
45	chr12:58133411-58133461	Hela-S3	cervix:	n/a
46	chr12:58133411-58133461	GM12892	blood:	n/a
47	chr12:58133411-58133461	HCPEpiC	choroid plexus:	n/a
48	chr12:58133411-58133461	NT2-D1	testis:	n/a
49	chr12:58133411-58133461	NH-A	brain:	n/a
50	chr12:58133411-58133461	HRE	kidney:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57914271..57916098-chr12:58131440..58134732,4	K562	blood:
2	chr12:57916381..57918711-chr12:58131475..58134282,2	MCF-7	breast:
3	chr12:57911286..57913384-chr12:58133067..58135116,2	K562	blood:
4	chr12:58133058..58135797-chr12:58239105..58241667,3	MCF-7	breast:
5	chr12:57909973..57915898-chr12:58127755..58134567,15	K562	blood:

No data

Variant related genes	Relation type
TSPAN31	TF binding region
AGAP2	TF binding region
TSPAN31	CpG island
AGAP2	CpG island
ENSG00000175197	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv899122	chr12:58118248-58137563	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv3363572	chr12:58129335-58133633	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
10	nsv826385	chr12:58129908-58133427	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	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
12	esv3408774	chr12:58130710-58133658	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
13	esv3429081	chr12:58131185-58133683	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
14	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

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58127800-58133600	Weak transcription	GM12878-XiMat	blood
2	chr12:58130200-58134200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:58131200-58133600	Active TSS	Brain Angular Gyrus	brain
4	chr12:58131200-58134400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:58131200-58138000	Weak transcription	K562	blood
6	chr12:58131600-58133600	Bivalent/Poised TSS	Left Ventricle	heart
7	chr12:58131600-58134600	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:58131800-58138000	Weak transcription	Lung	lung
9	chr12:58132000-58134800	Weak transcription	Spleen	Spleen
10	chr12:58132200-58138800	Weak transcription	Gastric	stomach
11	chr12:58132400-58133600	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr12:58132400-58133600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:58132400-58133800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr12:58132400-58134200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr12:58132400-58134400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:58132600-58133600	Enhancers	Primary B cells from cord blood	blood
17	chr12:58132600-58133600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:58132600-58133600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:58132600-58134200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:58132600-58134200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:58132800-58133600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:58132800-58133600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:58132800-58133600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr12:58132800-58133800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:58132800-58133800	Bivalent Enhancer	Fetal Brain Male	brain
26	chr12:58132800-58133800	Genic enhancers	Thymus	Thymus
27	chr12:58132800-58133800	Genic enhancers	Dnd41	blood
28	chr12:58132800-58134000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
29	chr12:58132800-58134000	Bivalent Enhancer	Fetal Stomach	stomach
30	chr12:58132800-58134600	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr12:58133000-58133600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:58133000-58133600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
33	chr12:58133000-58133600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:58133000-58133600	Genic enhancers	Fetal Thymus	thymus
35	chr12:58133000-58133800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:58133000-58133800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:58133000-58134000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr12:58133000-58134000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:58133000-58134000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr12:58133000-58134200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:58133000-58134400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr12:58133200-58133600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr12:58133200-58133600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
44	chr12:58133200-58133600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
45	chr12:58133200-58133600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
46	chr12:58133200-58133600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
47	chr12:58133200-58133600	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
48	chr12:58133200-58133600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr12:58133200-58133800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
50	chr12:58133200-58133800	Bivalent Enhancer	Fetal Brain Female	brain

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