Variant report

Variant	rs544986899
Chromosome Location	chr12:4386208-4386209
allele	A/G
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	POLR2A	chr12:4378383-4393977	GM12878	blood:	n/a	n/a
2	FOXP2	chr12:4386146-4386461	SK-N-MC	brain:	n/a	n/a
3	CTCF	chr12:4386163-4386434	LNCaP	prostate:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
4	CTCF	chr12:4386085-4386478	ECC-1	luminal epithelium:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
5	POLR2A	chr12:4385965-4389349	MCF10A-Er-Src	breast:	n/a	n/a
6	GTF2F1	chr12:4386115-4386426	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZEB1	chr12:4385989-4386461	GM12878	blood:	n/a	n/a
8	BCL11A	chr12:4386092-4386361	GM12878	blood:	n/a	n/a
9	MAX	chr12:4386170-4386423	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr12:4385862-4386526	GM12878	blood:	n/a	chr12:4386279-4386293
11	JUND	chr12:4386149-4386480	HepG2	liver:	n/a	n/a
12	CTCF	chr12:4386170-4386416	MCF-7	breast:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
13	POLR2A	chr12:4385944-4386661	K562	blood:	n/a	n/a
14	FOXA2	chr12:4386017-4386492	A549	lung:	n/a	n/a
15	POLR2A	chr12:4382575-4386671	PFSK-1	brain:	n/a	n/a
16	TEAD4	chr12:4385923-4386625	SK-N-SH	brain:	n/a	n/a
17	GTF2F1	chr12:4386150-4386445	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr12:4386200-4386350	AG09309	skin:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
19	CTCF	chr12:4386200-4386350	GM12872	blood:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
20	RAD21	chr12:4385940-4386505	Hela-S3	cervix:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
21	FOXM1	chr12:4385850-4386559	GM12878	blood:	n/a	n/a
22	EP300	chr12:4386191-4386389	HepG2	liver:	n/a	n/a
23	YY1	chr12:4386074-4386408	GM12891	blood:	n/a	n/a
24	YY1	chr12:4386034-4386434	GM12878	blood:	n/a	n/a
25	CHD2	chr12:4385973-4386429	HepG2	liver:	n/a	n/a
26	ZNF143	chr12:4385980-4386469	K562	blood:	n/a	n/a
27	RFX5	chr12:4386171-4386471	H1-hESC	embryonic stem cell:	n/a	n/a
28	TEAD4	chr12:4386052-4386505	K562	blood:	n/a	n/a
29	CTCF	chr12:4386143-4386443	NHEK	skin:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
30	CHD1	chr12:4386026-4386439	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr12:4386118-4386534	MCF-7	breast:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
32	EP300	chr12:4386050-4386441	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr12:4386050-4386597	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
34	CTCF	chr12:4385988-4386611	MCF-7	breast:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
35	RAD21	chr12:4386062-4386455	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
36	CTCF	chr12:4386200-4386350	HVMF	connective:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
37	STAT1	chr12:4385975-4386559	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:4385697-4406476	GM12892	blood:	n/a	n/a
39	STAT5A	chr12:4385848-4386487	GM12878	blood:	n/a	n/a
40	SMC3	chr12:4385702-4386630	SK-N-SH	brain:	n/a	chr12:4386279-4386293
41	MXI1	chr12:4385784-4386526	GM12878	blood:	n/a	n/a
42	EP300	chr12:4385893-4386446	K562	blood:	n/a	n/a
43	STAT3	chr12:4386186-4386386	MCF10A-Er-Src	breast:	n/a	n/a
44	EP300	chr12:4386059-4386488	HepG2	liver:	n/a	n/a
45	JUND	chr12:4386100-4386583	H1-hESC	embryonic stem cell:	n/a	n/a
46	TEAD4	chr12:4385978-4386537	HCT-116	colon:	n/a	n/a
47	YY1	chr12:4386004-4386449	GM12878	blood:	n/a	n/a
48	RAD21	chr12:4385947-4386596	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
49	CTCF	chr12:4386170-4386410	HepG2	liver:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
50	RAD21	chr12:4385980-4386531	HCT-116	colon:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:4386203-4386253	CMK	blood:	n/a
2	chr12:4386203-4386253	NHBE	bronchial:	n/a
3	chr12:4386203-4386253	AG10803	skin:	n/a
4	chr12:4386203-4386253	HCT-116	colon:	n/a
5	chr12:4386203-4386253	BJ	skin:	n/a
6	chr12:4386203-4386253	ProgFib	skin:	n/a
7	chr12:4386203-4386253	HCPEpiC	choroid plexus:	n/a
8	chr12:4386203-4386253	GM19239	blood:	n/a
9	chr12:4386203-4386253	SKMC	muscle:	n/a
10	chr12:4386203-4386253	NHDF-neo	bronchial:	n/a
11	chr12:4386203-4386253	SK-N-SH	brain:	n/a
12	chr12:4386203-4386253	HEK293	kidney:	embryo
13	chr12:4386203-4386253	Caco-2	colon:	n/a
14	chr12:4386203-4386253	GM12878	blood:	n/a
15	chr12:4386203-4386253	HEEpiC	esophagus:	n/a
16	chr12:4386203-4386253	PFSK-1	brain:	n/a
17	chr12:4386203-4386253	AG09319	gingival:	n/a
18	chr12:4386203-4386253	HAEpiC	amniotic membrane:	n/a
19	chr12:4386203-4386253	HMEC	breast:	n/a
20	chr12:4386203-4386253	ECC-1	luminal epithelium:	n/a
21	chr12:4386203-4386253	Jurkat	blood:	n/a
22	chr12:4386203-4386253	HPAEpiC	pulmonary alveolar:	n/a
23	chr12:4386203-4386253	PANC-1	pancreas:	n/a
24	chr12:4386203-4386253	HNPCEpiC	eye:	n/a
25	chr12:4386203-4386253	SAEC	small airway:	n/a
26	chr12:4386203-4386253	H1-hESC	embryonic stem cell:	embryo
27	chr12:4386203-4386253	BE2_C	brain:	n/a
28	chr12:4386203-4386253	IMR90	lung:	fetal
29	chr12:4386203-4386253	NB4	blood:	n/a
30	chr12:4386203-4386253	HRCEpiC	kidney:	n/a
31	chr12:4386203-4386253	GM12892	blood:	n/a
32	chr12:4386203-4386253	NH-A	brain:	n/a
33	chr12:4386203-4386253	U87	brain:	n/a
34	chr12:4386203-4386253	SK-N-MC	brain:	n/a
35	chr12:4386203-4386253	GM06990	blood:	n/a
36	chr12:4386203-4386253	K562	blood:	n/a
37	chr12:4386203-4386253	A549	lung:	n/a
38	chr12:4386203-4386253	HIPEpiC	eye:	n/a
39	chr12:4386203-4386253	HepG2	liver:	n/a
40	chr12:4386203-4386253	ovcar-3	ovarian:	n/a
41	chr12:4386203-4386253	HRE	kidney:	n/a
42	chr12:4386203-4386253	T-47D	breast:	n/a
43	chr12:4386203-4386253	RPTEC	kidney:	n/a
44	chr12:4386203-4386253	Hepatocyte	liver:	n/a
45	chr12:4386203-4386253	LNCaP	prostate:	n/a
46	chr12:4386203-4386253	AoSMC	blood vessel:	n/a
47	chr12:4386203-4386253	HCF	heart:	n/a
48	chr12:4386203-4386253	HRPEpiC	eye:	n/a
49	chr12:4386203-4386253	Hela-S3	cervix:	n/a
50	chr12:4386203-4386253	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:3994703..3995335-chr12:4385793..4386765,3	MCF-7	breast:
2	chr12:4216455..4217156-chr12:4385829..4386409,2	MCF-7	breast:
3	chr12:4216482..4217070-chr12:4385866..4386804,2	NB4	blood:
4	chr12:4104755..4105582-chr12:4385820..4386626,2	K562	blood:
5	chr12:4216655..4217210-chr12:4385805..4386330,2	K562	blood:
6	chr12:3992395..3993001-chr12:4385802..4386611,2	MCF-7	breast:
7	chr12:4104787..4105607-chr12:4385997..4386676,2	MCF-7	breast:

Variant related genes	Relation type
CCND2-AS1	TF binding region
CCND2	TF binding region
CCND2-AS2	TF binding region
CCND2	CpG island
CCND2-AS2	CpG island
CCND2-AS1	CpG island

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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541360	chr12:4338851-4389238	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv541361	chr12:4362258-4413849	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv275173	chr12:4385592-4386221	Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4382000-4388000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:4383600-4386400	Active TSS	Brain Angular Gyrus	brain
3	chr12:4384400-4388000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
4	chr12:4384400-4390600	Weak transcription	Gastric	stomach
5	chr12:4384600-4387000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
6	chr12:4384800-4386600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:4384800-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
8	chr12:4384800-4388200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr12:4385000-4386600	Transcr. at gene 5' and 3'	NHEK	skin
10	chr12:4385000-4387000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:4385000-4390000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
12	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
13	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
14	chr12:4385200-4386600	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
17	chr12:4385200-4386600	Transcr. at gene 5' and 3'	HMEC	breast
18	chr12:4385200-4386800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
19	chr12:4385200-4386800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
20	chr12:4385200-4387000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
21	chr12:4385200-4388200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
22	chr12:4385200-4388400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:4385200-4390800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:4385200-4390800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
25	chr12:4385200-4391000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
26	chr12:4385400-4386400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:4385400-4386400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:4385400-4386600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
29	chr12:4385400-4386600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
30	chr12:4385400-4386600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
31	chr12:4385400-4386600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:4385400-4386600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
33	chr12:4385400-4386600	Bivalent Enhancer	Stomach Mucosa	stomach
34	chr12:4385400-4386600	Bivalent Enhancer	NH-A	brain
35	chr12:4385400-4386800	Weak transcription	Esophagus	oesophagus
36	chr12:4385400-4386800	Bivalent Enhancer	HepG2	liver
37	chr12:4385400-4387200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
38	chr12:4385400-4388800	Genic enhancers	Primary hematopoietic stem cells	blood
39	chr12:4385400-4400000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
40	chr12:4385400-4404400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
41	chr12:4385600-4386400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:4385600-4386600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:4385600-4386600	Transcr. at gene 5' and 3'	HSMMtube	muscle
44	chr12:4385600-4387200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr12:4385600-4387200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:4385600-4387600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:4385600-4387800	Genic enhancers	Left Ventricle	heart
48	chr12:4385600-4388200	Enhancers	Adipose Nuclei	Adipose
49	chr12:4385600-4388200	Enhancers	Brain Anterior Caudate	brain
50	chr12:4385600-4389400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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