Variant report

Variant	rs558340404
Chromosome Location	chr12:63546069-63546070
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	CTCF	chr12:63545920-63546070	HCM	heart:	n/a	chr12:63546025-63546038
2	CTCF	chr12:63545901-63546144	GM13977	blood:	n/a	chr12:63546025-63546038
3	CTCF	chr12:63545836-63546178	ECC-1	luminal epithelium:	n/a	chr12:63546025-63546038
4	CTCF	chr12:63545940-63546090	HCPEpiC	choroid plexus:	n/a	chr12:63546025-63546038
5	GATA3	chr12:63545841-63546175	T-47D	breast:	n/a	n/a
6	CTCF	chr12:63545940-63546090	GM12868	blood:	n/a	chr12:63546025-63546038
7	CTCF	chr12:63545940-63546090	HMEC	breast:	n/a	chr12:63546025-63546038
8	RAD21	chr12:63545775-63546288	MCF-7	breast:	n/a	n/a
9	CTCF	chr12:63545897-63546166	K562	blood:	n/a	chr12:63546025-63546038
10	CTCF	chr12:63545855-63546174	MCF-7	breast:	n/a	chr12:63546025-63546038
11	ELF1	chr12:63545892-63546140	K562	blood:	n/a	n/a
12	CTCF	chr12:63545980-63546130	HEEpiC	esophagus:	n/a	chr12:63546025-63546038
13	CTCF	chr12:63545960-63546110	AG09319	gingival:	n/a	chr12:63546025-63546038
14	CTCF	chr12:63545960-63546110	RPTEC	kidney:	n/a	chr12:63546025-63546038
15	CTCF	chr12:63545885-63546127	SK-N-SH_RA	brain:	n/a	chr12:63546025-63546038
16	CTCF	chr12:63545960-63546110	AoAF	blood vessel:	n/a	chr12:63546025-63546038
17	CTCF	chr12:63545980-63546130	HPAF	blood vessel:	n/a	chr12:63546025-63546038
18	CTCF	chr12:63545980-63546130	HUVEC	blood vessel:	n/a	chr12:63546025-63546038
19	CTCF	chr12:63545980-63546130	BJ	skin:	n/a	chr12:63546025-63546038
20	CTCF	chr12:63545940-63546090	Caco-2	colon:	n/a	chr12:63546025-63546038
21	CTCF	chr12:63545960-63546110	HEEpiC	esophagus:	n/a	chr12:63546025-63546038
22	RAD21	chr12:63545975-63546077	K562	blood:	n/a	n/a
23	RAD21	chr12:63545717-63546386	MCF-7	breast:	n/a	chr12:63546321-63546335
24	RAD21	chr12:63545912-63546095	GM12878	blood:	n/a	n/a
25	CTCF	chr12:63545980-63546130	HepG2	liver:	n/a	chr12:63546025-63546038
26	RAD21	chr12:63545935-63546174	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr12:63545940-63546090	GM12874	blood:	n/a	chr12:63546025-63546038
28	CTCF	chr12:63545960-63546110	GM12871	blood:	n/a	chr12:63546025-63546038
29	CTCF	chr12:63545940-63546090	HEK293	kidney:	n/a	chr12:63546025-63546038
30	CTCF	chr12:63545853-63546126	K562	blood:	n/a	chr12:63546025-63546038
31	CTCF	chr12:63545903-63546126	Spleen_OC	spleen:	n/a	chr12:63546025-63546038
32	CTCF	chr12:63545940-63546090	HAc	cerebellar:	n/a	chr12:63546025-63546038
33	CTCF	chr12:63545621-63546650	A549	lung:	n/a	chr12:63546025-63546038
34	CTCF	chr12:63545960-63546110	Hela-S3	cervix:	n/a	chr12:63546025-63546038
35	SIN3A	chr12:63543863-63546155	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr12:63545826-63546202	A549	lung:	n/a	chr12:63546025-63546038
37	CTCF	chr12:63545869-63546174	Medullo	brain:	n/a	chr12:63546025-63546038
38	TCF12	chr12:63545776-63546083	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr12:63545822-63546238	HepG2	liver:	n/a	n/a
40	CTCF	chr12:63545940-63546090	NHDF-neo	bronchial:	n/a	chr12:63546025-63546038
41	RAD21	chr12:63545837-63546214	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr12:63545719-63546276	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr12:63545726-63546285	ECC-1	luminal epithelium:	n/a	n/a
44	CTCF	chr12:63545940-63546090	HCFaa	heart:	n/a	chr12:63546025-63546038
45	CTCF	chr12:63545908-63546196	A549	lung:	n/a	chr12:63546025-63546038
46	CTCF	chr12:63545920-63546070	HRE	kidney:	n/a	chr12:63546025-63546038
47	SMC3	chr12:63545956-63546154	K562	blood:	n/a	n/a
48	SMC3	chr12:63545851-63546217	GM12878	blood:	n/a	n/a
49	CTCF	chr12:63545940-63546090	AG04449	skin:	n/a	chr12:63546025-63546038
50	CTCF	chr12:63546000-63546150	GM12872	blood:	n/a	chr12:63546025-63546038

No.	Distal block	Cell Line	Cell type
1	chr12:63545428..63546206-chr12:63674883..63675724,2	MCF-7	breast:
2	chr12:63545448..63546470-chr12:63670124..63671316,6	MCF-7	breast:
3	chr12:63545419..63546376-chr12:64195555..64196413,2	MCF-7	breast:
4	chr12:63545559..63546473-chr12:63669896..63671149,5	MCF-7	breast:

Variant related genes	Relation type
AVPR1A	TF binding region

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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv469592	chr12:63486510-63679139	Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv482578	chr12:63486510-63679139	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv832436	chr12:63503993-63658112	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1035736	chr12:63526274-63920372	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv541510	chr12:63526274-63920372	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv2761742	chr12:63537412-63582333	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1035231	chr12:63537412-63582333	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv899164	chr12:63540476-63611633	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899165	chr12:63545986-63641641	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63543200-63546400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:63543800-63546200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:63543800-63546200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
4	chr12:63543800-63546800	Flanking Active TSS	Liver	Liver
5	chr12:63544200-63546200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
6	chr12:63544200-63546400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:63544200-63546400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
8	chr12:63544400-63546200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
9	chr12:63544600-63546200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:63545000-63546200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
11	chr12:63545400-63546400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
12	chr12:63545400-63546400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
13	chr12:63545400-63546400	Bivalent/Poised TSS	Fetal Brain Female	brain
14	chr12:63545400-63546400	Bivalent Enhancer	Fetal Heart	heart
15	chr12:63545600-63546200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
16	chr12:63545600-63546200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:63545600-63546200	Active TSS	Fetal Kidney	kidney
18	chr12:63545600-63546400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:63545600-63546400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
20	chr12:63545800-63546200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:63545800-63546200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:63545800-63546200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
23	chr12:63545800-63546200	Active TSS	Right Atrium	heart
24	chr12:63545800-63546400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:63545800-63546400	Active TSS	Colon Smooth Muscle	Colon
26	chr12:63546000-63546200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr12:63546000-63546200	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr12:63546000-63546200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr12:63546000-63546200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:63546000-63546200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:63546000-63546200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:63546000-63546200	Active TSS	Adipose Nuclei	Adipose
33	chr12:63546000-63546200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
34	chr12:63546000-63546200	Bivalent Enhancer	Brain Anterior Caudate	brain
35	chr12:63546000-63546200	Bivalent Enhancer	Fetal Stomach	stomach
36	chr12:63546000-63546200	Bivalent Enhancer	HUVEC	blood vessel
37	chr12:63546000-63546400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:63546000-63546400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
39	chr12:63546000-63546400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
40	chr12:63546000-63546400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
41	chr12:63546000-63546400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:63546000-63546400	Bivalent Enhancer	Fetal Brain Male	brain
43	chr12:63546000-63546400	Bivalent Enhancer	Fetal Thymus	thymus
44	chr12:63546000-63546400	Weak transcription	Right Ventricle	heart
45	chr12:63546000-63546400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr12:63546000-63546400	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
47	chr12:63546000-63546400	Bivalent Enhancer	A549	lung
48	chr12:63546000-63546600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:63546000-63546600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:63546000-63549200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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