Variant report

Variant	rs3741865
Chromosome Location	chr12:63544858-63544859
allele	C/T
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	CTBP2	chr12:63543651-63545351	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr12:63543589-63545750	H1-hESC	embryonic stem cell:	n/a	chr12:63544721-63544732 chr12:63545655-63545662 chr12:63543862-63543877 chr12:63544722-63544733 chr12:63544721-63544731 chr12:63545113-63545120 chr12:63545655-63545662 chr12:63544722-63544729 chr12:63545113-63545120 chr12:63544722-63544730 chr12:63544722-63544730 chr12:63543759-63543774 chr12:63545113-63545120 chr12:63545655-63545662
3	SIN3A	chr12:63543863-63546155	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr12:63543624-63545325	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr12:63544820-63544970	HAc	cerebellar:	n/a	n/a
6	TBP	chr12:63543836-63545000	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr12:63544853-63545540	A549	lung:	n/a	chr12:63545113-63545120 chr12:63545113-63545120 chr12:63545113-63545120
8	SUZ12	chr12:63543682-63545671	NT2-D1	testis:	n/a	n/a
9	CHD2	chr12:63544525-63544972	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr12:63544130-63545475	ECC-1	luminal epithelium:	n/a	chr12:63544931-63544940
11	MAX	chr12:63543776-63545400	H1-hESC	embryonic stem cell:	n/a	chr12:63544931-63544940
12	E2F6	chr12:63543627-63545405	H1-hESC	embryonic stem cell:	n/a	chr12:63544721-63544732 chr12:63543862-63543877 chr12:63544722-63544733 chr12:63544721-63544731 chr12:63545113-63545120 chr12:63544722-63544729 chr12:63545113-63545120 chr12:63544722-63544730 chr12:63544722-63544730 chr12:63543759-63543774 chr12:63545113-63545120
13	REST	chr12:63544707-63546100	H1-neurons	neurons:	n/a	chr12:63545053-63545066 chr12:63545777-63545786
14	MAX	chr12:63543660-63545455	H1-hESC	embryonic stem cell:	n/a	chr12:63544931-63544940
15	ZNF263	chr12:63544346-63546142	HEK293-T-REx	kidney:	n/a	chr12:63545887-63545896
16	ZNF143	chr12:63544003-63544962	H1-hESC	embryonic stem cell:	n/a	n/a
17	YY1	chr12:63544527-63545000	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr12:63544445-63545483	A549	lung:	n/a	chr12:63544931-63544940
19	KAP1	chr12:63544476-63546436	HEK293	kidney:	n/a	n/a
20	MAX	chr12:63543614-63545445	H1-hESC	embryonic stem cell:	n/a	chr12:63544931-63544940

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:63544857-63544907	BE2_C	brain:	n/a
2	chr12:63544857-63544907	NHBE	bronchial:	n/a
3	chr12:63544857-63544907	ProgFib	skin:	n/a
4	chr12:63544857-63544907	HRPEpiC	eye:	n/a
5	chr12:63544857-63544907	NB4	blood:	n/a
6	chr12:63544857-63544907	NT2-D1	testis:	n/a
7	chr12:63544857-63544907	LNCaP	prostate:	n/a
8	chr12:63544857-63544907	GM06990	blood:	n/a
9	chr12:63544857-63544907	GM12878	blood:	n/a
10	chr12:63544857-63544907	SAEC	small airway:	n/a
11	chr12:63544857-63544907	AG04450	lung:	fetal
12	chr12:63544857-63544907	HPAEpiC	pulmonary alveolar:	n/a
13	chr12:63544857-63544907	GM12891	blood:	n/a
14	chr12:63544857-63544907	PrEC	prostate:	n/a
15	chr12:63544857-63544907	HUVEC	blood vessel:	n/a
16	chr12:63544857-63544907	HCPEpiC	choroid plexus:	n/a
17	chr12:63544857-63544907	K562	blood:	n/a
18	chr12:63544857-63544907	NH-A	brain:	n/a
19	chr12:63544857-63544907	H1-hESC	embryonic stem cell:	embryo
20	chr12:63544857-63544907	HL-60	blood:	n/a
21	chr12:63544857-63544907	PANC-1	pancreas:	n/a
22	chr12:63544857-63544907	AoSMC	blood vessel:	n/a
23	chr12:63544857-63544907	Hepatocyte	liver:	n/a
24	chr12:63544857-63544907	GM12892	blood:	n/a
25	chr12:63544857-63544907	A549	lung:	n/a
26	chr12:63544857-63544907	SK-N-SH	brain:	n/a
27	chr12:63544857-63544907	HNPCEpiC	eye:	n/a
28	chr12:63544857-63544907	ovcar-3	ovarian:	n/a
29	chr12:63544857-63544907	U87	brain:	n/a
30	chr12:63544857-63544907	HIPEpiC	eye:	n/a
31	chr12:63544857-63544907	RPTEC	kidney:	n/a
32	chr12:63544857-63544907	HCT-116	colon:	n/a
33	chr12:63544857-63544907	ECC-1	luminal epithelium:	n/a
34	chr12:63544857-63544907	HMEC	breast:	n/a
35	chr12:63544857-63544907	HAEpiC	amniotic membrane:	n/a
36	chr12:63544857-63544907	Hela-S3	cervix:	n/a
37	chr12:63544857-63544907	HRE	kidney:	n/a
38	chr12:63544857-63544907	HCM	heart:	n/a
39	chr12:63544857-63544907	HEK293	kidney:	embryo
40	chr12:63544857-63544907	SKMC	muscle:	n/a
41	chr12:63544857-63544907	HEEpiC	esophagus:	n/a
42	chr12:63544857-63544907	CMK	blood:	n/a
43	chr12:63544857-63544907	SK-N-MC	brain:	n/a
44	chr12:63544857-63544907	IMR90	lung:	fetal
45	chr12:63544857-63544907	HepG2	liver:	n/a
46	chr12:63544857-63544907	MCF-7	breast:	n/a
47	chr12:63544857-63544907	HCF	heart:	n/a
48	chr12:63544857-63544907	GM19239	blood:	n/a
49	chr12:63544857-63544907	NHDF-neo	bronchial:	n/a
50	chr12:63544857-63544907	SK-N-SH_RA	brain:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MON2-3	chr12:63544845-63544872	ENSG00000257973.1

Variant related genes	Relation type
AVPR1A	TF binding region
AVPR1A	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10877966	0.93[ASN][1000 genomes]
rs10877967	0.99[ASN][1000 genomes]
rs10877968	0.81[CHD][hapmap]
rs10877969	0.80[CHD][hapmap]
rs10877978	0.96[ASN][1000 genomes]
rs10877982	0.93[ASN][1000 genomes]
rs11174804	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11174808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11174810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11174816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11174828	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11174840	0.96[ASN][1000 genomes]
rs11174841	0.96[ASN][1000 genomes]
rs12227476	0.97[ASN][1000 genomes]
rs12297389	0.96[ASN][1000 genomes]
rs1774	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1812476	0.93[ASN][1000 genomes]
rs3021528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218817	0.93[ASN][1000 genomes]
rs61353632	0.99[ASN][1000 genomes]
rs61554779	0.96[ASN][1000 genomes]
rs7358710	0.96[ASN][1000 genomes]
rs7954346	0.99[ASN][1000 genomes]
rs7967990	0.99[ASN][1000 genomes]
rs7976075	0.93[ASN][1000 genomes]
rs7980289	0.97[ASN][1000 genomes]
rs962862	0.99[ASN][1000 genomes]
rs9805119	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63542600-63545200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:63542800-63545000	Bivalent Enhancer	Fetal Brain Male	brain
3	chr12:63543200-63546400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:63543600-63545000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:63543600-63545200	ZNF genes & repeats	Spleen	Spleen
6	chr12:63543600-63545400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:63543600-63545800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:63543600-63546000	Flanking Active TSS	Pancreas	Pancrea
9	chr12:63543600-63546000	Bivalent/Poised TSS	Psoas Muscle	Psoas
10	chr12:63543600-63546000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
11	chr12:63543800-63545000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
12	chr12:63543800-63545200	Flanking Active TSS	Gastric	stomach
13	chr12:63543800-63545200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
14	chr12:63543800-63545400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:63543800-63545400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
16	chr12:63543800-63545400	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
17	chr12:63543800-63545400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr12:63543800-63545600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr12:63543800-63545600	Bivalent/Poised TSS	Fetal Kidney	kidney
20	chr12:63543800-63546000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr12:63543800-63546000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
22	chr12:63543800-63546000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
24	chr12:63543800-63546000	Active TSS	Aorta	Aorta
25	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr12:63543800-63546000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
28	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
29	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr12:63543800-63546000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
31	chr12:63543800-63546200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr12:63543800-63546200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr12:63543800-63546800	Flanking Active TSS	Liver	Liver
34	chr12:63544000-63545000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:63544000-63545400	Flanking Bivalent TSS/Enh	Thymus	Thymus
36	chr12:63544000-63545800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:63544000-63546000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr12:63544000-63546000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:63544200-63545400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:63544200-63545400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
46	chr12:63544200-63545400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
47	chr12:63544200-63545800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:63544200-63545800	Flanking Active TSS	Right Ventricle	heart
49	chr12:63544200-63546000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links