Variant report

Variant	rs2456507
Chromosome Location	chr15:53077634-53077635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr15:53077263-53077757	HepG2	liver:	n/a	chr15:53077604-53077613 chr15:53077482-53077492
2	EP300	chr15:53077272-53077656	HepG2	liver:	n/a	chr15:53077604-53077613 chr15:53077482-53077492
3	SUZ12	chr15:53076297-53078338	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr15:53077191-53077682	HepG2	liver:	n/a	n/a
5	YY1	chr15:53077272-53077714	HepG2	liver:	n/a	chr15:53077606-53077615
6	RXRA	chr15:53077262-53077663	HepG2	liver:	n/a	n/a
7	FOXA1	chr15:53077323-53077698	HepG2	liver:	n/a	n/a
8	SP1	chr15:53077243-53077700	HepG2	liver:	n/a	chr15:53077542-53077554 chr15:53077543-53077553 chr15:53077544-53077553 chr15:53077542-53077554
9	SIN3A	chr15:53077575-53078162	H1-hESC	embryonic stem cell:	n/a	chr15:53077729-53077743
10	HEY1	chr15:53077181-53077635	HepG2	liver:	n/a	n/a
11	ZNF143	chr15:53077602-53077729	H1-hESC	embryonic stem cell:	n/a	chr15:53077647-53077665
12	CTBP2	chr15:53075555-53079670	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:53077609-53077659	HIPEpiC	eye:	n/a
2	chr15:53077609-53077659	HCM	heart:	n/a
3	chr15:53077609-53077659	HRCEpiC	kidney:	n/a
4	chr15:53077609-53077659	NHBE	bronchial:	n/a
5	chr15:53077609-53077659	HPAEpiC	pulmonary alveolar:	n/a
6	chr15:53077609-53077659	GM06990	blood:	n/a
7	chr15:53077609-53077659	NB4	blood:	n/a
8	chr15:53077609-53077659	U87	brain:	n/a
9	chr15:53077609-53077659	NT2-D1	testis:	n/a
10	chr15:53077609-53077659	ProgFib	skin:	n/a
11	chr15:53077609-53077659	MCF-7	breast:	n/a
12	chr15:53077609-53077659	RPTEC	kidney:	n/a
13	chr15:53077609-53077659	BJ	skin:	n/a
14	chr15:53077609-53077659	HEK293	kidney:	embryo
15	chr15:53077609-53077659	Caco-2	colon:	n/a
16	chr15:53077609-53077659	GM19239	blood:	n/a
17	chr15:53077609-53077659	HUVEC	blood vessel:	n/a
18	chr15:53077609-53077659	PANC-1	pancreas:	n/a
19	chr15:53077609-53077659	GM12878	blood:	n/a
20	chr15:53077609-53077659	HAEpiC	amniotic membrane:	n/a
21	chr15:53077609-53077659	Hepatocyte	liver:	n/a
22	chr15:53077609-53077659	SAEC	small airway:	n/a
23	chr15:53077609-53077659	GM12891	blood:	n/a
24	chr15:53077609-53077659	CMK	blood:	n/a
25	chr15:53077609-53077659	NH-A	brain:	n/a
26	chr15:53077609-53077659	ovcar-3	ovarian:	n/a
27	chr15:53077609-53077659	IMR90	lung:	fetal
28	chr15:53077609-53077659	SK-N-SH	brain:	n/a
29	chr15:53077609-53077659	AG09319	gingival:	n/a
30	chr15:53077609-53077659	NHDF-neo	bronchial:	n/a
31	chr15:53077609-53077659	A549	lung:	n/a
32	chr15:53077609-53077659	K562	blood:	n/a
33	chr15:53077609-53077659	ECC-1	luminal epithelium:	n/a
34	chr15:53077609-53077659	HMEC	breast:	n/a
35	chr15:53077609-53077659	HRE	kidney:	n/a
36	chr15:53077609-53077659	HRPEpiC	eye:	n/a
37	chr15:53077609-53077659	AG10803	skin:	n/a
38	chr15:53077609-53077659	AG09309	skin:	n/a
39	chr15:53077609-53077659	AoSMC	blood vessel:	n/a
40	chr15:53077609-53077659	SKMC	muscle:	n/a
41	chr15:53077609-53077659	LNCaP	prostate:	n/a
42	chr15:53077609-53077659	H1-hESC	embryonic stem cell:	embryo
43	chr15:53077609-53077659	GM12892	blood:	n/a
44	chr15:53077609-53077659	HCF	heart:	n/a
45	chr15:53077609-53077659	HL-60	blood:	n/a
46	chr15:53077609-53077659	PFSK-1	brain:	n/a
47	chr15:53077609-53077659	HNPCEpiC	eye:	n/a
48	chr15:53077609-53077659	SK-N-SH_RA	brain:	n/a
49	chr15:53077609-53077659	BE2_C	brain:	n/a
50	chr15:53077609-53077659	Hela-S3	cervix:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52611004..52613000-chr15:53076080..53077962,2	K562	blood:
2	chr15:53076988..53078899-chr16:3071890..3073813,2	MCF-7	breast:

No data

Variant related genes	Relation type
ONECUT1	TF binding region
ONECUT1	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120450	0.85[EUR][1000 genomes]
rs2243790	0.89[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2440317	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2440322	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2440376	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs2456522	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456524	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456525	0.93[EUR][1000 genomes]
rs2456526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456529	0.91[EUR][1000 genomes]
rs2456530	0.89[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2456532	0.89[CEU][hapmap];0.93[EUR][1000 genomes]
rs28475375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60065065	0.95[EUR][1000 genomes]
rs7180600	0.88[EUR][1000 genomes]

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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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 target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2456507	ORMDL3	trans	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53075200-53078000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:53075400-53078800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
3	chr15:53075400-53081000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
4	chr15:53075400-53082000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr15:53075600-53078000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
6	chr15:53075600-53078200	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr15:53075600-53079200	Active TSS	Pancreas	Pancrea
8	chr15:53075600-53079800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr15:53075600-53081200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:53075600-53082000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr15:53075600-53083600	Bivalent Enhancer	Fetal Brain Male	brain
12	chr15:53075800-53077800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr15:53075800-53078000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:53075800-53082200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
15	chr15:53076200-53078000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr15:53076200-53078200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:53076200-53079400	Enhancers	Gastric	stomach
18	chr15:53076200-53079600	Bivalent Enhancer	Left Ventricle	heart
19	chr15:53076400-53078200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:53076400-53078400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr15:53076400-53078400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
22	chr15:53076400-53083800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr15:53076600-53078200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
24	chr15:53076600-53078200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
25	chr15:53076600-53080600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:53076600-53081800	Bivalent Enhancer	Spleen	Spleen
27	chr15:53076800-53078200	Bivalent Enhancer	Brain Anterior Caudate	brain
28	chr15:53076800-53078200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
29	chr15:53076800-53078400	Bivalent Enhancer	Adipose Nuclei	Adipose
30	chr15:53077000-53077800	Bivalent Enhancer	Brain Substantia Nigra	brain
31	chr15:53077000-53077800	Bivalent Enhancer	Colonic Mucosa	Colon
32	chr15:53077000-53077800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
33	chr15:53077000-53078000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr15:53077000-53078000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr15:53077000-53078000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr15:53077000-53078200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr15:53077000-53078400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:53077000-53079600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:53077200-53078000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
40	chr15:53077200-53078200	Bivalent Enhancer	Fetal Stomach	stomach
41	chr15:53077200-53078800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr15:53077200-53078800	Flanking Active TSS	HepG2	liver
43	chr15:53077200-53080400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:53077200-53080600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:53077400-53077800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr15:53077400-53077800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr15:53077400-53077800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
48	chr15:53077400-53078000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
49	chr15:53077400-53078000	Bivalent/Poised TSS	Right Ventricle	heart
50	chr15:53077400-53078200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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