Variant report

Variant	rs2440316
Chromosome Location	chr15:53083614-53083615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:53083480-53083630	HCM	heart:	n/a	n/a
2	ZNF143	chr15:53083230-53084069	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr15:53083480-53083630	BJ	skin:	n/a	n/a
4	E2F6	chr15:53083089-53083629	H1-hESC	embryonic stem cell:	n/a	chr15:53083235-53083244 chr15:53083108-53083115 chr15:53083552-53083561
5	BACH1	chr15:53083442-53084110	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr15:53083500-53083650	GM12872	blood:	n/a	n/a
7	RAD21	chr15:53083248-53083738	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr15:53083480-53083630	GM12868	blood:	n/a	n/a
9	SIN3A	chr15:53083187-53083653	H1-hESC	embryonic stem cell:	n/a	chr15:53083366-53083375
10	CTCF	chr15:53083480-53083630	HPAF	blood vessel:	n/a	n/a
11	RAD21	chr15:53083352-53083661	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTBP2	chr15:53079913-53083729	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr15:53083480-53083630	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr15:53083480-53083630	GM12873	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:53083587-53083637	HepG2	liver:	n/a
2	chr15:53083587-53083637	HL-60	blood:	n/a
3	chr15:53083587-53083637	NHBE	bronchial:	n/a
4	chr15:53083587-53083637	HMEC	breast:	n/a
5	chr15:53083587-53083637	SK-N-SH	brain:	n/a
6	chr15:53083587-53083637	CMK	blood:	n/a
7	chr15:53083587-53083637	SAEC	small airway:	n/a
8	chr15:53083587-53083637	PrEC	prostate:	n/a
9	chr15:53083587-53083637	AG04450	lung:	fetal
10	chr15:53083587-53083637	Caco-2	colon:	n/a
11	chr15:53083587-53083637	LNCaP	prostate:	n/a
12	chr15:53083587-53083637	NB4	blood:	n/a
13	chr15:53083587-53083637	HEEpiC	esophagus:	n/a
14	chr15:53083587-53083637	GM06990	blood:	n/a
15	chr15:53083587-53083637	Hepatocyte	liver:	n/a
16	chr15:53083587-53083637	ProgFib	skin:	n/a
17	chr15:53083587-53083637	SKMC	muscle:	n/a
18	chr15:53083587-53083637	SK-N-SH_RA	brain:	n/a
19	chr15:53083587-53083637	HPAEpiC	pulmonary alveolar:	n/a
20	chr15:53083587-53083637	HNPCEpiC	eye:	n/a
21	chr15:53083587-53083637	AG04449	skin:	fetal
22	chr15:53083587-53083637	NT2-D1	testis:	n/a
23	chr15:53083587-53083637	HAEpiC	amniotic membrane:	n/a
24	chr15:53083587-53083637	T-47D	breast:	n/a
25	chr15:53083587-53083637	NHDF-neo	bronchial:	n/a
26	chr15:53083587-53083637	BE2_C	brain:	n/a
27	chr15:53083587-53083637	ECC-1	luminal epithelium:	n/a
28	chr15:53083587-53083637	AoSMC	blood vessel:	n/a
29	chr15:53083587-53083637	HRPEpiC	eye:	n/a
30	chr15:53083587-53083637	HRE	kidney:	n/a
31	chr15:53083587-53083637	HIPEpiC	eye:	n/a
32	chr15:53083587-53083637	HCT-116	colon:	n/a
33	chr15:53083587-53083637	A549	lung:	n/a
34	chr15:53083587-53083637	PFSK-1	brain:	n/a
35	chr15:53083587-53083637	GM12891	blood:	n/a
36	chr15:53083587-53083637	MCF-7	breast:	n/a
37	chr15:53083587-53083637	U87	brain:	n/a
38	chr15:53083587-53083637	H1-hESC	embryonic stem cell:	embryo
39	chr15:53083587-53083637	SK-N-MC	brain:	n/a
40	chr15:53083587-53083637	Jurkat	blood:	n/a
41	chr15:53083587-53083637	HUVEC	blood vessel:	n/a
42	chr15:53083587-53083637	HCPEpiC	choroid plexus:	n/a
43	chr15:53083587-53083637	HCF	heart:	n/a
44	chr15:53083587-53083637	AG10803	skin:	n/a
45	chr15:53083587-53083637	RPTEC	kidney:	n/a
46	chr15:53083587-53083637	AG09309	skin:	n/a
47	chr15:53083587-53083637	HCM	heart:	n/a
48	chr15:53083587-53083637	GM12878	blood:	n/a
49	chr15:53083587-53083637	AG09319	gingival:	n/a
50	chr15:53083587-53083637	MCF10A-Er-Src	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:45913793..45915528-chr15:53082604..53084932,2	MCF-7	breast:

No data

Variant related genes	Relation type
ONECUT1	TF binding region
ONECUT1	CpG island
ENSG00000133112	Chromatin interaction
ENSG00000170919	Chromatin interaction
ENSG00000273149	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1899752	0.97[EUR][1000 genomes]
rs2165991	0.90[EUR][1000 genomes]
rs2440315	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440374	0.90[EUR][1000 genomes]
rs2456506	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2456523	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2456525	0.97[ASN][1000 genomes]
rs2456531	0.97[EUR][1000 genomes]
rs2460	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28687152	0.94[EUR][1000 genomes]
rs60065065	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7180600	0.92[ASN][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

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53076400-53083800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr15:53080600-53083800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:53081200-53083800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr15:53081200-53083800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr15:53081600-53083800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
6	chr15:53081600-53083800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:53081600-53083800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
8	chr15:53081800-53083800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:53081800-53083800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr15:53081800-53084000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:53082000-53083800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:53082000-53083800	Bivalent/Poised TSS	Fetal Brain Female	brain
13	chr15:53082200-53083800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr15:53082200-53083800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:53082200-53083800	Active TSS	Brain Substantia Nigra	brain
16	chr15:53082600-53084000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:53083000-53083800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
18	chr15:53083000-53083800	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr15:53083000-53083800	Bivalent/Poised TSS	Right Ventricle	heart
20	chr15:53083200-53083800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
21	chr15:53083200-53084000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:53083400-53083800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr15:53083400-53083800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr15:53083400-53083800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr15:53083400-53083800	Bivalent Enhancer	Placenta	Placenta
26	chr15:53083400-53084000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
27	chr15:53083400-53084000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr15:53083400-53084000	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr15:53083600-53083800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr15:53083600-53083800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:53083600-53083800	Bivalent/Poised TSS	Primary B cells from cord blood	blood
32	chr15:53083600-53083800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
33	chr15:53083600-53083800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
34	chr15:53083600-53083800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:53083600-53083800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:53083600-53083800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:53083600-53083800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:53083600-53083800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr15:53083600-53083800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
40	chr15:53083600-53083800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr15:53083600-53083800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
42	chr15:53083600-53084000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr15:53083600-53084000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:53083600-53084000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:53083600-53088400	Weak transcription	Pancreas	Pancrea
46	chr15:53083600-53088600	Weak transcription	Liver	Liver

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