Variant report

Variant	rs2456506
Chromosome Location	chr15:53076326-53076327
allele	A/C
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	chr15:53076200-53076490	HCT-116	colon:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
2	CTCF	chr15:53076240-53076390	GM12864	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
3	MAX	chr15:53076070-53076463	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr15:53076156-53076415	SK-N-SH_RA	brain:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
5	CTCF	chr15:53076200-53076350	GM12866	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
6	MAX	chr15:53076176-53076617	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr15:53076260-53076410	HRE	kidney:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
8	CTCF	chr15:53076139-53076506	H1-hESC	embryonic stem cell:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
9	CTCF	chr15:53076220-53076370	HMF	breast:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
10	CTCF	chr15:53076052-53076496	H1-hESC	embryonic stem cell:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
11	CTCF	chr15:53076260-53076410	NHLF	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
12	CTCF	chr15:53076200-53076350	WI-38	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
13	CTCF	chr15:53076200-53076350	AoAF	blood vessel:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
14	REST	chr15:53076135-53076451	PFSK-1	brain:	n/a	n/a
15	MAX	chr15:53076078-53076802	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr15:53076170-53076409	K562	blood:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
17	CTCF	chr15:53076240-53076390	K562	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
18	CTCF	chr15:53076240-53076390	AG04450	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
19	CTCF	chr15:53075999-53076598	K562	blood:	n/a	chr15:53076531-53076544 chr15:53076277-53076295 chr15:53076280-53076293
20	CTCF	chr15:53075885-53076647	A549	lung:	n/a	chr15:53076531-53076544 chr15:53076277-53076295 chr15:53076280-53076293
21	CTCF	chr15:53076200-53076350	GM12865	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
22	CTCF	chr15:53076220-53076370	HCPEpiC	choroid plexus:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
23	REST	chr15:53075317-53076405	SK-N-SH	brain:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
24	CTCF	chr15:53076260-53076410	HFF	foreskin:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
25	CTCF	chr15:53076114-53076467	GM12878	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
26	CTCF	chr15:53076260-53076410	HA-sp	spinal cord:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
27	CTCF	chr15:53076200-53076350	HMF	breast:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
28	POLR2A	chr15:53076034-53076559	H1-neurons	neurons:	n/a	n/a
29	CTCF	chr15:53076066-53076456	A549	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
30	CTCF	chr15:53076220-53076370	AG09309	skin:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
31	CTCF	chr15:53076260-53076410	HAc	cerebellar:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
32	SUZ12	chr15:53076297-53078338	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr15:53076200-53076350	HPF	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
34	BACH1	chr15:53076053-53076451	H1-hESC	embryonic stem cell:	n/a	n/a
35	E2F6	chr15:53076217-53076350	K562	blood:	n/a	chr15:53076286-53076295
36	CTCF	chr15:53076220-53076370	GM12865	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
37	CTCF	chr15:53076220-53076370	AG09319	gingival:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
38	CTCF	chr15:53076163-53076416	H1-hESC	embryonic stem cell:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
39	CTCF	chr15:53076260-53076410	HFF-Myc	foreskin:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
40	CTCF	chr15:53076211-53076386	Fibrobl	skin:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
41	CTCF	chr15:53076168-53076393	LNCaP	prostate:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
42	MAX	chr15:53076016-53076594	A549	lung:	n/a	n/a
43	CTCF	chr15:53076240-53076390	BE2_C	brain:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
44	CTCF	chr15:53076202-53076368	GM13976	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
45	CTCF	chr15:53076193-53076416	GM19239	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
46	RAD21	chr15:53076003-53076698	H1-hESC	embryonic stem cell:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
47	CTCF	chr15:53076180-53076330	GM12865	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
48	MYC	chr15:53076003-53076364	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr15:53076200-53076350	HRPEpiC	eye:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
50	CTCF	chr15:53076220-53076370	GM12867	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:53075751..53076563-chr15:53489418..53490178,2	K562	blood:
2	chr15:52611004..52613000-chr15:53076080..53077962,2	K562	blood:

Variant related genes	Relation type
ONECUT1	TF binding region

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

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

rs_ID	r²[population]
rs1899752	0.94[EUR][1000 genomes]
rs2165991	0.86[EUR][1000 genomes]
rs2440315	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440316	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440374	0.86[EUR][1000 genomes]
rs2456523	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2456525	0.98[ASN][1000 genomes]
rs2456531	0.94[EUR][1000 genomes]
rs2460	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687152	0.91[EUR][1000 genomes]
rs60065065	0.98[ASN][1000 genomes]
rs7180600	0.93[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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53075200-53076600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr15:53075200-53077000	Flanking Active TSS	Liver	Liver
3	chr15:53075200-53077600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
4	chr15:53075200-53078000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:53075400-53076400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:53075400-53076400	Bivalent Enhancer	Spleen	Spleen
7	chr15:53075400-53076600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
8	chr15:53075400-53076600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr15:53075400-53076800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr15:53075400-53076800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr15:53075400-53077200	Enhancers	HepG2	liver
12	chr15:53075400-53077600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:53075400-53078800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr15:53075400-53081000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr15:53075400-53082000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr15:53075600-53076400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:53075600-53076400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr15:53075600-53076400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
19	chr15:53075600-53076400	Bivalent Enhancer	Lung	lung
20	chr15:53075600-53076400	Enhancers	Right Atrium	heart
21	chr15:53075600-53076600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:53075600-53076600	Bivalent Enhancer	Fetal Thymus	thymus
23	chr15:53075600-53076800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
24	chr15:53075600-53077000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:53075600-53077000	Bivalent Enhancer	Right Ventricle	heart
26	chr15:53075600-53078000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr15:53075600-53078200	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr15:53075600-53079200	Active TSS	Pancreas	Pancrea
29	chr15:53075600-53079800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr15:53075600-53081200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
31	chr15:53075600-53082000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr15:53075600-53083600	Bivalent Enhancer	Fetal Brain Male	brain
33	chr15:53075800-53076400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr15:53075800-53076600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
35	chr15:53075800-53076600	Bivalent Enhancer	Psoas Muscle	Psoas
36	chr15:53075800-53076800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
37	chr15:53075800-53077000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr15:53075800-53077600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:53075800-53077600	Bivalent Enhancer	Fetal Heart	heart
40	chr15:53075800-53077800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
41	chr15:53075800-53078000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:53075800-53082200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr15:53076000-53076400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:53076000-53076400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
45	chr15:53076000-53076400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
46	chr15:53076000-53076600	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr15:53076000-53077000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:53076000-53077400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
49	chr15:53076200-53076400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:53076200-53076400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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