Variant report

Variant	rs62023489
Chromosome Location	chr15:53076118-53076119
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	MAX	chr15:53076070-53076463	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:53076052-53076496	H1-hESC	embryonic stem cell:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
3	MAX	chr15:53076078-53076802	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:53075999-53076598	K562	blood:	n/a	chr15:53076531-53076544 chr15:53076277-53076295 chr15:53076280-53076293
5	CTCF	chr15:53075885-53076647	A549	lung:	n/a	chr15:53076531-53076544 chr15:53076277-53076295 chr15:53076280-53076293
6	REST	chr15:53075317-53076405	SK-N-SH	brain:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
7	CTCF	chr15:53076114-53076467	GM12878	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
8	POLR2A	chr15:53076034-53076559	H1-neurons	neurons:	n/a	n/a
9	CTCF	chr15:53076066-53076456	A549	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
10	CTCF	chr15:53076040-53076190	HFF-Myc	foreskin:	n/a	n/a
11	BACH1	chr15:53076053-53076451	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr15:53076016-53076594	A549	lung:	n/a	n/a
13	RAD21	chr15:53076003-53076698	H1-hESC	embryonic stem cell:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
14	MYC	chr15:53076003-53076364	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr15:53076066-53076476	A549	lung:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
16	YY1	chr15:53076038-53076657	H1-hESC	embryonic stem cell:	n/a	chr15:53076283-53076297 chr15:53076295-53076306 chr15:53076290-53076304
17	CEBPB	chr15:53075756-53076401	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr15:53076104-53076442	A549	lung:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
19	CTCF	chr15:53076020-53076170	GM12864	blood:	n/a	n/a
20	CHD1	chr15:53075713-53076383	H1-hESC	embryonic stem cell:	n/a	chr15:53076203-53076210
21	RAD21	chr15:53076083-53076510	H1-hESC	embryonic stem cell:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
22	MXI1	chr15:53075413-53076405	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr15:53075239-53076400	PFSK-1	brain:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
24	REST	chr15:53075258-53076668	H1-neurons	neurons:	n/a	chr15:53076445-53076454 chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
25	REST	chr15:53075238-53076449	H1-hESC	embryonic stem cell:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
26	RAD21	chr15:53076108-53076413	SK-N-SH_RA	brain:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
27	RAD21	chr15:53076058-53076625	A549	lung:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
28	REST	chr15:53075336-53076565	ECC-1	luminal epithelium:	n/a	chr15:53076445-53076454 chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
29	RAD21	chr15:53076023-53076421	A549	lung:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
30	REST	chr15:53075300-53076453	H1-hESC	embryonic stem cell:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
31	CTCF	chr15:53076116-53076381	SK-N-SH_RA	brain:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
32	RAD21	chr15:53075577-53076572	H1-hESC	embryonic stem cell:	n/a	chr15:53076279-53076293 chr15:53076283-53076293
33	CTCF	chr15:53076080-53076230	GM12872	blood:	n/a	n/a
34	E2F6	chr15:53076046-53076874	H1-hESC	embryonic stem cell:	n/a	chr15:53076203-53076210 chr15:53076286-53076295
35	CTCF	chr15:53076020-53076170	HAc	cerebellar:	n/a	n/a
36	POLR2A	chr15:53076022-53076725	H1-neurons	neurons:	n/a	n/a
37	REST	chr15:53075378-53076318	A549	lung:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
38	SIN3A	chr15:53075325-53077329	H1-hESC	embryonic stem cell:	n/a	chr15:53075700-53075714 chr15:53075699-53075709
39	TBP	chr15:53076072-53076216	K562	blood:	n/a	n/a
40	MAX	chr15:53076117-53076583	A549	lung:	n/a	n/a
41	CTCF	chr15:53076087-53076465	K562	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
42	CTCF	chr15:53076116-53076423	K562	blood:	n/a	chr15:53076277-53076295 chr15:53076280-53076293
43	TEAD4	chr15:53076117-53076742	H1-hESC	embryonic stem cell:	n/a	n/a
44	REST	chr15:53075357-53076189	PANC-1	pancreas:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
45	REST	chr15:53075253-53076433	ECC-1	luminal epithelium:	n/a	chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
46	CTCF	chr15:53075890-53076943	SK-N-SH	brain:	n/a	chr15:53076531-53076544 chr15:53076277-53076295 chr15:53076280-53076293
47	SMC3	chr15:53076019-53076451	K562	blood:	n/a	chr15:53076283-53076293 chr15:53076279-53076293
48	CTBP2	chr15:53075555-53079670	H1-hESC	embryonic stem cell:	n/a	n/a
49	REST	chr15:53075236-53076488	HL-60	blood:	n/a	chr15:53076445-53076454 chr15:53075700-53075709 chr15:53075698-53075711 chr15:53075695-53075715 chr15:53075701-53075715
50	TCF7L2	chr15:53076084-53076433	PANC-1	pancreas:	n/a	n/a

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: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1357	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16965171	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16965179	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17543338	0.80[EUR][1000 genomes]
rs55781920	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61735385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62023486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62023487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62023488	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62023490	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62023492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62023493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8025128	0.84[AMR][1000 genomes];0.97[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

No data

Chromatin state (count:67 , 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	chr15:53075400-53076200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
6	chr15:53075400-53076200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
7	chr15:53075400-53076200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:53075400-53076400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:53075400-53076400	Bivalent Enhancer	Spleen	Spleen
10	chr15:53075400-53076600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
11	chr15:53075400-53076600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
12	chr15:53075400-53076800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr15:53075400-53076800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr15:53075400-53077200	Enhancers	HepG2	liver
15	chr15:53075400-53077600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:53075400-53078800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
17	chr15:53075400-53081000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr15:53075400-53082000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr15:53075600-53076200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:53075600-53076200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
21	chr15:53075600-53076200	Weak transcription	Gastric	stomach
22	chr15:53075600-53076400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr15:53075600-53076400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr15:53075600-53076400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
25	chr15:53075600-53076400	Bivalent Enhancer	Lung	lung
26	chr15:53075600-53076400	Enhancers	Right Atrium	heart
27	chr15:53075600-53076600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:53075600-53076600	Bivalent Enhancer	Fetal Thymus	thymus
29	chr15:53075600-53076800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
30	chr15:53075600-53077000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:53075600-53077000	Bivalent Enhancer	Right Ventricle	heart
32	chr15:53075600-53078000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr15:53075600-53078200	Bivalent Enhancer	Fetal Muscle Leg	muscle
34	chr15:53075600-53079200	Active TSS	Pancreas	Pancrea
35	chr15:53075600-53079800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr15:53075600-53081200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr15:53075600-53082000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr15:53075600-53083600	Bivalent Enhancer	Fetal Brain Male	brain
39	chr15:53075800-53076200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr15:53075800-53076200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:53075800-53076200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:53075800-53076200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:53075800-53076200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:53075800-53076200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:53075800-53076200	Bivalent Enhancer	Brain Hippocampus Middle	brain
46	chr15:53075800-53076200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
47	chr15:53075800-53076200	Bivalent Enhancer	HUVEC	blood vessel
48	chr15:53075800-53076400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr15:53075800-53076600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
50	chr15:53075800-53076600	Bivalent Enhancer	Psoas Muscle	Psoas

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