Variant report

Variant	rs56135201
Chromosome Location	chr15:40602256-40602257
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	SMC3	chr15:40602206-40602599	GM12878	blood:	n/a	chr15:40602405-40602419
2	RAD21	chr15:40602196-40602606	IMR90	lung:	n/a	chr15:40602401-40602420
3	CBX3	chr15:40602223-40602586	K562	blood:	n/a	n/a
4	SMC3	chr15:40602224-40602599	K562	blood:	n/a	chr15:40602405-40602419
5	RAD21	chr15:40602161-40602621	HepG2	liver:	n/a	chr15:40602401-40602420
6	RAD21	chr15:40602226-40602656	A549	lung:	n/a	chr15:40602401-40602420
7	CTCF	chr15:40602221-40602524	T-47D	breast:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
8	CTCF	chr15:40602216-40602591	A549	lung:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
9	RAD21	chr15:40602217-40602647	K562	blood:	n/a	chr15:40602401-40602420
10	HCFC1	chr15:40602233-40602501	K562	blood:	n/a	n/a
11	PAX5	chr15:40602243-40602530	GM12878	blood:	n/a	n/a
12	MAZ	chr15:40602220-40602639	K562	blood:	n/a	n/a
13	CTCF	chr15:40602144-40602597	K562	blood:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
14	RAD21	chr15:40602203-40602590	HepG2	liver:	n/a	chr15:40602401-40602420
15	RAD21	chr15:40602207-40602612	GM12878	blood:	n/a	chr15:40602401-40602420
16	RAD21	chr15:40602100-40602632	ECC-1	luminal epithelium:	n/a	chr15:40602401-40602420
17	SMC3	chr15:40601960-40602955	SK-N-SH	brain:	n/a	chr15:40602405-40602419
18	RCOR1	chr15:40602225-40602575	K562	blood:	n/a	n/a
19	CTCF	chr15:40602069-40602670	K562	blood:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
20	RAD21	chr15:40602180-40602554	SK-N-SH_RA	brain:	n/a	chr15:40602401-40602420
21	MYC	chr15:40602250-40602510	K562	blood:	n/a	n/a
22	CTCF	chr15:40602016-40602865	HCT-116	colon:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
23	TEAD4	chr15:40602177-40602706	K562	blood:	n/a	n/a
24	RAD21	chr15:40602232-40602558	K562	blood:	n/a	chr15:40602401-40602420
25	MAX	chr15:40602240-40602573	K562	blood:	n/a	n/a
26	RAD21	chr15:40602145-40602649	SK-N-SH_RA	brain:	n/a	chr15:40602401-40602420
27	RAD21	chr15:40602207-40602668	ECC-1	luminal epithelium:	n/a	chr15:40602401-40602420
28	RAD21	chr15:40602041-40602663	A549	lung:	n/a	chr15:40602401-40602420
29	CTCF	chr15:40602220-40602370	HAc	cerebellar:	n/a	n/a
30	RAD21	chr15:40602178-40602521	H1-hESC	embryonic stem cell:	n/a	chr15:40602401-40602420
31	RAD21	chr15:40601822-40602860	SK-N-SH	brain:	n/a	chr15:40602401-40602420
32	RAD21	chr15:40602113-40602661	H1-hESC	embryonic stem cell:	n/a	chr15:40602401-40602420
33	RAD21	chr15:40602045-40602652	MCF-7	breast:	n/a	chr15:40602401-40602420
34	TBL1XR1	chr15:40602242-40602590	K562	blood:	n/a	n/a
35	CTCF	chr15:40602221-40602709	A549	lung:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
36	MXI1	chr15:40602004-40602823	SK-N-SH	brain:	n/a	n/a
37	RAD21	chr15:40602240-40602564	HepG2	liver:	n/a	chr15:40602401-40602420
38	EBF1	chr15:40602237-40602560	GM12878	blood:	n/a	chr15:40602374-40602385
39	MYC	chr15:40602217-40602571	NB4	blood:	n/a	n/a
40	EBF1	chr15:40602213-40602528	GM12878	blood:	n/a	chr15:40602374-40602385
41	CTCF	chr15:40602146-40602559	H1-hESC	embryonic stem cell:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
42	MAX	chr15:40602241-40602606	NB4	blood:	n/a	n/a
43	MAZ	chr15:40602227-40602573	GM12878	blood:	n/a	n/a
44	CTCF	chr15:40602215-40602589	IMR90	lung:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
45	CTCF	chr15:40601997-40602921	SK-N-SH	brain:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
46	CTCF	chr15:40602053-40602719	HCT-116	colon:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
47	RAD21	chr15:40602250-40602512	K562	blood:	n/a	chr15:40602401-40602420
48	RAD21	chr15:40602144-40602664	A549	lung:	n/a	chr15:40602401-40602420
49	CTCF	chr15:40602177-40602642	H1-hESC	embryonic stem cell:	n/a	chr15:40602403-40602421 chr15:40602409-40602418 chr15:40602398-40602419
50	RAD21	chr15:40602186-40602633	H1-hESC	embryonic stem cell:	n/a	chr15:40602401-40602420

No.	Distal block	Cell Line	Cell type
1	chr15:40571488..40572288-chr15:40601921..40602727,4	MCF-7	breast:
2	chr15:40589397..40592046-chr15:40601245..40604242,2	K562	blood:
3	chr15:40574576..40575096-chr15:40601978..40602927,2	MCF-7	breast:
4	chr15:40601618..40604143-chr15:40604739..40606593,2	MCF-7	breast:
5	chr15:40571308..40572301-chr15:40601892..40603242,9	K562	blood:
6	chr15:40526580..40529009-chr15:40601249..40602782,2	K562	blood:
7	chr15:40601542..40603378-chr15:40607620..40610047,2	MCF-7	breast:
8	chr15:40574436..40575203-chr15:40602112..40602659,2	MCF-7	breast:
9	chr15:40574768..40575283-chr15:40601903..40602861,2	K562	blood:
10	chr15:40509144..40510009-chr15:40601917..40602437,2	K562	blood:
11	chr15:40571286..40572270-chr15:40601478..40602969,9	MCF-7	breast:
12	chr15:40566645..40567517-chr15:40601865..40602542,3	K562	blood:
13	chr15:40602041..40603902-chr15:40615864..40618409,2	K562	blood:
14	chr15:40585291..40587794-chr15:40600413..40602999,2	K562	blood:
15	chr15:40601564..40604029-chr15:40608282..40611704,3	K562	blood:
16	chr15:40573917..40574516-chr15:40601900..40602438,2	MCF-7	breast:

Variant related genes	Relation type
PLCB2	TF binding region
ENSG00000259198	TF binding region
ENSG00000230778	Chromatin interaction
ENSG00000244705	Chromatin interaction
ENSG00000259288	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259198	Chromatin interaction
ENSG00000156970	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1123487	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305645	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3743138	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3784399	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55927878	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56203022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62021888	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8023550	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv457118	chr15:40565705-40606484	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv569227	chr15:40565705-40606484	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40584200-40614800	Weak transcription	Gastric	stomach
2	chr15:40598000-40602400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr15:40598400-40602400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:40598600-40602400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr15:40598800-40602400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:40599400-40605600	Weak transcription	Right Atrium	heart
7	chr15:40599800-40602400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:40600000-40602400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:40600000-40605600	Weak transcription	HSMM	muscle
10	chr15:40600000-40614600	Weak transcription	Brain Substantia Nigra	brain
11	chr15:40600200-40602400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr15:40601000-40602400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
13	chr15:40601000-40602400	Enhancers	Fetal Heart	heart
14	chr15:40601200-40602400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr15:40601200-40604600	Weak transcription	Pancreas	Pancrea
16	chr15:40601200-40605800	Weak transcription	HUVEC	blood vessel
17	chr15:40601200-40612800	Weak transcription	Right Ventricle	heart
18	chr15:40601400-40602400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:40601400-40602400	Enhancers	Stomach Mucosa	stomach
20	chr15:40601400-40602600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:40601400-40602600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:40601400-40602600	Enhancers	Fetal Thymus	thymus
23	chr15:40601400-40602800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:40601400-40603000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr15:40601400-40603200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:40601400-40605600	Weak transcription	Lung	lung
27	chr15:40601400-40606400	Weak transcription	Esophagus	oesophagus
28	chr15:40601600-40602400	Enhancers	Primary T cells from cord blood	blood
29	chr15:40601600-40602400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:40601600-40602400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr15:40601600-40602600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:40601600-40602600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr15:40601600-40602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:40601600-40602800	Enhancers	Primary B cells from peripheral blood	blood
35	chr15:40601600-40602800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr15:40601600-40603000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr15:40601800-40602400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
38	chr15:40601800-40602400	Enhancers	K562	blood
39	chr15:40601800-40602800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr15:40601800-40602800	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr15:40601800-40605600	Weak transcription	Colonic Mucosa	Colon
42	chr15:40601800-40605600	Weak transcription	Thymus	Thymus
43	chr15:40602000-40602400	Enhancers	Fetal Brain Male	brain
44	chr15:40602000-40602600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:40602000-40612600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:40602000-40613000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:40602000-40614600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:40602200-40602400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:40602200-40602600	Enhancers	Primary B cells from cord blood	blood
50	chr15:40602200-40602600	Enhancers	Primary hematopoietic stem cells	blood

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