Variant report

Variant	nsv549561
Chromosome Location	chr1:247279549-247282233
allele	n/a
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	ATF2	chr1:247282166-247282519	H1-hESC	embryonic stem cell:	n/a	n/a
2	ATF2	chr1:247282209-247282493	H1-hESC	embryonic stem cell:	n/a	n/a
3	BHLHE40	chr1:247282190-247282604	HepG2	liver:	n/a	n/a
4	CBX3	chr1:247279956-247280480	K562	blood:	n/a	n/a
5	CBX3	chr1:247280963-247282452	K562	blood:	n/a	n/a
6	CBX3	chr1:247279022-247279825	K562	blood:	n/a	n/a
7	CBX3	chr1:247280516-247280801	K562	blood:	n/a	n/a
8	CBX3	chr1:247278814-247282541	K562	blood:	n/a	n/a
9	CTCF	chr1:247282224-247282515	GM12892	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
10	CTCF	chr1:247282204-247282504	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
11	CTCF	chr1:247282171-247282608	GM12878	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
12	CTCF	chr1:247282210-247282590	HCT-116	colon:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
13	CTCF	chr1:247282133-247282562	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
14	CTCF	chr1:247282154-247282523	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
15	CTCF	chr1:247282209-247282501	HepG2	liver:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
16	CTCF	chr1:247282228-247282511	HepG2	liver:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
17	CTCF	chr1:247282220-247282370	GM12865	blood:	n/a	chr1:247282312-247282330 chr1:247282308-247282317 chr1:247282314-247282327
18	CTCF	chr1:247282184-247282780	SK-N-SH	brain:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282711-247282724 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282664-247282673 chr1:247282314-247282327
19	CTCF	chr1:247282207-247282634	H1-hESC	embryonic stem cell:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
20	CTCF	chr1:247282215-247282598	H1-hESC	embryonic stem cell:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
21	CTCF	chr1:247282190-247282740	A549	lung:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282711-247282724 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282664-247282673 chr1:247282314-247282327
22	CTCF	chr1:247282052-247282603	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
23	CTCF	chr1:247282216-247282520	Hela-S3	cervix:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
24	CTCF	chr1:247282231-247282648	MCF-7	breast:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
25	CTCF	chr1:247282232-247282494	K562	blood:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
26	CTCF	chr1:247282225-247282563	H1-hESC	embryonic stem cell:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
27	CTCF	chr1:247282186-247282621	IMR90	lung:	n/a	chr1:247282440-247282461 chr1:247282312-247282330 chr1:247282439-247282455 chr1:247282441-247282454 chr1:247282438-247282456 chr1:247282308-247282317 chr1:247282314-247282327
28	EGR1	chr1:247282204-247282398	K562	blood:	n/a	chr1:247282368-247282381
29	EGR1	chr1:247282195-247282447	K562	blood:	n/a	chr1:247282368-247282381
30	JUND	chr1:247282159-247282525	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAFF	chr1:247282170-247282469	HepG2	liver:	n/a	n/a
32	MAZ	chr1:247282187-247282498	K562	blood:	n/a	n/a
33	MXI1	chr1:247282168-247282513	HepG2	liver:	n/a	n/a
34	NR2F2	chr1:247280413-247282550	K562	blood:	n/a	n/a
35	NR2F2	chr1:247279088-247280368	K562	blood:	n/a	n/a
36	NR2F2	chr1:247279103-247282442	K562	blood:	n/a	n/a
37	RAD21	chr1:247282226-247282546	IMR90	lung:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
38	RAD21	chr1:247282188-247282756	SK-N-SH	brain:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
39	RAD21	chr1:247282206-247282518	HepG2	liver:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282444-247282456 chr1:247282313-247282326
40	RAD21	chr1:247282153-247282610	HepG2	liver:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
41	RAD21	chr1:247282219-247282486	GM12878	blood:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282444-247282456 chr1:247282313-247282326
42	RAD21	chr1:247282198-247282545	HCT-116	colon:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
43	RAD21	chr1:247282187-247282553	H1-hESC	embryonic stem cell:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
44	RAD21	chr1:247282204-247282658	ECC-1	luminal epithelium:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
45	RAD21	chr1:247282196-247282708	HCT-116	colon:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
46	RAD21	chr1:247282174-247282666	H1-hESC	embryonic stem cell:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
47	RAD21	chr1:247282172-247282510	Hela-S3	cervix:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282444-247282456 chr1:247282313-247282326
48	RAD21	chr1:247282199-247282577	ECC-1	luminal epithelium:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326
49	RAD21	chr1:247282192-247282504	SK-N-SH_RA	brain:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282444-247282456 chr1:247282313-247282326
50	RAD21	chr1:247282181-247282580	HepG2	liver:	n/a	chr1:247282439-247282458 chr1:247282310-247282329 chr1:247282537-247282544 chr1:247282444-247282456 chr1:247282313-247282326

No.	Distal block	Cell Line	Cell type
1	chr1:247273239..247275061-chr1:247277041..247280302,3	K562	blood:
2	chr1:247274786..247276587-chr1:247277453..247279795,2	MCF-7	breast:
3	chr1:247241666..247243646-chr1:247278123..247279948,2	K562	blood:

Variant related genes	Relation type
C1orf229	TF binding region
FGFR3P6	TF binding region
ENSG00000221953	chromatin interactions
ENSG00000135747	chromatin interactions

Extended variants
information (count: 35 )
Associated
traits (count: 30 )

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs28489280	chr1:247279582-247279583	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs28606523	chr1:247279584-247279585	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs28612339	chr1:247279645-247279646	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs28705205	chr1:247279665-247279666	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs28507145	chr1:247279667-247279668	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs200139656	chr1:247279691-247279692	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs55815441	chr1:247279802-247279803	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs201706516	chr1:247279873-247279874	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs201274933	chr1:247279962-247279963	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs200698161	chr1:247280136-247280137	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs373975432	chr1:247280273-247280274	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs55851721	chr1:247280312-247280313	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs200448724	chr1:247280466-247280467	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs201450624	chr1:247280700-247280701	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs200371324	chr1:247281295-247281296	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs566569058	chr1:247281328-247281329	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs1212570	chr1:247281510-247281511	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs1212898	chr1:247281525-247281526	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs1212899	chr1:247281602-247281603	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs55787515	chr1:247281769-247281770	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs538005065	chr1:247281874-247281875	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs367889905	chr1:247281904-247281905	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs12748377	chr1:247281942-247281943	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs371998562	chr1:247281950-247281951	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs12748386	chr1:247281963-247281964	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs12748393	chr1:247281982-247281983	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs1192845	chr1:247282077-247282078	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs555954667	chr1:247282104-247282105	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs12748601	chr1:247282123-247282124	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs567984731	chr1:247282150-247282151	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs376364523	chr1:247282169-247282170	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs113806528	chr1:247282180-247282181	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs372735385	chr1:247282201-247282202	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs12121338	chr1:247282226-247282227	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs34942837	chr1:247282229-247282230	Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:30)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	17060936	CNVD
Multiple myeloma	16616336	CNVD
Cutaneous malignant melanoma	18794153	CNVD
Astrocytoma	17934521	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Breast cancer	20409316	CNVD
Fibroblasts	17951408	CNVD
Lung cancer	17951408	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247276600-247284600	Weak transcription	Right Ventricle	heart
2	chr1:247276800-247283000	Weak transcription	Spleen	Spleen
3	chr1:247279000-247290800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:247279200-247282400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:247282200-247282600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:247282200-247283600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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