Variant report

Variant	nsv960875
Chromosome Location	chr19:56244736-56265968
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:305)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr19:56252920-56252934	A549	lung:	n/a	n/a
2	CEBPB	chr19:56258745-56258858	HepG2	liver:	n/a	chr19:56258809-56258820
3	CEBPB	chr19:56252761-56252952	K562	blood:	n/a	chr19:56252917-56252928
4	CEBPB	chr19:56252893-56252942	HepG2	liver:	n/a	chr19:56252917-56252928
5	CTCF	chr19:56258247-56258265	MCF-7	breast:	n/a	n/a
6	CTCF	chr19:56258305-56258414	MCF-7	breast:	n/a	n/a
7	CTCF	chr19:56264236-56264269	Lung_OC	lung:	n/a	n/a
8	CTCF	chr19:56258237-56258238	GM19239	blood:	n/a	n/a
9	CTCF	chr19:56258240-56258344	GM19239	blood:	n/a	n/a
10	E2F4	chr19:56252193-56252357	MCF10A-Er-Src	breast:	n/a	n/a
11	GATA3	chr19:56248412-56248612	SH-SY5Y	brain:	n/a	n/a
12	MYC	chr19:56258306-56258412	MCF-7	breast:	n/a	n/a
13	MYC	chr19:56258308-56258414	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:56259003-56259128	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:56248663-56248772	MCF-7	breast:	n/a	n/a
16	TAL1	chr19:56255612-56255727	K562	blood:	n/a	n/a
17	TCF7L2	chr19:56265960-56266143	Hela-S3	cervix:	n/a	chr19:56265962-56265978 chr19:56265962-56265978 chr19:56265963-56265977 chr19:56265965-56265974
18	ZNF384	chr19:56252891-56253112	K562	blood:	n/a	n/a

(count:305 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56249291-56249341	NB4	blood:	n/a
2	chr19:56249743-56249793	AG10803	skin:	n/a
3	chr19:56250127-56250177	HCT-116	colon:	n/a
4	chr19:56249291-56249341	CMK	blood:	n/a
5	chr19:56250127-56250177	MCF-7	breast:	n/a
6	chr19:56250127-56250177	HPAEpiC	pulmonary alveolar:	n/a
7	chr19:56249743-56249793	Hela-S3	cervix:	n/a
8	chr19:56249743-56249793	PFSK-1	brain:	n/a
9	chr19:56250652-56250702	GM19239	blood:	n/a
10	chr19:56249743-56249793	HCT-116	colon:	n/a
11	chr19:56250652-56250702	PFSK-1	brain:	n/a
12	chr19:56249743-56249793	NH-A	brain:	n/a
13	chr19:56249891-56249941	HRCEpiC	kidney:	n/a
14	chr19:56249891-56249941	BJ	skin:	n/a
15	chr19:56250127-56250177	CMK	blood:	n/a
16	chr19:56249743-56249793	AG09309	skin:	n/a
17	chr19:56249891-56249941	GM19239	blood:	n/a
18	chr19:56249291-56249341	HEEpiC	esophagus:	n/a
19	chr19:56250652-56250702	A549	lung:	n/a
20	chr19:56250127-56250177	LNCaP	prostate:	n/a
21	chr19:56249891-56249941	SK-N-SH	brain:	n/a
22	chr19:56249743-56249793	GM12891	blood:	n/a
23	chr19:56250127-56250177	SK-N-MC	brain:	n/a
24	chr19:56249891-56249941	HRPEpiC	eye:	n/a
25	chr19:56249743-56249793	T-47D	breast:	n/a
26	chr19:56249891-56249941	K562	blood:	n/a
27	chr19:56249743-56249793	HCPEpiC	choroid plexus:	n/a
28	chr19:56250127-56250177	AG04449	skin:	fetal
29	chr19:56249291-56249341	MCF-7	breast:	n/a
30	chr19:56250652-56250702	HEK293	kidney:	embryo
31	chr19:56249291-56249341	HEK293	kidney:	embryo
32	chr19:56249891-56249941	HEEpiC	esophagus:	n/a
33	chr19:56249291-56249341	NHDF-neo	bronchial:	n/a
34	chr19:56250127-56250177	Hela-S3	cervix:	n/a
35	chr19:56249743-56249793	HEEpiC	esophagus:	n/a
36	chr19:56249291-56249341	Hela-S3	cervix:	n/a
37	chr19:56249891-56249941	NT2-D1	testis:	n/a
38	chr19:56250652-56250702	HCPEpiC	choroid plexus:	n/a
39	chr19:56249891-56249941	HCF	heart:	n/a
40	chr19:56250127-56250177	NHBE	bronchial:	n/a
41	chr19:56250127-56250177	NT2-D1	testis:	n/a
42	chr19:56249291-56249341	HMEC	breast:	n/a
43	chr19:56249291-56249341	GM12892	blood:	n/a
44	chr19:56250127-56250177	ECC-1	luminal epithelium:	n/a
45	chr19:56249891-56249941	U87	brain:	n/a
46	chr19:56250652-56250702	SKMC	muscle:	n/a
47	chr19:56249891-56249941	GM12878	blood:	n/a
48	chr19:56250127-56250177	HMEC	breast:	n/a
49	chr19:56249743-56249793	HAEpiC	amniotic membrane:	n/a
50	chr19:56250127-56250177	AG09319	gingival:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56252523..56255492-chr19:56257324..56260762,3	K562	blood:
2	chr19:56252523..56255492-chr19:56257324..56260762,3	K562	blood:
3	chr19:56238198..56240970-chr19:56241234..56244950,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFPL4A-1	chr19:56248651-56248966	NONHSAT068080

No data

Variant related genes	Relation type
RN7SKP109	TF binding region
RFPL4A	TF binding region
NLRP9	TF binding region
RN7SKP109	CpG island
RFPL4A	CpG island
NLRP9	CpG island

Extended variants
information (count: 173 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:173 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs45597436	chr19:56244837-56244838	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs372283899	chr19:56244838-56244839	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs376663019	chr19:56244845-56244846	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs534639462	chr19:56244859-56244860	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs139300317	chr19:56244911-56244912	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs369608035	chr19:56244929-56244930	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs373742721	chr19:56244942-56244943	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs566617976	chr19:56244970-56244971	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs538706869	chr19:56245012-56245013	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs558630577	chr19:56245070-56245071	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs573236439	chr19:56245121-56245122	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs190650329	chr19:56245128-56245129	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs543270036	chr19:56245175-56245176	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs558175237	chr19:56248468-56248469	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs541862989	chr19:56248469-56248470	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs184929950	chr19:56248472-56248473	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs189787871	chr19:56248518-56248519	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs573838900	chr19:56248526-56248527	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs571287225	chr19:56248560-56248561	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs538831580	chr19:56248561-56248562	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs371550588	chr19:56248606-56248607	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs532179882	chr19:56248654-56248655	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs555098156	chr19:56248692-56248693	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs571920789	chr19:56248700-56248701	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs114683555	chr19:56248711-56248712	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs368454091	chr19:56248724-56248725	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs182439669	chr19:56248750-56248751	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs532919896	chr19:56248770-56248771	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs543084352	chr19:56248774-56248775	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs34736097	chr19:56248775-56248776	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs10403433	chr19:56248780-56248781	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs550574399	chr19:56248799-56248800	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs10402884	chr19:56248807-56248808	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs549101197	chr19:56248820-56248821	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs8103725	chr19:56248837-56248838	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs115268376	chr19:56248839-56248840	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs112172984	chr19:56248888-56248889	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs370767891	chr19:56249743-56249744	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
39	rs141752595	chr19:56249744-56249745	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
40	rs559472872	chr19:56249750-56249751	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
41	rs201668498	chr19:56249783-56249784	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
42	rs189047566	chr19:56249891-56249892	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
43	rs565298299	chr19:56249892-56249893	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
44	rs10417652	chr19:56249933-56249934	Inactive region	CpG island	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs150560665	chr19:56250170-56250171	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
46	rs117513746	chr19:56250653-56250654	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
47	rs566316870	chr19:56250699-56250700	Inactive region	CpG island	1 gene(s)	Overlapped CNVs	n/a
48	rs77318755	chr19:56252193-56252194	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs35905323	chr19:56252200-56252201	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs190241095	chr19:56252246-56252247	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Breast cancer	20459607	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Breast cancer	21509527	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56244800-56245200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:56264400-56265000	Enhancers	Liver	Liver
3	chr19:56264800-56265600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr19:56265000-56265400	Flanking Active TSS	Liver	Liver
5	chr19:56265000-56266000	Enhancers	Pancreas	Pancrea
6	chr19:56265400-56265600	Enhancers	Liver	Liver
7	chr19:56265400-56265800	Enhancers	Gastric	stomach
8	chr19:56265600-56265800	Flanking Active TSS	Liver	Liver
9	chr19:56265800-56268200	Weak transcription	Liver	Liver

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