Variant report

Variant	nsv978820
Chromosome Location	chr19:42212524-42214379
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:245)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:42213936-42214015	Kidney_OC	kidney:	n/a	n/a
2	POLR2A	chr19:42212489-42212698	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:42212454-42212719	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:42212379-42212705	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:42212708-42212709	MCF-7	breast:	n/a	n/a
6	USF1	chr19:42212352-42212573	K562	blood:	n/a	n/a
7	USF1	chr19:42212251-42212730	HCT-116	colon:	n/a	n/a
8	USF1	chr19:42212362-42212646	A549	lung:	n/a	n/a
9	USF1	chr19:42212421-42212641	ECC-1	luminal epithelium:	n/a	n/a
10	USF2	chr19:42212394-42212574	Hela-S3	cervix:	n/a	n/a
11	ZNF263	chr19:42212358-42212874	HEK293-T-REx	kidney:	n/a	chr19:42212742-42212751

(count:245 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:42212594-42212644	NH-A	brain:	n/a
2	chr19:42212594-42212644	NH-A	brain:	n/a
3	chr19:42213763-42213813	ovcar-3	ovarian:	n/a
4	chr19:42213020-42213070	IMR90	lung:	fetal
5	chr19:42213763-42213813	A549	lung:	n/a
6	chr19:42212594-42212644	A549	lung:	n/a
7	chr19:42213020-42213070	HAEpiC	amniotic membrane:	n/a
8	chr19:42213763-42213813	NHBE	bronchial:	n/a
9	chr19:42213763-42213813	AG04449	skin:	fetal
10	chr19:42213020-42213070	T-47D	breast:	n/a
11	chr19:42213020-42213070	HCPEpiC	choroid plexus:	n/a
12	chr19:42212501-42212551	HMEC	breast:	n/a
13	chr19:42212594-42212644	HEEpiC	esophagus:	n/a
14	chr19:42213020-42213070	HNPCEpiC	eye:	n/a
15	chr19:42213763-42213813	AG09319	gingival:	n/a
16	chr19:42213020-42213070	HUVEC	blood vessel:	n/a
17	chr19:42213020-42213070	NB4	blood:	n/a
18	chr19:42213763-42213813	AG10803	skin:	n/a
19	chr19:42212501-42212551	GM19239	blood:	n/a
20	chr19:42212501-42212551	HPAEpiC	pulmonary alveolar:	n/a
21	chr19:42213763-42213813	HMEC	breast:	n/a
22	chr19:42212501-42212551	GM06990	blood:	n/a
23	chr19:42213763-42213813	Jurkat	blood:	n/a
24	chr19:42212594-42212644	Caco-2	colon:	n/a
25	chr19:42212594-42212644	HPAEpiC	pulmonary alveolar:	n/a
26	chr19:42212501-42212551	ovcar-3	ovarian:	n/a
27	chr19:42213020-42213070	NH-A	brain:	n/a
28	chr19:42213763-42213813	MCF-7	breast:	n/a
29	chr19:42212594-42212644	HNPCEpiC	eye:	n/a
30	chr19:42212501-42212551	MCF10A-Er-Src	breast:	n/a
31	chr19:42213020-42213070	SK-N-SH	brain:	n/a
32	chr19:42212594-42212644	HMEC	breast:	n/a
33	chr19:42213763-42213813	SK-N-SH_RA	brain:	n/a
34	chr19:42212594-42212644	SK-N-SH_RA	brain:	n/a
35	chr19:42212594-42212644	PFSK-1	brain:	n/a
36	chr19:42212501-42212551	AG04449	skin:	fetal
37	chr19:42213020-42213070	PrEC	prostate:	n/a
38	chr19:42213020-42213070	HRPEpiC	eye:	n/a
39	chr19:42212501-42212551	PANC-1	pancreas:	n/a
40	chr19:42213020-42213070	BE2_C	brain:	n/a
41	chr19:42213020-42213070	ECC-1	luminal epithelium:	n/a
42	chr19:42213763-42213813	AG09309	skin:	n/a
43	chr19:42212501-42212551	IMR90	lung:	fetal
44	chr19:42212594-42212644	ECC-1	luminal epithelium:	n/a
45	chr19:42213763-42213813	LNCaP	prostate:	n/a
46	chr19:42212501-42212551	GM12892	blood:	n/a
47	chr19:42212594-42212644	SK-N-SH	brain:	n/a
48	chr19:42213020-42213070	NHDF-neo	bronchial:	n/a
49	chr19:42212594-42212644	AG10803	skin:	n/a
50	chr19:42212594-42212644	PANC-1	pancreas:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42211076..42212814-chr19:42288522..42291440,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CEACAM6-1	chr19:42213599-42214002	NONHSAT066483
2	lnc-CEACAM6-1	chr19:42212540-42212714	NONHSAT066483

No data

Variant related genes	Relation type
ENSG00000267881	TF binding region
CEACAM5	TF binding region
CEACAM7	TF binding region
ENSG00000267881	CpG island
CEACAM5	CpG island
CEACAM7	CpG island
ENSG00000268833	chromatin interactions

Extended variants
information (count: 111 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550897851	chr19:42212526-42212527	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs45537140	chr19:42212613-42212614	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
3	rs190377739	chr19:42212621-42212622	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
4	rs45614132	chr19:42212622-42212623	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
5	rs115233397	chr19:42212644-42212645	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs267605502	chr19:42212661-42212662	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs201518445	chr19:42212664-42212665	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs200391100	chr19:42212689-42212690	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs200859918	chr19:42212701-42212702	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs538013635	chr19:42212739-42212740	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs144340352	chr19:42212744-42212745	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs200207181	chr19:42212745-42212746	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs111973464	chr19:42212753-42212754	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs72455487	chr19:42212754-42212755	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs3217253	chr19:42212755-42212756	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs114263190	chr19:42212797-42212798	Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs544755548	chr19:42212811-42212812	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs8113098	chr19:42212819-42212820	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
19	rs182639723	chr19:42212826-42212827	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs542655390	chr19:42212874-42212875	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
21	rs562323116	chr19:42212908-42212909	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs187608648	chr19:42212919-42212920	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs544761106	chr19:42212941-42212942	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs76806056	chr19:42212974-42212975	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs369318726	chr19:42212981-42212982	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs533603769	chr19:42213000-42213001	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs551460723	chr19:42213014-42213015	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs529125196	chr19:42213027-42213028	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	CpG island	2 gene(s)	Overlapped CNVs	n/a
29	rs73545178	chr19:42213029-42213030	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	CpG island	2 gene(s)	Overlapped CNVs	n/a
30	rs547621122	chr19:42213030-42213031	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	CpG island	2 gene(s)	Overlapped CNVs	n/a
31	rs527630512	chr19:42213066-42213067	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	CpG island	2 gene(s)	Overlapped CNVs	n/a
32	rs548985087	chr19:42213104-42213105	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs567514133	chr19:42213112-42213113	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs565830362	chr19:42213122-42213123	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs539766150	chr19:42213128-42213129	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs112637399	chr19:42213137-42213138	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs537734302	chr19:42213162-42213163	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs556449609	chr19:42213192-42213193	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs117222609	chr19:42213223-42213224	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs569702888	chr19:42213240-42213241	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs538875906	chr19:42213243-42213244	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs553862876	chr19:42213252-42213253	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs572175711	chr19:42213261-42213262	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs4802127	chr19:42213276-42213277	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs554620558	chr19:42213277-42213278	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs555480936	chr19:42213291-42213292	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs111736472	chr19:42213295-42213296	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs375743111	chr19:42213359-42213360	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs544559768	chr19:42213360-42213361	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs147741773	chr19:42213407-42213408	Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

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
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	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
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42211000-42214200	Active TSS	Rectal Smooth Muscle	rectum
2	chr19:42211200-42212600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr19:42211400-42212600	Weak transcription	Fetal Intestine Small	intestine
4	chr19:42211600-42212600	Weak transcription	Fetal Intestine Large	intestine
5	chr19:42212000-42216200	Active TSS	Esophagus	oesophagus
6	chr19:42212000-42222800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:42212400-42213200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr19:42212400-42213800	Active TSS	Colonic Mucosa	Colon
9	chr19:42212400-42214400	Active TSS	Stomach Mucosa	stomach
10	chr19:42212600-42212800	Enhancers	Fetal Intestine Large	intestine
11	chr19:42212600-42212800	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr19:42212600-42212800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
13	chr19:42212600-42214000	Active TSS	Small Intestine	intestine
14	chr19:42212600-42215200	Active TSS	Fetal Intestine Small	intestine
15	chr19:42212800-42213000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr19:42212800-42213800	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr19:42213000-42213400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr19:42213000-42213600	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:42213000-42215000	Active TSS	Fetal Stomach	stomach
20	chr19:42213200-42213600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr19:42213600-42214000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:42213600-42217200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
23	chr19:42213800-42216600	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
24	chr19:42213800-42216600	Transcr. at gene 5' and 3'	Sigmoid Colon	Sigmoid Colon
25	chr19:42214000-42214600	Bivalent/Poised TSS	Small Intestine	intestine
26	chr19:42214000-42217000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
27	chr19:42214200-42214600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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