Variant report

Variant	nsv9718
Chromosome Location	chr19:37839070-37852872
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	CEBPB	chr19:37838989-37839353	HepG2	liver:	n/a	chr19:37839167-37839176 chr19:37839165-37839176 chr19:37839167-37839178
2	CEBPB	chr19:37839034-37839295	K562	blood:	n/a	chr19:37839167-37839176 chr19:37839165-37839176 chr19:37839167-37839178
3	CEBPB	chr19:37838998-37839346	A549	lung:	n/a	chr19:37839167-37839176 chr19:37839165-37839176 chr19:37839167-37839178
4	CEBPB	chr19:37850269-37850370	HepG2	liver:	n/a	chr19:37850288-37850299
5	CEBPB	chr19:37838996-37839331	IMR90	lung:	n/a	chr19:37839167-37839176 chr19:37839165-37839176 chr19:37839167-37839178
6	CTCF	chr19:37839801-37839886	GM13976	blood:	n/a	n/a
7	GATA2	chr19:37841481-37841781	SH-SY5Y	brain:	n/a	n/a
8	JUND	chr19:37840038-37840238	HepG2	liver:	n/a	n/a
9	MAFK	chr19:37839341-37839508	HepG2	liver:	n/a	chr19:37839427-37839442
10	MAFK	chr19:37839330-37839530	HepG2	liver:	n/a	chr19:37839427-37839442
11	POLR2A	chr19:37852871-37853431	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr19:37839543-37839566	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:37852835-37853349	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr19:37843837-37844068	A549	lung:	n/a	n/a
15	SPI1	chr19:37845646-37845909	GM12878	blood:	n/a	n/a
16	SPI1	chr19:37845642-37845810	GM12878	blood:	n/a	n/a
17	SPI1	chr19:37845552-37845817	GM12891	blood:	n/a	n/a
18	STAT3	chr19:37838886-37839324	MCF10A-Er-Src	breast:	n/a	chr19:37839155-37839163 chr19:37839167-37839175
19	STAT3	chr19:37839009-37839333	MCF10A-Er-Src	breast:	n/a	chr19:37839155-37839163 chr19:37839167-37839175
20	STAT3	chr19:37839016-37839329	MCF10A-Er-Src	breast:	n/a	chr19:37839155-37839163 chr19:37839167-37839175
21	STAT3	chr19:37838990-37839233	MCF10A-Er-Src	breast:	n/a	chr19:37839155-37839163 chr19:37839167-37839175

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:37840935-37840985	HPAEpiC	pulmonary alveolar:	n/a
2	chr19:37840935-37840985	AoSMC	blood vessel:	n/a
3	chr19:37840935-37840985	HRE	kidney:	n/a
4	chr19:37840935-37840985	BE2_C	brain:	n/a
5	chr19:37840935-37840985	A549	lung:	n/a
6	chr19:37840935-37840985	SAEC	small airway:	n/a
7	chr19:37840935-37840985	SK-N-SH_RA	brain:	n/a
8	chr19:37840935-37840985	AG04449	skin:	fetal
9	chr19:37840935-37840985	AG04450	lung:	fetal
10	chr19:37840935-37840985	GM12892	blood:	n/a
11	chr19:37840935-37840985	SKMC	muscle:	n/a
12	chr19:37840935-37840985	NHBE	bronchial:	n/a
13	chr19:37840935-37840985	ovcar-3	ovarian:	n/a
14	chr19:37840935-37840985	AG10803	skin:	n/a
15	chr19:37840935-37840985	GM06990	blood:	n/a
16	chr19:37840935-37840985	RPTEC	kidney:	n/a
17	chr19:37840935-37840985	NT2-D1	testis:	n/a
18	chr19:37840935-37840985	GM12891	blood:	n/a
19	chr19:37840935-37840985	T-47D	breast:	n/a
20	chr19:37840935-37840985	Jurkat	blood:	n/a
21	chr19:37840935-37840985	Hepatocyte	liver:	n/a
22	chr19:37840935-37840985	Caco-2	colon:	n/a
23	chr19:37840935-37840985	HUVEC	blood vessel:	n/a
24	chr19:37840935-37840985	MCF-7	breast:	n/a
25	chr19:37840935-37840985	AG09319	gingival:	n/a
26	chr19:37840935-37840985	HAEpiC	amniotic membrane:	n/a
27	chr19:37840935-37840985	HepG2	liver:	n/a
28	chr19:37840935-37840985	PrEC	prostate:	n/a
29	chr19:37840935-37840985	SK-N-SH	brain:	n/a
30	chr19:37840935-37840985	HMEC	breast:	n/a
31	chr19:37840935-37840985	NHDF-neo	bronchial:	n/a
32	chr19:37840935-37840985	K562	blood:	n/a
33	chr19:37840935-37840985	IMR90	lung:	fetal
34	chr19:37840935-37840985	PANC-1	pancreas:	n/a
35	chr19:37840935-37840985	PFSK-1	brain:	n/a
36	chr19:37840935-37840985	H1-hESC	embryonic stem cell:	embryo
37	chr19:37840935-37840985	AG09309	skin:	n/a
38	chr19:37840935-37840985	HEK293	kidney:	embryo
39	chr19:37840935-37840985	HEEpiC	esophagus:	n/a
40	chr19:37840935-37840985	GM12878	blood:	n/a
41	chr19:37840935-37840985	Hela-S3	cervix:	n/a
42	chr19:37840935-37840985	U87	brain:	n/a
43	chr19:37840935-37840985	NH-A	brain:	n/a
44	chr19:37840935-37840985	GM19239	blood:	n/a
45	chr19:37840935-37840985	MCF10A-Er-Src	breast:	n/a
46	chr19:37840935-37840985	BJ	skin:	n/a
47	chr19:37840935-37840985	HRPEpiC	eye:	n/a
48	chr19:37840935-37840985	HNPCEpiC	eye:	n/a
49	chr19:37840935-37840985	HIPEpiC	eye:	n/a
50	chr19:37840935-37840985	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37838063..37840096-chr19:37846657..37849398,2	MCF-7	breast:
2	chr19:37851946..37854387-chr19:37859960..37862069,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF527-4	chr19:37848864-37848941	NONHSAT066106

Variant related genes	Relation type
HKR1	TF binding region
HKR1	CpG island
ENSG00000189164	chromatin interactions
ENSG00000181666	chromatin interactions

Extended variants
information (count: 532 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:532 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10405407	chr19:37839164-37839165	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs578197332	chr19:37839193-37839194	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs190419342	chr19:37839258-37839259	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs34757761	chr19:37839276-37839277	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs560743549	chr19:37839313-37839314	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs528004251	chr19:37839330-37839331	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs2972598	chr19:37839352-37839353	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs182646456	chr19:37839381-37839382	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs543233008	chr19:37839394-37839395	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs561812705	chr19:37839486-37839487	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs528934585	chr19:37839526-37839527	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs550314236	chr19:37839606-37839607	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs568801823	chr19:37839656-37839657	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs117519141	chr19:37839707-37839708	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs548781593	chr19:37839734-37839735	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs187818098	chr19:37839809-37839810	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs566414792	chr19:37839829-37839830	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs2921561	chr19:37839871-37839872	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs142444039	chr19:37839897-37839898	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs79258984	chr19:37839939-37839940	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs11667380	chr19:37839945-37839946	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs146641191	chr19:37839972-37839973	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs556303204	chr19:37839981-37839982	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs577989607	chr19:37840063-37840064	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs545402481	chr19:37840090-37840091	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs147902852	chr19:37840109-37840110	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs572772919	chr19:37840114-37840115	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs543245100	chr19:37840136-37840137	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs35830725	chr19:37840188-37840189	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs193156633	chr19:37840200-37840201	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs528996636	chr19:37840205-37840206	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs544267835	chr19:37840210-37840211	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs183314926	chr19:37840232-37840233	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs374996828	chr19:37840241-37840242	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs189123271	chr19:37840324-37840325	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs551744891	chr19:37840343-37840344	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs550955497	chr19:37840387-37840388	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs566480041	chr19:37840388-37840389	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs193072981	chr19:37840420-37840421	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs548778498	chr19:37840421-37840422	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs567424203	chr19:37840443-37840444	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs537620134	chr19:37840451-37840452	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs550383176	chr19:37840457-37840458	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs183726786	chr19:37840523-37840524	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs188143628	chr19:37840545-37840546	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs368289499	chr19:37840563-37840564	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs539081181	chr19:37840595-37840596	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs148885622	chr19:37840599-37840600	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs143531610	chr19:37840605-37840606	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs60346583	chr19:37840688-37840689	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:60)

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
Pleomorphic liposarcoma	18784837	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
Disorders of sex development	21048976	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
Lung cancer	18438408	CNVD
Glioma	17123091	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:566 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37826200-37853200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37826600-37848800	Weak transcription	Small Intestine	intestine
3	chr19:37826600-37856200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:37826600-37861600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:37826800-37846600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:37826800-37847000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:37826800-37852600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37826800-37853400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:37827000-37845800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:37827000-37853400	Weak transcription	Stomach Mucosa	stomach
11	chr19:37828000-37855800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:37830000-37846800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:37830000-37853600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:37830800-37853200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:37831800-37840400	Strong transcription	Ovary	ovary
16	chr19:37831800-37840600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:37831800-37842000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:37831800-37846400	Strong transcription	Dnd41	blood
19	chr19:37832000-37842000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr19:37832200-37840600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:37832200-37840800	Strong transcription	Primary T cells from cord blood	blood
22	chr19:37832200-37842000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr19:37832600-37843200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:37832600-37852200	Weak transcription	Fetal Thymus	thymus
25	chr19:37832800-37850800	Weak transcription	HMEC	breast
26	chr19:37832800-37852400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:37833000-37845400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:37833600-37840800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:37833800-37840800	Strong transcription	Thymus	Thymus
30	chr19:37833800-37843400	Strong transcription	Adipose Nuclei	Adipose
31	chr19:37834200-37840200	ZNF genes & repeats	Liver	Liver
32	chr19:37834200-37841800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:37834400-37840000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:37834400-37840400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:37834400-37840400	Strong transcription	Fetal Lung	lung
36	chr19:37834400-37840800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:37834400-37841600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:37834400-37842000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:37834400-37843000	Strong transcription	Placenta	Placenta
40	chr19:37834400-37843200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:37834400-37844200	Strong transcription	Fetal Stomach	stomach
42	chr19:37834400-37845200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:37834400-37847800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr19:37834600-37840000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr19:37834600-37840200	Strong transcription	Fetal Brain Female	brain
46	chr19:37834600-37840200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:37834600-37840400	Strong transcription	HSMMtube	muscle
48	chr19:37834600-37840600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:37834600-37840800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:37834600-37841400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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