Variant report

Variant	esv1804308
Chromosome Location	chr19:56864731-56877187
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	ARID3A	chr19:56866390-56867520	HepG2	liver:	n/a	n/a
2	BACH1	chr19:56868468-56868645	K562	blood:	n/a	n/a
3	CBX3	chr19:56868338-56868616	K562	blood:	n/a	n/a
4	CBX3	chr19:56868281-56868662	K562	blood:	n/a	n/a
5	CEBPB	chr19:56866960-56867199	HepG2	liver:	n/a	n/a
6	CEBPB	chr19:56867598-56867926	HepG2	liver:	n/a	chr19:56867757-56867768
7	CEBPB	chr19:56868669-56868820	HepG2	liver:	n/a	n/a
8	CTCF	chr19:56871227-56871255	GM13976	blood:	n/a	n/a
9	CTCF	chr19:56870343-56870393	LNCaP	prostate:	n/a	n/a
10	CTCF	chr19:56869292-56869357	LNCaP	prostate:	n/a	n/a
11	EP300	chr19:56866783-56867261	HepG2	liver:	n/a	n/a
12	EP300	chr19:56866943-56867306	HepG2	liver:	n/a	n/a
13	FOXA1	chr19:56866747-56867374	HepG2	liver:	n/a	chr19:56867126-56867138
14	FOXA1	chr19:56866798-56867266	HepG2	liver:	n/a	chr19:56867126-56867138
15	FOXA1	chr19:56866754-56867348	HepG2	liver:	n/a	chr19:56867126-56867138
16	FOXA1	chr19:56866757-56867170	HepG2	liver:	n/a	chr19:56867126-56867138
17	FOXA2	chr19:56866419-56867578	HepG2	liver:	n/a	chr19:56867126-56867138
18	FOXA2	chr19:56866848-56867211	HepG2	liver:	n/a	chr19:56867126-56867138
19	GATA3	chr19:56872313-56872613	SK-N-SH	brain:	n/a	n/a
20	HNF4A	chr19:56866857-56867210	HepG2	liver:	n/a	chr19:56867018-56867031 chr19:56867017-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867018-56867030 chr19:56867015-56867033 chr19:56867018-56867031
21	HNF4A	chr19:56866844-56867258	HepG2	liver:	n/a	chr19:56867018-56867031 chr19:56867017-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867018-56867030 chr19:56867015-56867033 chr19:56867018-56867031
22	HNF4G	chr19:56866916-56867138	HepG2	liver:	n/a	chr19:56867018-56867031 chr19:56867017-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867017-56867031 chr19:56867018-56867030 chr19:56867018-56867030 chr19:56867017-56867032 chr19:56867015-56867033 chr19:56867018-56867031
23	JUND	chr19:56868461-56868610	K562	blood:	n/a	chr19:56868533-56868544
24	JUND	chr19:56868515-56868638	HepG2	liver:	n/a	chr19:56868533-56868544
25	KAP1	chr19:56867955-56868625	K562	blood:	n/a	n/a
26	KAP1	chr19:56872011-56872462	K562	blood:	n/a	n/a
27	MAFF	chr19:56868354-56868666	K562	blood:	n/a	n/a
28	MAFK	chr19:56874537-56874757	HepG2	liver:	n/a	n/a
29	MAFK	chr19:56876857-56877067	HepG2	liver:	n/a	n/a
30	MAFK	chr19:56868446-56868656	K562	blood:	n/a	n/a
31	MAFK	chr19:56874542-56874718	HepG2	liver:	n/a	n/a
32	NFIC	chr19:56866807-56867338	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:56866837-56866897	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr19:56873708-56873812	A549	lung:	n/a	n/a
35	RCOR1	chr19:56868480-56868514	K562	blood:	n/a	n/a
36	RXRA	chr19:56866913-56867231	HepG2	liver:	n/a	chr19:56867017-56867026
37	SP1	chr19:56866842-56867321	HepG2	liver:	n/a	n/a
38	STAT3	chr19:56867222-56867414	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr19:56871337-56871457	MCF10A-Er-Src	breast:	n/a	n/a
40	TCF7L2	chr19:56866788-56867248	HepG2	liver:	n/a	n/a
41	TRIM28	chr19:56868272-56868676	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56861231..56863974-chr19:56864374..56866865,3	K562	blood:
2	chr19:56861231..56864651-chr19:56864910..56868187,3	K562	blood:
3	chr19:56874655..56877497-chr19:56878126..56879780,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN5A-3	chr19:56876325-56876366	ENSG00000267606.1
2	lnc-ZSCAN5A-3	chr19:56877085-56877318	ENSG00000267606.1
3	lnc-ZSCAN5A-3	chr19:56877085-56877115	NONHSAT068109
4	lnc-ZSCAN5A-3	chr19:56874604-56874767	ENSG00000267606.1
5	lnc-ZSCAN5A-3	chr19:56876325-56876426	ENSG00000267606.1
6	lnc-ZSCAN5A-3	chr19:56865862-56866010	ENSG00000267606.1
7	lnc-ZSCAN5A-3	chr19:56877084-56877318	ENSG00000267606.1
8	lnc-ZSCAN5A-3	chr19:56874604-56874767	NONHSAT068109
9	lnc-ZSCAN5A-3	chr19:56874545-56874767	ENSG00000267606.1

Variant related genes	Relation type
ZNF542	TF binding region
ENSG00000267606	TF binding region
ENSG00000131848	chromatin interactions
ENSG00000240225	chromatin interactions
ENSG00000267606	chromatin interactions

Extended variants
information (count: 513 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:513 , 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	rs2869162	chr19:56864731-56864732	Weak transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs193012104	chr19:56864752-56864753	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs539344300	chr19:56864780-56864781	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs535577086	chr19:56864813-56864814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs555872423	chr19:56864814-56864815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs386811210	chr19:56864853-56864854	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs112879825	chr19:56864854-56864855	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs2017421	chr19:56864860-56864861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs138305035	chr19:56864866-56864867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs576693370	chr19:56864893-56864894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs185582985	chr19:56864904-56864905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs12104159	chr19:56864905-56864906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs576226645	chr19:56864907-56864908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs369854353	chr19:56864910-56864911	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs189256470	chr19:56864914-56864915	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs12104160	chr19:56864928-56864929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs527402891	chr19:56864940-56864941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs547380568	chr19:56864942-56864943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs56374537	chr19:56864960-56864961	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs372782884	chr19:56864961-56864962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs112441225	chr19:56864964-56864965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs547790062	chr19:56864980-56864981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs8102637	chr19:56864997-56864998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs368619512	chr19:56865005-56865006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs536010167	chr19:56865009-56865010	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs149525290	chr19:56865020-56865021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs12104156	chr19:56865024-56865025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs534808124	chr19:56865025-56865026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs371908679	chr19:56865039-56865040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs12104157	chr19:56865046-56865047	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs201284094	chr19:56865057-56865058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs564666898	chr19:56865068-56865069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs577661656	chr19:56865070-56865071	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs539343360	chr19:56865075-56865076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs556382317	chr19:56865076-56865077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs183749996	chr19:56865083-56865084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs201804534	chr19:56865094-56865095	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs112784589	chr19:56865097-56865098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs199926740	chr19:56865099-56865100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs386811211	chr19:56865105-56865106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs12104315	chr19:56865107-56865108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs12104316	chr19:56865125-56865126	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs112382847	chr19:56865137-56865138	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs113972626	chr19:56865144-56865145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs564070526	chr19:56865154-56865155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs12977903	chr19:56865156-56865157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs532988034	chr19:56865174-56865175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs549522845	chr19:56865175-56865176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs563962880	chr19:56865181-56865182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs529583792	chr19:56865201-56865202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
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
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Glioma	20126413	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56855000-56870200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr19:56859400-56872800	Weak transcription	Ovary	ovary
3	chr19:56862000-56868400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:56862400-56866400	Weak transcription	Right Atrium	heart
5	chr19:56863000-56872800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56864400-56864800	ZNF genes & repeats	Liver	Liver
7	chr19:56864600-56865600	Weak transcription	Brain Substantia Nigra	brain
8	chr19:56864600-56865800	Weak transcription	HepG2	liver
9	chr19:56864800-56865400	Weak transcription	Liver	Liver
10	chr19:56865400-56865800	Active TSS	Liver	Liver
11	chr19:56865800-56867200	Enhancers	Liver	Liver
12	chr19:56865800-56867200	Enhancers	HepG2	liver
13	chr19:56866200-56871000	Weak transcription	Primary T cells from cord blood	blood
14	chr19:56866800-56867600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:56867200-56867600	Flanking Active TSS	HepG2	liver
16	chr19:56867200-56867800	Flanking Active TSS	Liver	Liver
17	chr19:56867600-56867800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:56867600-56868400	Enhancers	HepG2	liver
19	chr19:56867800-56868000	Enhancers	Liver	Liver
20	chr19:56868400-56868800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56869400-56872400	Weak transcription	Left Ventricle	heart
22	chr19:56871000-56871200	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr19:56871600-56877400	ZNF genes & repeats	Liver	Liver
24	chr19:56872200-56879400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:56872400-56872600	ZNF genes & repeats	Brain Hippocampus Middle	brain
26	chr19:56872400-56873200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
27	chr19:56872400-56873800	Strong transcription	Left Ventricle	heart
28	chr19:56872600-56872800	Weak transcription	Fetal Heart	heart
29	chr19:56872600-56873200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr19:56872600-56873200	ZNF genes & repeats	Brain Anterior Caudate	brain
31	chr19:56872600-56875400	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:56872800-56873200	ZNF genes & repeats	Aorta	Aorta
33	chr19:56872800-56873200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr19:56872800-56873200	ZNF genes & repeats	Fetal Kidney	kidney
35	chr19:56872800-56873200	ZNF genes & repeats	Fetal Lung	lung
36	chr19:56872800-56873200	ZNF genes & repeats	Ovary	ovary
37	chr19:56872800-56873200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
38	chr19:56872800-56873400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:56873000-56874400	Weak transcription	Fetal Heart	heart
40	chr19:56873200-56874200	Weak transcription	Fetal Lung	lung
41	chr19:56873200-56874200	ZNF genes & repeats	Fetal Stomach	stomach
42	chr19:56873200-56874600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:56873200-56874800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:56873400-56875200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:56873800-56874000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:56873800-56879000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:56873800-56879200	Weak transcription	Left Ventricle	heart
48	chr19:56874000-56876600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr19:56874000-56878400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:56874200-56874600	Weak transcription	Fetal Stomach	stomach

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