Variant report

Variant	esv1804860
Chromosome Location	chr19:23461424-23466657
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	chr19:23464504-23464974	HepG2	liver:	n/a	n/a
2	BHLHE40	chr19:23465524-23465669	GM12878	blood:	n/a	n/a
3	CEBPB	chr19:23464853-23465097	HepG2	liver:	n/a	n/a
4	CTCF	chr19:23466597-23467215	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr19:23464540-23464690	HepG2	liver:	n/a	n/a
6	CTCF	chr19:23466540-23466690	HCM	heart:	n/a	n/a
7	CTCF	chr19:23464980-23465130	HMF	breast:	n/a	n/a
8	EP300	chr19:23464587-23464881	HepG2	liver:	n/a	n/a
9	EP300	chr19:23464430-23464769	HepG2	liver:	n/a	chr19:23464522-23464536 chr19:23464458-23464472
10	FOXA1	chr19:23460988-23461427	HepG2	liver:	n/a	n/a
11	FOXA1	chr19:23460934-23461424	HepG2	liver:	n/a	n/a
12	FOXA1	chr19:23464530-23465051	HepG2	liver:	n/a	chr19:23464719-23464731 chr19:23464723-23464735 chr19:23464734-23464746
13	FOXA1	chr19:23464527-23464845	HepG2	liver:	n/a	chr19:23464719-23464731 chr19:23464723-23464735 chr19:23464734-23464746
14	FOXA1	chr19:23464540-23464921	HepG2	liver:	n/a	chr19:23464719-23464731 chr19:23464723-23464735 chr19:23464734-23464746
15	HNF4A	chr19:23464525-23464761	HepG2	liver:	n/a	chr19:23464688-23464702 chr19:23464541-23464549 chr19:23464686-23464704 chr19:23464687-23464702 chr19:23464688-23464703 chr19:23464688-23464702
16	HNF4A	chr19:23464518-23464894	HepG2	liver:	n/a	chr19:23464688-23464702 chr19:23464541-23464549 chr19:23464686-23464704 chr19:23464687-23464702 chr19:23464688-23464703 chr19:23464688-23464702
17	HNF4G	chr19:23464534-23464777	HepG2	liver:	n/a	chr19:23464688-23464702 chr19:23464541-23464549 chr19:23464686-23464704 chr19:23464686-23464701 chr19:23464688-23464703 chr19:23464688-23464702
18	POLR2A	chr19:23464463-23464706	HepG2	liver:	n/a	n/a
19	RAD21	chr19:23464629-23464684	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr19:23466636-23467117	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr19:23466523-23467147	SK-N-SH	brain:	n/a	n/a
22	SMC3	chr19:23466528-23467232	SK-N-SH	brain:	n/a	n/a
23	STAT3	chr19:23464694-23464815	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:56735011..56736549-chr19:23464937..23466566,2	MCF-7	breast:
2	chr19:23456110..23458063-chr19:23465875..23467770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213971	TF binding region
ENSG00000269107	TF binding region
VN1R90P	TF binding region
ENSG00000213971	chromatin interactions

Extended variants
information (count: 265 )
Associated
traits (count: 41 )

Variant overlapped rSNPs/rCNVs (count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1658216	chr19:23461424-23461425	Active TSS Weak transcription Enhancers	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs556139129	chr19:23461437-23461438	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs79151024	chr19:23461439-23461440	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs574364254	chr19:23461444-23461445	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs369437800	chr19:23461447-23461448	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs541469227	chr19:23461484-23461485	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs559748714	chr19:23461489-23461490	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs147056416	chr19:23461527-23461528	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs138330414	chr19:23461537-23461538	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs551496005	chr19:23461551-23461552	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs397859443	chr19:23461585-23461586	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs397859870	chr19:23461586-23461587	Active TSS Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs564134911	chr19:23461604-23461605	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs578218517	chr19:23461611-23461612	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs540820757	chr19:23461613-23461614	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs531574332	chr19:23461621-23461622	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs549563012	chr19:23461625-23461626	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs207477058	chr19:23461638-23461639	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs561675796	chr19:23461645-23461646	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs443473	chr19:23461657-23461658	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs368449401	chr19:23461705-23461706	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs572959448	chr19:23461710-23461711	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs111929694	chr19:23461711-23461712	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs547005182	chr19:23461736-23461737	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs565644218	chr19:23461782-23461783	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs147443870	chr19:23461789-23461790	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs551419302	chr19:23461791-23461792	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569644258	chr19:23461811-23461812	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs554127499	chr19:23461910-23461911	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs34803165	chr19:23461946-23461947	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs148482915	chr19:23461961-23461962	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs116081286	chr19:23461999-23462000	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs574399681	chr19:23462023-23462024	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs112671500	chr19:23462024-23462025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs567876682	chr19:23462059-23462060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs377227126	chr19:23462062-23462063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs536906696	chr19:23462099-23462100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs529854451	chr19:23462100-23462101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs67145045	chr19:23462103-23462104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs552281179	chr19:23462104-23462105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs34595072	chr19:23462110-23462111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs376848411	chr19:23462111-23462112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs369294518	chr19:23462156-23462157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs11883091	chr19:23462161-23462162	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs545063848	chr19:23462162-23462163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs112605538	chr19:23462178-23462179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs183525824	chr19:23462185-23462186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs543248524	chr19:23462189-23462190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs188520042	chr19:23462200-23462201	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs529173257	chr19:23462253-23462254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:41)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Prostate cancer	16573809	CNVD
Chordoma	18071362	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	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
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Colorectal cancer	20459617	CNVD
Ductal carcinoma	22052326	CNVD
Cancer	20164920	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23457600-23470400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:23457800-23464200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr19:23458600-23464400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:23461200-23461600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:23461400-23462000	Enhancers	HepG2	liver
6	chr19:23461600-23462000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:23462000-23462800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:23462000-23463400	Weak transcription	HepG2	liver
9	chr19:23463400-23464800	Enhancers	HepG2	liver
10	chr19:23464200-23464400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:23464200-23466000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr19:23464200-23467000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr19:23464400-23465200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:23464400-23467000	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr19:23464600-23466000	Enhancers	Primary T cells from cord blood	blood
16	chr19:23464800-23465000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:23464800-23465000	Flanking Active TSS	HepG2	liver
18	chr19:23465000-23465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:23465000-23465400	Enhancers	HepG2	liver
20	chr19:23465200-23466000	Enhancers	Dnd41	blood
21	chr19:23465200-23466200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr19:23465200-23466600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:23465400-23465600	Flanking Active TSS	HepG2	liver
24	chr19:23465600-23465800	Enhancers	HepG2	liver
25	chr19:23465800-23466000	Flanking Active TSS	HepG2	liver
26	chr19:23466000-23466800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:23466000-23467000	Enhancers	HepG2	liver
28	chr19:23466200-23466600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:23466400-23470600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:23466600-23467000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:23466600-23467200	Enhancers	Primary T cells fromperipheralblood	blood

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