Variant report

Variant	esv19824
Chromosome Location	chr3:97904245-97914149
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:280)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:280 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr3:97907429-97907720	GM12878	blood:	n/a	n/a
2	BRCA1	chr3:97907317-97907430	GM12878	blood:	n/a	n/a
3	CHD1	chr3:97907603-97907803	GM12878	blood:	n/a	n/a
4	CHD2	chr3:97907426-97907647	GM12878	blood:	n/a	n/a
5	CTCF	chr3:97907505-97907660	GM13976	blood:	n/a	n/a
6	CTCF	chr3:97907420-97907570	HEEpiC	esophagus:	n/a	n/a
7	CTCF	chr3:97907480-97907630	HPAF	blood vessel:	n/a	n/a
8	CTCF	chr3:97907361-97907709	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr3:97907510-97907651	Kidney_OC	kidney:	n/a	n/a
10	CTCF	chr3:97907548-97907635	Pancreas_OC	pancreas:	n/a	n/a
11	CTCF	chr3:97907500-97907650	HL-60	blood:	n/a	n/a
12	CTCF	chr3:97907560-97907710	GM12872	blood:	n/a	n/a
13	CTCF	chr3:97904113-97904299	HepG2	liver:	n/a	n/a
14	CTCF	chr3:97907473-97907694	LNCaP	prostate:	n/a	n/a
15	CTCF	chr3:97904120-97904270	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:97907460-97907610	BJ	skin:	n/a	n/a
17	CTCF	chr3:97907540-97907690	AG10803	skin:	n/a	n/a
18	CTCF	chr3:97907360-97907510	HFF-Myc	foreskin:	n/a	n/a
19	CTCF	chr3:97907480-97907630	NHEK	skin:	n/a	n/a
20	CTCF	chr3:97907490-97907658	GM10266	blood:	n/a	n/a
21	CTCF	chr3:97907500-97907650	HMEC	breast:	n/a	n/a
22	CTCF	chr3:97904013-97904486	HCT-116	colon:	n/a	n/a
23	CTCF	chr3:97907325-97907855	MCF-7	breast:	n/a	n/a
24	CTCF	chr3:97904100-97904250	GM12865	blood:	n/a	n/a
25	CTCF	chr3:97904160-97904310	GM12869	blood:	n/a	n/a
26	CTCF	chr3:97907321-97907742	MCF-7	breast:	n/a	n/a
27	CTCF	chr3:97907499-97907682	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr3:97907500-97907650	GM12872	blood:	n/a	n/a
29	CTCF	chr3:97904189-97904246	K562	blood:	n/a	n/a
30	CTCF	chr3:97907460-97907610	GM12870	blood:	n/a	n/a
31	CTCF	chr3:97903808-97904617	HCT-116	colon:	n/a	n/a
32	CTCF	chr3:97904183-97904274	GM10266	blood:	n/a	n/a
33	CTCF	chr3:97907480-97907630	HMF	breast:	n/a	n/a
34	CTCF	chr3:97907560-97907710	HVMF	connective:	n/a	n/a
35	CTCF	chr3:97904046-97904409	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:97907487-97907682	Medullo	brain:	n/a	n/a
37	CTCF	chr3:97907540-97907690	GM12865	blood:	n/a	n/a
38	CTCF	chr3:97907500-97907669	GM20000	blood:	n/a	n/a
39	CTCF	chr3:97904140-97904290	GM12870	blood:	n/a	n/a
40	CTCF	chr3:97907227-97907960	A549	lung:	n/a	n/a
41	CTCF	chr3:97907500-97907650	BE2_C	brain:	n/a	n/a
42	CTCF	chr3:97907500-97907650	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr3:97907464-97907674	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:97904240-97904390	A549	lung:	n/a	n/a
45	CTCF	chr3:97907425-97907690	HepG2	liver:	n/a	n/a
46	CTCF	chr3:97907483-97907663	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr3:97907449-97907782	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:97904131-97904263	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr3:97904160-97904310	HEEpiC	esophagus:	n/a	n/a
50	CTCF	chr3:97907540-97907690	GM06990	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:97907135..97908282-chr3:98048120..98049025,6	MCF-7	breast:
2	chr3:97758293..97759189-chr3:97903652..97904697,9	MCF-7	breast:
3	chr3:97757849..97759434-chr3:97903672..97904727,17	MCF-7	breast:
4	chr3:97904894..97907628-chr3:98045904..98048505,2	K562	blood:
5	chr3:97907135..97908080-chr3:98062563..98063391,2	MCF-7	breast:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733
2	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
3	lnc-OR5H15-1	chr3:97912268-97912342	XLOC_002733
4	lnc-OR5H15-1	chr3:97910049-97910454	XLOC_002733
5	lnc-MINA-6	chr3:97904268-97904295	NONHSAT090787

No data

Variant related genes	Relation type
OR5H5P	TF binding region
TGFB2	miRNA target sites
LYPD3	miRNA target sites

Extended variants
information (count: 720 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:720 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs386663669	chr3:97904247-97904248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs71618720	chr3:97904256-97904257	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs9848177	chr3:97904257-97904258	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs9848199	chr3:97904293-97904294	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs564647511	chr3:97904335-97904336	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs151338372	chr3:97904354-97904355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs559848517	chr3:97904358-97904359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs67055113	chr3:97904379-97904380	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs545907227	chr3:97904385-97904386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs562618269	chr3:97904393-97904394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs386663671	chr3:97904412-97904413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs71113891	chr3:97904422-97904423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs67479571	chr3:97904453-97904454	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs561547008	chr3:97904477-97904478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs373734702	chr3:97904481-97904482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs66496940	chr3:97904505-97904506	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs67894920	chr3:97904531-97904532	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs386663672	chr3:97904555-97904556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs13088901	chr3:97904563-97904564	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs189432739	chr3:97904566-97904567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs537967507	chr3:97904568-97904569	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs13088925	chr3:97904594-97904595	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs13084315	chr3:97904616-97904617	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs140605913	chr3:97904652-97904653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs13084481	chr3:97904673-97904674	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs13089085	chr3:97904680-97904681	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs545841900	chr3:97904685-97904686	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150445255	chr3:97904687-97904688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs570012424	chr3:97904706-97904707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs576171024	chr3:97904711-97904712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs541964712	chr3:97904720-97904721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs561275681	chr3:97904731-97904732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs145361645	chr3:97904761-97904762	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs540559693	chr3:97904769-97904770	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs560869674	chr3:97904817-97904818	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs532359543	chr3:97904829-97904830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs552120780	chr3:97904874-97904875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs374775866	chr3:97904883-97904884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs13069991	chr3:97904885-97904886	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs7429620	chr3:97904897-97904898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs531647118	chr3:97904901-97904902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs548672149	chr3:97904908-97904909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs13090781	chr3:97904911-97904912	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs201111693	chr3:97904946-97904947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs376995144	chr3:97904948-97904949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs553759088	chr3:97904960-97904961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs57616527	chr3:97904961-97904962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs80001903	chr3:97904964-97904965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs13070139	chr3:97904965-97904966	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs539759923	chr3:97904981-97904982	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97902000-97907000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:97902200-97906400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:97902200-97907200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:97902400-97907000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:97906400-97906800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:97906800-97907000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:97906800-97907000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:97906800-97908000	Enhancers	Primary hematopoietic stem cells	blood
9	chr3:97906800-97908400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:97907000-97907400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:97907000-97908000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:97907000-97908000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:97907000-97908200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:97907000-97910200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:97907200-97907600	Enhancers	Primary T cells from cord blood	blood
16	chr3:97907200-97907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:97907200-97907600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:97907200-97907600	Enhancers	GM12878-XiMat	blood
19	chr3:97907200-97907800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:97907400-97908400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:97908200-97908600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:97908400-97910000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:97908600-97908800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:97908800-97910800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:97910000-97912200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr3:97910200-97910400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:97910200-97910800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:97910400-97913600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:97910800-97911400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:97910800-97913800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr3:97911400-97911600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:97911600-97912000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:97912000-97912600	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:97912200-97914600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr3:97912600-97916000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:97913600-97913800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:97913600-97914400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:97913800-97915400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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