Variant report

Variant	nsv893646
Chromosome Location	chr9:104993672-105046926
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	chr9:105045700-105045900	A549	lung:	n/a	n/a
2	CEBPB	chr9:105015369-105015524	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr9:105045628-105045943	HepG2	liver:	n/a	n/a
4	CEBPB	chr9:104999513-104999769	HepG2	liver:	n/a	chr9:104999628-104999639
5	CTCF	chr9:105015420-105015570	Caco-2	colon:	n/a	n/a
6	CTCF	chr9:104997625-104997683	Fibrobl	skin:	n/a	n/a
7	CTCF	chr9:105015540-105015690	WERI-Rb-1	eye:	n/a	chr9:105015565-105015573
8	CTCF	chr9:105015460-105015610	HEK293	kidney:	n/a	chr9:105015565-105015573
9	CTCF	chr9:105015408-105015699	H1-hESC	embryonic stem cell:	n/a	chr9:105015565-105015573
10	CTCF	chr9:105015420-105015729	H1-hESC	embryonic stem cell:	n/a	chr9:105015565-105015573
11	CTCF	chr9:105015517-105015635	MCF-7	breast:	n/a	chr9:105015565-105015573
12	CTCF	chr9:105015460-105015610	MCF-7	breast:	n/a	chr9:105015565-105015573
13	CTCF	chr9:105007369-105007413	GM20000	blood:	n/a	n/a
14	CTCF	chr9:105019456-105019525	GM13976	blood:	n/a	n/a
15	CTCF	chr9:105018830-105018903	GM10266	blood:	n/a	n/a
16	CTCF	chr9:105015506-105015634	MCF-7	breast:	n/a	chr9:105015565-105015573
17	CTCF	chr9:105017180-105017330	GM12866	blood:	n/a	n/a
18	CTCF	chr9:105029673-105029679	GM10248	blood:	n/a	n/a
19	CTCF	chr9:105015560-105015710	WERI-Rb-1	eye:	n/a	chr9:105015565-105015573
20	CTCF	chr9:105039793-105039858	Kidney_OC	kidney:	n/a	n/a
21	E2F4	chr9:105018969-105019169	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F4	chr9:105036415-105036556	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr9:105006785-105007034	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr9:105041290-105041457	MCF10A-Er-Src	breast:	n/a	n/a
25	E2F4	chr9:104995456-104995731	MCF10A-Er-Src	breast:	n/a	n/a
26	E2F4	chr9:105046506-105046792	MCF10A-Er-Src	breast:	n/a	n/a
27	E2F4	chr9:105025079-105025217	MCF10A-Er-Src	breast:	n/a	n/a
28	EGR1	chr9:104999892-105000088	K562	blood:	n/a	n/a
29	EGR1	chr9:104999898-105000117	K562	blood:	n/a	n/a
30	EP300	chr9:105026378-105026917	GM12878	blood:	n/a	chr9:105026435-105026449
31	EP300	chr9:104999780-104999807	GM12878	blood:	n/a	n/a
32	FOS	chr9:105005505-105005531	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr9:105017660-105017923	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr9:105017647-105017981	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr9:105036291-105036608	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
36	FOS	chr9:105036246-105036626	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
37	FOS	chr9:105036247-105036631	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
38	FOS	chr9:105017646-105017952	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr9:105036308-105036641	MCF10A-Er-Src	breast:	n/a	chr9:105036451-105036460
40	GATA3	chr9:105012859-105013100	T-47D	breast:	n/a	chr9:105012908-105012917
41	GTF2F1	chr9:105015554-105015583	H1-hESC	embryonic stem cell:	n/a	n/a
42	JUND	chr9:105002606-105002737	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAFK	chr9:105018716-105018720	HepG2	liver:	n/a	n/a
44	MAX	chr9:105011592-105011818	NB4	blood:	n/a	chr9:105011651-105011661
45	MXI1	chr9:105015495-105015612	H1-hESC	embryonic stem cell:	n/a	n/a
46	MXI1	chr9:104995047-104995110	GM12878	blood:	n/a	n/a
47	MYC	chr9:104997652-104997685	MCF-7	breast:	n/a	n/a
48	MYC	chr9:105036319-105036522	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr9:105045635-105045785	MCF10A-Er-Src	breast:	n/a	chr9:105045692-105045703 chr9:105045692-105045703 chr9:105045692-105045702 chr9:105045692-105045703 chr9:105045691-105045704
50	MYC	chr9:104999988-105000028	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:104996734..105000664-chr9:105001906..105004565,3	K562	blood:
2	chr10:9229922..9230664-chr9:104997433..104997933,2	MCF-7	breast:
3	chr9:104998428..105001146-chr9:105002179..105004444,3	K562	blood:
4	chr9:104998428..105001146-chr9:105002179..105004444,3	K562	blood:
5	chr9:104996734..105000664-chr9:105001906..105004565,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf107-2	chr9:104998737-104998845	XLOC_007494
2	lnc-C9orf107-6	chr9:105022063-105022447	NONHSAT133760
3	lnc-C9orf107-6	chr9:105022537-105022636	NONHSAT133760
4	lnc-C9orf107-2	chr9:105000314-105000407	XLOC_007494
5	lnc-C9orf107-2	chr9:104997647-104997890	FPKM1_group_33624_transcript_3
6	lnc-C9orf107-2	chr9:104997351-104999003	FPKM1_group_33624_transcript_3
7	lnc-C9orf107-2	chr9:105000311-105000554	NONHSAT133757
8	lnc-C9orf107-6	chr9:105022063-105022447	FPKM1_group_33627_transcript_2
9	lnc-C9orf107-6	chr9:105022537-105022537	FPKM1_group_33627_transcript_2
10	lnc-C9orf107-5	chr9:105045829-105045892	NONHSAT133761
11	lnc-GRIN3A-3	chr9:105029817-105029914	NONHSAT133756
12	lnc-C9orf107-2	chr9:104997351-104999003	NONHSAT133757
13	lnc-GRIN3A-3	chr9:105029817-105029914	ucscGeneNc_uc004bbt_2

Variant related genes	Relation type
RNU6-329P	TF binding region

Extended variants
information (count: 575 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:575 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535745189	chr9:104997352-104997353	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs554762055	chr9:104997382-104997383	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs569448926	chr9:104997387-104997388	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs140504945	chr9:104997401-104997402	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs543709997	chr9:104997403-104997404	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs556313523	chr9:104997417-104997418	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs576371755	chr9:104997419-104997420	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs572224914	chr9:104997438-104997439	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs191265647	chr9:104997440-104997441	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs565377254	chr9:104997444-104997445	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs527734611	chr9:104997473-104997474	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs541235967	chr9:104997482-104997483	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs561112639	chr9:104997485-104997486	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs530348879	chr9:104997495-104997496	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs550433364	chr9:104997496-104997497	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs58902315	chr9:104997510-104997511	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs138300596	chr9:104997518-104997519	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs142827548	chr9:104997543-104997544	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs545702318	chr9:104997558-104997559	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs534669398	chr9:104997563-104997564	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs554823228	chr9:104997582-104997583	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs1115733	chr9:104997660-104997661	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs576042875	chr9:104997673-104997674	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs558208883	chr9:104997722-104997723	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs545470985	chr9:104997730-104997731	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs536983618	chr9:104997750-104997751	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs145067906	chr9:104997754-104997755	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs576407150	chr9:104997763-104997764	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs545390729	chr9:104997841-104997842	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs80173272	chr9:104997889-104997890	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs572224373	chr9:104997933-104997934	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs147590027	chr9:104997948-104997949	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs541098065	chr9:104997980-104997981	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs561347088	chr9:104998011-104998012	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs368895023	chr9:104998037-104998038	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs34196755	chr9:104998045-104998046	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs73659294	chr9:104998064-104998065	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs574682697	chr9:104998080-104998081	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs543808174	chr9:104998081-104998082	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs148339438	chr9:104998087-104998088	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs372898009	chr9:104998134-104998135	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs1156746	chr9:104998144-104998145	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs541283871	chr9:104998156-104998157	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs148203555	chr9:104998166-104998167	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs150072086	chr9:104998168-104998169	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs559360961	chr9:104998216-104998217	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs528220305	chr9:104998220-104998221	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs150902627	chr9:104998279-104998280	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs568304752	chr9:104998318-104998319	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs187184297	chr9:104998324-104998325	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Neuroblastoma	20406844	CNVD
Schizophrenia	23813976	CNVD
Basal cell lymphoma	21115979	CNVD

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104997400-104997600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr9:104997800-104998800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:104998800-104999200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:105024600-105024800	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr9:105024600-105026200	Enhancers	Fetal Kidney	kidney
6	chr9:105026200-105026800	Weak transcription	Fetal Kidney	kidney
7	chr9:105026600-105027200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr9:105026800-105027000	Enhancers	Fetal Kidney	kidney
9	chr9:105032000-105032600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:105032600-105036000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:105036000-105036200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:105036200-105036600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:105036200-105037000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:105036600-105037000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:105042400-105043000	Enhancers	Fetal Kidney	kidney
16	chr9:105043000-105043600	Weak transcription	Fetal Kidney	kidney
17	chr9:105043600-105043800	Enhancers	Fetal Kidney	kidney

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