Variant report

Variant	nsv1045322
Chromosome Location	chr9:86666993-86701912
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	chr9:86669576-86669976	HepG2	liver:	n/a	n/a
2	BACH1	chr9:86669741-86669772	H1-hESC	embryonic stem cell:	n/a	n/a
3	BCL3	chr9:86669538-86669804	GM12878	blood:	n/a	n/a
4	BHLHE40	chr9:86691048-86691355	K562	blood:	n/a	n/a
5	BHLHE40	chr9:86691087-86691287	HepG2	liver:	n/a	n/a
6	CBX3	chr9:86685563-86685798	K562	blood:	n/a	n/a
7	CEBPB	chr9:86669613-86669768	HepG2	liver:	n/a	n/a
8	CEBPB	chr9:86669528-86669868	HepG2	liver:	n/a	n/a
9	CEBPB	chr9:86700997-86701030	HepG2	liver:	n/a	chr9:86701006-86701017
10	CHD2	chr9:86685589-86685878	H1-hESC	embryonic stem cell:	n/a	n/a
11	CHD2	chr9:86669667-86669717	HepG2	liver:	n/a	n/a
12	CHD2	chr9:86685570-86685904	HepG2	liver:	n/a	n/a
13	CHD2	chr9:86685568-86685955	K562	blood:	n/a	n/a
14	CTCF	chr9:86694073-86694138	Lung_OC	lung:	n/a	n/a
15	CTCF	chr9:86674836-86674960	MCF-7	breast:	n/a	n/a
16	CTCF	chr9:86674816-86674982	MCF-7	breast:	n/a	n/a
17	CTCF	chr9:86674800-86674950	MCF-7	breast:	n/a	n/a
18	CTCF	chr9:86674820-86674970	MCF-7	breast:	n/a	n/a
19	E2F6	chr9:86685566-86685766	K562	blood:	n/a	n/a
20	E2F6	chr9:86685425-86685924	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELK1	chr9:86683861-86684157	K562	blood:	n/a	n/a
22	EP300	chr9:86670419-86670734	HepG2	liver:	n/a	chr9:86670616-86670626
23	EP300	chr9:86669513-86669875	HepG2	liver:	n/a	n/a
24	EP300	chr9:86669638-86669759	HepG2	liver:	n/a	n/a
25	ESR1	chr9:86671119-86671539	T-47D	breast:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
26	ESR1	chr9:86671126-86671486	T-47D	breast:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
27	ESR1	chr9:86671112-86671453	T-47D	breast:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
28	ESR1	chr9:86671095-86671531	T-47D	breast:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
29	ESR1	chr9:86671142-86671370	T-47D	breast:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
30	ESR1	chr9:86671155-86671394	ECC-1	luminal epithelium:	n/a	chr9:86671324-86671341 chr9:86671323-86671340
31	FOS	chr9:86677687-86677878	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr9:86680661-86680775	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr9:86677743-86677886	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr9:86680634-86680857	MCF10A-Er-Src	breast:	n/a	n/a
35	FOSL2	chr9:86669591-86669842	HepG2	liver:	n/a	n/a
36	FOSL2	chr9:86669496-86669913	HepG2	liver:	n/a	n/a
37	FOXA1	chr9:86669617-86669955	HepG2	liver:	n/a	n/a
38	FOXA1	chr9:86693806-86694037	T-47D	breast:	n/a	n/a
39	FOXA1	chr9:86669628-86670086	HepG2	liver:	n/a	n/a
40	FOXA1	chr9:86669571-86669965	HepG2	liver:	n/a	n/a
41	FOXA1	chr9:86693841-86693994	T-47D	breast:	n/a	n/a
42	GATA2	chr9:86695755-86696225	SH-SY5Y	brain:	n/a	n/a
43	GATA3	chr9:86693300-86693423	SH-SY5Y	brain:	n/a	n/a
44	GATA3	chr9:86671148-86671491	MCF-7	breast:	n/a	chr9:86671148-86671157
45	GATA3	chr9:86695889-86696262	SH-SY5Y	brain:	n/a	n/a
46	HNF4A	chr9:86669540-86669797	HepG2	liver:	n/a	chr9:86669670-86669688 chr9:86669729-86669737
47	HNF4A	chr9:86669500-86669840	HepG2	liver:	n/a	chr9:86669670-86669688 chr9:86669729-86669737
48	HNF4G	chr9:86669402-86669860	HepG2	liver:	n/a	chr9:86669460-86669475 chr9:86669460-86669475 chr9:86669670-86669688 chr9:86669460-86669475 chr9:86669460-86669475 chr9:86669729-86669737
49	HNF4G	chr9:86669553-86669795	HepG2	liver:	n/a	chr9:86669670-86669688 chr9:86669729-86669737
50	JUND	chr9:86698720-86698752	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86693838..86695435-chr9:86695774..86698504,2	MCF-7	breast:
2	chr9:86671448..86673966-chr9:86679778..86681333,2	MCF-7	breast:
3	chr9:86671448..86673966-chr9:86679778..86681333,2	MCF-7	breast:
4	chr9:86693838..86695435-chr9:86695774..86698504,2	MCF-7	breast:
5	chr9:86541635..86544345-chr9:86665548..86667347,2	K562	blood:
6	chr9:86674506..86675321-chr9:86876055..86876581,2	MCF-7	breast:
7	chr9:86594149..86596782-chr9:86685649..86687855,2	K562	blood:
8	chr9:86663038..86665601-chr9:86690355..86692187,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RMI1-2	chr9:86678358-86678444	NONHSAT132769
2	lnc-RMI1-2	chr9:86698867-86699316	ENSG00000227463.2
3	lnc-RMI1-2	chr9:86690576-86690763	ENSG00000227463.1
4	lnc-RMI1-2	chr9:86692821-86693002	ENSG00000227463.2
5	lnc-RMI1-8	chr9:86693499-86693772	NONHSAT132772
6	lnc-RMI1-2	chr9:86696853-86696907	ENSG00000227463.1
7	lnc-RMI1-2	chr9:86697386-86697691	ENSG00000227463.1
8	lnc-RMI1-2	chr9:86697386-86697691	ENSG00000227463.2
9	lnc-RMI1-2	chr9:86678358-86678444	ENSG00000227463.2
10	lnc-RMI1-2	chr9:86690343-86690763	ENSG00000227463.2
11	lnc-RMI1-2	chr9:86696853-86696924	ENSG00000227463.2
12	lnc-RMI1-2	chr9:86682210-86682342	ENSG00000227463.2

Variant related genes	Relation type
ENSG00000270166	TF binding region
ENSG00000227463	TF binding region
ENSG00000178966	chromatin interactions
ENSG00000165119	chromatin interactions

Extended variants
information (count: 815 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:815 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs376320172	chr9:86668605-86668606	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs540920289	chr9:86668672-86668673	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs146557778	chr9:86668678-86668679	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs184168273	chr9:86668685-86668686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs544169449	chr9:86668717-86668718	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs375320360	chr9:86668749-86668750	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs531843211	chr9:86668755-86668756	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs200456916	chr9:86668777-86668778	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs140524880	chr9:86668783-86668784	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs150627464	chr9:86668791-86668792	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs374002707	chr9:86668792-86668793	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs11140342	chr9:86668794-86668795	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs373774403	chr9:86668795-86668796	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs111584945	chr9:86668796-86668797	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs141190065	chr9:86668824-86668825	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs190784136	chr9:86668854-86668855	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs568432909	chr9:86668861-86668862	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs529359749	chr9:86668914-86668915	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs547344158	chr9:86668920-86668921	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs565737340	chr9:86668989-86668990	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs367890649	chr9:86668990-86668991	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs539343876	chr9:86669077-86669078	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs542245549	chr9:86669164-86669165	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs564329471	chr9:86669219-86669220	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs11140343	chr9:86669293-86669294	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs11140344	chr9:86669301-86669302	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs11140345	chr9:86669330-86669331	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs528557845	chr9:86669379-86669380	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs567507953	chr9:86669403-86669404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs573620646	chr9:86669404-86669405	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs534717122	chr9:86669410-86669411	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs552958793	chr9:86669422-86669423	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs10746730	chr9:86669426-86669427	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs377169120	chr9:86669438-86669439	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs544400043	chr9:86669477-86669478	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs182019702	chr9:86669478-86669479	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs201662584	chr9:86669482-86669483	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs568356545	chr9:86669580-86669581	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs537415388	chr9:86669583-86669584	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs368884403	chr9:86669653-86669654	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs186058695	chr9:86669666-86669667	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs543618245	chr9:86669701-86669702	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188909228	chr9:86669737-86669738	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs150219960	chr9:86669777-86669778	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs556939814	chr9:86669813-86669814	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs373071091	chr9:86669868-86669869	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs11140346	chr9:86669915-86669916	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs115815367	chr9:86669958-86669959	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs12344728	chr9:86669978-86669979	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs111444677	chr9:86670031-86670032	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

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
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Urothelial cell carcinoma	18451213	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Renal cell carcinoma	18765545	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86668600-86669000	Enhancers	Ovary	ovary
2	chr9:86668600-86669600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr9:86668800-86669200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr9:86668800-86671400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr9:86669000-86669400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:86669000-86669400	Weak transcription	Ovary	ovary
7	chr9:86669000-86670600	Enhancers	HepG2	liver
8	chr9:86669200-86669800	Enhancers	Liver	Liver
9	chr9:86669200-86673000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr9:86669400-86669600	Enhancers	Ovary	ovary
11	chr9:86669400-86669800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:86669600-86669800	Enhancers	Fetal Muscle Leg	muscle
13	chr9:86669600-86669800	Enhancers	Left Ventricle	heart
14	chr9:86669600-86670000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:86669600-86670200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr9:86669600-86671200	Weak transcription	Ovary	ovary
17	chr9:86669800-86671000	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:86670000-86671000	Weak transcription	Left Ventricle	heart
19	chr9:86670200-86673400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr9:86671000-86671400	Enhancers	Left Ventricle	heart
21	chr9:86671000-86673400	Enhancers	Fetal Muscle Leg	muscle
22	chr9:86671200-86671600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:86671200-86671600	Enhancers	Ovary	ovary
24	chr9:86671200-86671600	Enhancers	Psoas Muscle	Psoas
25	chr9:86671200-86672000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:86671400-86672400	Enhancers	Fetal Muscle Trunk	muscle
27	chr9:86671600-86672000	Weak transcription	Psoas Muscle	Psoas
28	chr9:86672000-86672800	Enhancers	Psoas Muscle	Psoas
29	chr9:86672000-86676600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:86672400-86673200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:86672800-86673000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:86672800-86676400	Weak transcription	Psoas Muscle	Psoas
33	chr9:86673000-86676600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:86673400-86673600	Enhancers	Fetal Muscle Trunk	muscle
35	chr9:86673400-86676600	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:86673400-86677000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:86674800-86675000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:86675200-86676400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:86676000-86676800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr9:86676400-86677200	Enhancers	Colon Smooth Muscle	Colon
41	chr9:86676400-86677200	Enhancers	Psoas Muscle	Psoas
42	chr9:86676400-86677200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr9:86676400-86677400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr9:86676400-86678600	Enhancers	Stomach Mucosa	stomach
45	chr9:86676400-86679200	Enhancers	Fetal Heart	heart
46	chr9:86676600-86676800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr9:86676600-86677600	Enhancers	Fetal Muscle Leg	muscle
48	chr9:86676600-86678600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr9:86676800-86677200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:86677000-86677200	Enhancers	Skeletal Muscle Female	skeletal muscle

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