Variant report

Variant	nsv466416
Chromosome Location	chr9:72479046-72513240
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	chr9:72492804-72493198	HepG2	liver:	n/a	n/a
2	BCL3	chr9:72500239-72500884	A549	lung:	n/a	n/a
3	BCL3	chr9:72500373-72500859	A549	lung:	n/a	n/a
4	BHLHE40	chr9:72492881-72493119	K562	blood:	n/a	n/a
5	BRCA1	chr9:72492781-72493014	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr9:72513027-72513373	Hela-S3	cervix:	n/a	chr9:72513289-72513300 chr9:72513179-72513192
7	CEBPB	chr9:72500311-72500919	A549	lung:	n/a	n/a
8	CEBPB	chr9:72504152-72504319	IMR90	lung:	n/a	n/a
9	CEBPB	chr9:72513030-72513315	HepG2	liver:	n/a	chr9:72513289-72513300 chr9:72513179-72513192
10	CEBPB	chr9:72505957-72506205	A549	lung:	n/a	chr9:72506059-72506070
11	CEBPB	chr9:72487016-72487296	HepG2	liver:	n/a	chr9:72487123-72487134 chr9:72487123-72487136
12	CEBPB	chr9:72492836-72493227	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr9:72513117-72513260	H1-hESC	embryonic stem cell:	n/a	chr9:72513179-72513192
14	CEBPB	chr9:72492867-72493277	MCF-7	breast:	n/a	n/a
15	CEBPB	chr9:72500415-72500866	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr9:72505931-72506206	HepG2	liver:	n/a	chr9:72506059-72506070
17	CEBPB	chr9:72513039-72513361	IMR90	lung:	n/a	chr9:72513289-72513300 chr9:72513179-72513192
18	CEBPB	chr9:72492697-72493282	HCT-116	colon:	n/a	n/a
19	CEBPB	chr9:72500375-72500924	ECC-1	luminal epithelium:	n/a	n/a
20	CEBPB	chr9:72500396-72500764	ECC-1	luminal epithelium:	n/a	n/a
21	CEBPB	chr9:72500443-72500828	A549	lung:	n/a	n/a
22	CEBPB	chr9:72492782-72493145	K562	blood:	n/a	n/a
23	CEBPB	chr9:72509814-72509856	HepG2	liver:	n/a	n/a
24	CEBPB	chr9:72487002-72487270	IMR90	lung:	n/a	chr9:72487123-72487134 chr9:72487123-72487136
25	CHD2	chr9:72500396-72500867	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr9:72492772-72493184	ECC-1	luminal epithelium:	n/a	n/a
27	CTCF	chr9:72492900-72493050	GM12864	blood:	n/a	n/a
28	CTCF	chr9:72492920-72493070	HEK293	kidney:	n/a	n/a
29	CTCF	chr9:72492805-72493211	K562	blood:	n/a	n/a
30	CTCF	chr9:72478940-72479090	AG10803	skin:	n/a	chr9:72479067-72479076 chr9:72479062-72479078 chr9:72479064-72479074 chr9:72479056-72479077 chr9:72479061-72479079
31	CTCF	chr9:72492731-72493144	HCT-116	colon:	n/a	n/a
32	CTCF	chr9:72482420-72482570	HBMEC	blood vessel:	n/a	n/a
33	CTCF	chr9:72492846-72493058	T-47D	breast:	n/a	n/a
34	CTCF	chr9:72492860-72493010	AG04450	lung:	n/a	n/a
35	CTCF	chr9:72492873-72493096	A549	lung:	n/a	n/a
36	CTCF	chr9:72492900-72493050	MCF-7	breast:	n/a	n/a
37	CTCF	chr9:72492566-72493475	SK-N-SH	brain:	n/a	n/a
38	CTCF	chr9:72492920-72493070	GM12865	blood:	n/a	n/a
39	CTCF	chr9:72492960-72493110	NHEK	skin:	n/a	n/a
40	CTCF	chr9:72479118-72479149	GM12878	blood:	n/a	n/a
41	CTCF	chr9:72492887-72493082	Lung_OC	lung:	n/a	n/a
42	CTCF	chr9:72492785-72493104	T-47D	breast:	n/a	n/a
43	CTCF	chr9:72492851-72493100	HepG2	liver:	n/a	n/a
44	CTCF	chr9:72478940-72479090	HRPEpiC	eye:	n/a	chr9:72479067-72479076 chr9:72479062-72479078 chr9:72479064-72479074 chr9:72479056-72479077 chr9:72479061-72479079
45	CTCF	chr9:72492980-72493130	HCT-116	colon:	n/a	n/a
46	CTCF	chr9:72492920-72493070	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr9:72492880-72493030	GM12871	blood:	n/a	n/a
48	CTCF	chr9:72492920-72493070	GM12864	blood:	n/a	n/a
49	CTCF	chr9:72492940-72493090	AG09319	gingival:	n/a	n/a
50	CTCF	chr9:72482420-72482570	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:72373598..72376289-chr9:72500894..72503778,2	K562	blood:
2	chr9:72287581..72288559-chr9:72492736..72493419,3	MCF-7	breast:
3	chr9:72512582..72514126-chr9:72872792..72874503,2	MCF-7	breast:
4	chr9:72505375..72507864-chr9:72508984..72510952,2	K562	blood:
5	chr9:72480266..72482674-chr9:72527396..72529225,2	K562	blood:
6	chr9:72505375..72507864-chr9:72508984..72510952,2	K562	blood:
7	chr9:72170921..72173288-chr9:72491881..72494788,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAMDC2-3	chr9:72501754-72501811	NONHSAT131791
2	lnc-PTAR1-3	chr9:72499279-72499566	NONHSAT131792
3	lnc-MAMDC2-3	chr9:72499969-72500038	NONHSAT131791

Variant related genes	Relation type
RN7SL570P	TF binding region
ENSG00000261447	chromatin interactions
ENSG00000188647	chromatin interactions
ENSG00000268364	chromatin interactions
ENSG00000198887	chromatin interactions

Extended variants
information (count: 1321 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1321 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2035921	chr9:72479046-72479047	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs191936758	chr9:72479085-72479086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs558135124	chr9:72479087-72479088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs566810789	chr9:72479088-72479089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs534304418	chr9:72479096-72479097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs555573259	chr9:72479109-72479110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs573907109	chr9:72479118-72479119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs544499574	chr9:72479133-72479134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs1389123	chr9:72479172-72479173	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs138726969	chr9:72479213-72479214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs3070538	chr9:72479247-72479248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs62569935	chr9:72479263-72479264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs577561664	chr9:72479309-72479310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs544639716	chr9:72479318-72479319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs113160903	chr9:72479350-72479351	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs1389124	chr9:72479356-72479357	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs527370574	chr9:72479357-72479358	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs553691132	chr9:72479397-72479398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs573536205	chr9:72479398-72479399	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs188419037	chr9:72479411-72479412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs78875301	chr9:72479584-72479585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs2871283	chr9:72479591-72479592	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs550861300	chr9:72479636-72479637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs10868224	chr9:72479663-72479664	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs370306586	chr9:72479670-72479671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs11140722	chr9:72479744-72479745	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs12345382	chr9:72479835-72479836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs566880281	chr9:72479873-72479874	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs534263678	chr9:72479878-72479879	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs139103538	chr9:72479922-72479923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs567457334	chr9:72479923-72479924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs10117766	chr9:72479989-72479990	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs149473909	chr9:72480039-72480040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs372321692	chr9:72480054-72480055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs536944569	chr9:72480098-72480099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs547215038	chr9:72480100-72480101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs577827647	chr9:72480152-72480153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs532168396	chr9:72480171-72480172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs551914453	chr9:72480197-72480198	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs538948631	chr9:72480216-72480217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs553469674	chr9:72480219-72480220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs565643179	chr9:72480251-72480252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs571743524	chr9:72480280-72480281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs112282614	chr9:72480320-72480321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs560697828	chr9:72480331-72480332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs143875940	chr9:72480414-72480415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs148611627	chr9:72480429-72480430	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs182014015	chr9:72480437-72480438	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs563112101	chr9:72480438-72480439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs766003	chr9:72480440-72480441	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:65)

Disease	PMID	Source
Breast cancer	17133270	CNVD
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
Melanoma	22183965	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
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD
Intellectual disability	21811512	CNVD
Autism	21484199	CNVD
Breast cancer	22737080	CNVD
Malignant peripheral nerve sheath tumor	22811580	CNVD
Leprosy	22719964	CNVD
Primary ovarian insufficiency	22879975	CNVD
Malignant melanoma	17260012	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:307 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72442800-72480200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:72471000-72481800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:72475000-72487000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:72475400-72487600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:72475400-72495200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:72476200-72492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:72476400-72481000	Weak transcription	Osteobl	bone
8	chr9:72476400-72481800	Weak transcription	NH-A	brain
9	chr9:72481000-72483400	Enhancers	Osteobl	bone
10	chr9:72481400-72483400	Enhancers	HUVEC	blood vessel
11	chr9:72481800-72482000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:72481800-72483200	Enhancers	NH-A	brain
13	chr9:72482200-72482800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:72482200-72483000	Enhancers	NHDF-Ad	bronchial
15	chr9:72482400-72482800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:72482400-72482800	Enhancers	NHLF	lung
17	chr9:72482400-72483000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:72482600-72483400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:72482800-72485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:72482800-72486200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:72483000-72486200	Weak transcription	NHDF-Ad	bronchial
22	chr9:72485400-72485600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:72485600-72486000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:72486000-72487000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:72486200-72486800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:72486200-72486800	Enhancers	NHDF-Ad	bronchial
27	chr9:72486800-72488400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:72486800-72488800	Weak transcription	NHDF-Ad	bronchial
29	chr9:72487000-72488200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr9:72487000-72488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:72487400-72487600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:72487400-72487800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:72487400-72490000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr9:72487600-72488400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:72487600-72489200	Enhancers	Psoas Muscle	Psoas
36	chr9:72487600-72489600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:72487800-72488000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr9:72487800-72490600	Enhancers	Fetal Heart	heart
39	chr9:72488000-72488400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:72488000-72488600	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr9:72488200-72488800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:72488200-72492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr9:72488400-72489000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:72488400-72489000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:72488400-72489400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr9:72488400-72492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:72488600-72489000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr9:72488600-72489200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:72488800-72489000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:72488800-72489200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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