Variant report

Variant	nsv1037684
Chromosome Location	chr9:115720902-115769814
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	BACH1	chr9:115724795-115724810	H1-hESC	embryonic stem cell:	n/a	n/a
2	CBX3	chr9:115759519-115759832	K562	blood:	n/a	n/a
3	CBX3	chr9:115759331-115759906	K562	blood:	n/a	n/a
4	CEBPB	chr9:115726947-115727252	HepG2	liver:	n/a	chr9:115727095-115727108 chr9:115727096-115727107
5	CEBPB	chr9:115726973-115727204	A549	lung:	n/a	chr9:115727095-115727108 chr9:115727096-115727107
6	CEBPB	chr9:115726948-115727258	IMR90	lung:	n/a	chr9:115727095-115727108 chr9:115727096-115727107
7	CEBPB	chr9:115726931-115727160	Hela-S3	cervix:	n/a	chr9:115727095-115727108 chr9:115727096-115727107
8	CTCF	chr9:115733775-115734002	GM12891	blood:	n/a	n/a
9	CTCF	chr9:115733380-115733530	NHDF-neo	bronchial:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
10	CTCF	chr9:115733760-115733910	AG04449	skin:	n/a	n/a
11	CTCF	chr9:115733800-115733950	BJ	skin:	n/a	n/a
12	CTCF	chr9:115733340-115733490	HEK293	kidney:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
13	CTCF	chr9:115733780-115733930	HRPEpiC	eye:	n/a	n/a
14	CTCF	chr9:115733751-115734015	MCF-7	breast:	n/a	n/a
15	CTCF	chr9:115733780-115733930	HPF	lung:	n/a	n/a
16	CTCF	chr9:115733313-115734061	K562	blood:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
17	CTCF	chr9:115733800-115733950	HVMF	connective:	n/a	n/a
18	CTCF	chr9:115733320-115733470	HMF	breast:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
19	CTCF	chr9:115733300-115733450	AoAF	blood vessel:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
20	CTCF	chr9:115733820-115733970	HA-sp	spinal cord:	n/a	n/a
21	CTCF	chr9:115722843-115722920	LNCaP	prostate:	n/a	n/a
22	CTCF	chr9:115733581-115734092	HCT-116	colon:	n/a	n/a
23	CTCF	chr9:115733220-115733370	GM12867	blood:	n/a	n/a
24	CTCF	chr9:115733768-115733988	A549	lung:	n/a	n/a
25	CTCF	chr9:115733360-115733510	HVMF	connective:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
26	CTCF	chr9:115733760-115733910	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr9:115733800-115733950	GM12869	blood:	n/a	n/a
28	CTCF	chr9:115733800-115733950	WI-38	lung:	n/a	n/a
29	CTCF	chr9:115733780-115733930	HRE	kidney:	n/a	n/a
30	CTCF	chr9:115733780-115733930	GM12878	blood:	n/a	n/a
31	CTCF	chr9:115733680-115733830	GM12868	blood:	n/a	n/a
32	CTCF	chr9:115733779-115733983	HepG2	liver:	n/a	n/a
33	CTCF	chr9:115733380-115733530	BE2_C	brain:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
34	CTCF	chr9:115733780-115733930	AoAF	blood vessel:	n/a	n/a
35	CTCF	chr9:115733820-115733970	HMEC	breast:	n/a	n/a
36	CTCF	chr9:115733393-115733472	ProgFib	skin:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
37	CTCF	chr9:115733740-115733890	GM12873	blood:	n/a	n/a
38	CTCF	chr9:115733721-115733988	K562	blood:	n/a	n/a
39	CTCF	chr9:115733800-115733950	GM12865	blood:	n/a	n/a
40	CTCF	chr9:115733773-115733988	Gliobla	brain:	n/a	n/a
41	CTCF	chr9:115733760-115733910	HPF	lung:	n/a	n/a
42	CTCF	chr9:115733360-115733510	HMEC	breast:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
43	CTCF	chr9:115733749-115734008	MCF-7	breast:	n/a	n/a
44	CTCF	chr9:115733780-115733930	HepG2	liver:	n/a	n/a
45	CTCF	chr9:115733282-115733505	A549	lung:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
46	CTCF	chr9:115733840-115733990	AoAF	blood vessel:	n/a	n/a
47	CTCF	chr9:115733340-115733490	HCPEpiC	choroid plexus:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
48	CTCF	chr9:115733440-115733590	RPTEC	kidney:	n/a	n/a
49	CTCF	chr9:115733225-115733588	HepG2	liver:	n/a	chr9:115733410-115733431 chr9:115733408-115733426
50	CTCF	chr9:115733300-115733450	HEEpiC	esophagus:	n/a	chr9:115733410-115733431 chr9:115733408-115733426

No.	Distal block	Cell Line	Cell type
1	chr9:115753371..115755961-chr9:115757044..115759989,3	K562	blood:
2	chr9:115733155..115735067-chr9:115738207..115740660,2	K562	blood:
3	chr9:115737840..115740130-chr9:115746954..115748821,2	K562	blood:
4	chr9:115687229..115687831-chr9:115733126..115733994,2	MCF-7	breast:
5	chr9:115761496..115766057-chr9:115772281..115775505,7	K562	blood:
6	chr9:115753371..115755961-chr9:115757044..115759989,3	K562	blood:
7	chr9:115761833..115763545-chr9:115767333..115769730,2	K562	blood:
8	chr9:115732761..115734046-chr9:115874470..115875680,10	MCF-7	breast:
9	chr9:115733155..115735067-chr9:115738207..115740660,2	K562	blood:
10	chr9:115761496..115763178-chr9:115772919..115775096,2	K562	blood:
11	chr9:115732989..115733848-chr9:115873467..115873994,3	MCF-7	breast:
12	chr9:115752326..115754565-chr9:115761394..115764104,2	K562	blood:
13	chr9:115761833..115763545-chr9:115767333..115769730,2	K562	blood:
14	chr9:115683256..115684613-chr9:115733098..115734013,7	MCF-7	breast:
15	chr9:115733381..115734140-chr9:115873498..115874197,3	MCF-7	breast:
16	chr9:115733547..115734542-chr9:115874910..115875666,2	MCF-7	breast:
17	chr9:115687126..115687971-chr9:115732295..115733102,2	K562	blood:
18	chr9:115737840..115740130-chr9:115746954..115748821,2	K562	blood:
19	chr9:115686542..115688045-chr9:115732880..115734329,5	MCF-7	breast:
20	chr9:115752326..115754565-chr9:115761394..115764104,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC46A2-3	chr9:115724446-115724541	NONHSAT134029
2	lnc-SLC46A2-3	chr9:115721414-115721451	NONHSAT134029
3	lnc-SLC46A2-3	chr9:115721630-115721731	NONHSAT134029
4	lnc-SLC46A2-3	chr9:115722073-115722183	NONHSAT134029
5	lnc-SLC46A2-3	chr9:115723954-115724094	NONHSAT134029
6	lnc-SLC46A2-3	chr9:115723165-115723242	NONHSAT134029

Variant related genes	Relation type
MUPP	TF binding region
ENSG00000228623	chromatin interactions
ENSG00000225684	chromatin interactions
ENSG00000231528	chromatin interactions

Extended variants
information (count: 826 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:826 , 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	rs559378616	chr9:115721414-115721415	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs528580660	chr9:115721428-115721429	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs75088381	chr9:115721447-115721448	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs145972292	chr9:115721449-115721450	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs183416377	chr9:115721645-115721646	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs557271040	chr9:115721647-115721648	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs546868438	chr9:115721670-115721671	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs187301072	chr9:115721697-115721698	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs146133602	chr9:115721722-115721723	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs542565566	chr9:115721729-115721730	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs551232969	chr9:115722074-115722075	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs571801168	chr9:115722100-115722101	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs537206709	chr9:115722119-115722120	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs553142409	chr9:115722127-115722128	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs374616465	chr9:115722142-115722143	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs60984221	chr9:115722149-115722150	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs7041451	chr9:115723175-115723176	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs111415142	chr9:115723232-115723233	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs529820897	chr9:115723957-115723958	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs553301014	chr9:115723977-115723978	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs189031028	chr9:115724082-115724083	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs542480745	chr9:115724449-115724450	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs10981559	chr9:115724471-115724472	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs141653449	chr9:115724474-115724475	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs146204226	chr9:115724475-115724476	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs3903908	chr9:115724490-115724491	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs574435559	chr9:115724505-115724506	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs540353070	chr9:115724506-115724507	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs564907306	chr9:115724507-115724508	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs560514737	chr9:115724526-115724527	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs78322887	chr9:115724800-115724801	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs369607478	chr9:115726072-115726073	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs112044406	chr9:115726077-115726078	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs545022416	chr9:115726185-115726186	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs545246755	chr9:115726186-115726187	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs565280481	chr9:115726187-115726188	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs188275096	chr9:115726220-115726221	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs553702695	chr9:115726255-115726256	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs570491484	chr9:115726337-115726338	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs527866126	chr9:115726339-115726340	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs536029683	chr9:115726492-115726493	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs1925082	chr9:115726513-115726514	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs572682198	chr9:115726555-115726556	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs144336864	chr9:115726590-115726591	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs75613430	chr9:115726595-115726596	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs115966024	chr9:115726599-115726600	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs16917642	chr9:115726941-115726942	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs7035634	chr9:115726957-115726958	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs150978144	chr9:115726964-115726965	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs535230506	chr9:115727006-115727007	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	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
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
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Lung cancer	19147751	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	22522925	CNVD
Melanoma	20877625	CNVD

Chromatin state (count:164 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115726400-115726600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:115727600-115729000	Enhancers	Stomach Mucosa	stomach
3	chr9:115732000-115732200	Enhancers	Osteobl	bone
4	chr9:115752000-115752600	ZNF genes & repeats	Fetal Brain Female	brain
5	chr9:115753800-115768800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr9:115754600-115756600	ZNF genes & repeats	Brain Hippocampus Middle	brain
7	chr9:115754600-115756800	ZNF genes & repeats	Brain Substantia Nigra	brain
8	chr9:115754600-115758000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr9:115754800-115758000	ZNF genes & repeats	Liver	Liver
10	chr9:115755000-115756600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr9:115755000-115758000	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr9:115755200-115756400	ZNF genes & repeats	Fetal Brain Female	brain
13	chr9:115755400-115756800	ZNF genes & repeats	Brain Anterior Caudate	brain
14	chr9:115755400-115765200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr9:115755800-115756600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:115755800-115756600	ZNF genes & repeats	Pancreas	Pancrea
17	chr9:115756000-115756600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:115756000-115756600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
19	chr9:115756000-115756800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:115757400-115757800	ZNF genes & repeats	Brain Angular Gyrus	brain
21	chr9:115757600-115757800	ZNF genes & repeats	Fetal Brain Female	brain
22	chr9:115757800-115759200	Weak transcription	Brain Angular Gyrus	brain
23	chr9:115758000-115759200	Weak transcription	Adipose Nuclei	Adipose
24	chr9:115758000-115759200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr9:115758000-115760600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr9:115758400-115762400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:115759200-115760200	ZNF genes & repeats	Brain Angular Gyrus	brain
28	chr9:115759200-115761000	ZNF genes & repeats	Liver	Liver
29	chr9:115759200-115761800	ZNF genes & repeats	Fetal Brain Male	brain
30	chr9:115759200-115762000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:115759200-115762200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
32	chr9:115759200-115762200	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr9:115759200-115762400	ZNF genes & repeats	Brain Substantia Nigra	brain
34	chr9:115759200-115763000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:115759200-115763000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr9:115759200-115764400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:115759200-115764400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:115759200-115764400	ZNF genes & repeats	Fetal Lung	lung
39	chr9:115759200-115765400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
40	chr9:115759200-115767000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:115759200-115768800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr9:115759200-115769000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr9:115759200-115773000	ZNF genes & repeats	Fetal Brain Female	brain
44	chr9:115759400-115761000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr9:115759400-115762200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
46	chr9:115759400-115762200	ZNF genes & repeats	Fetal Kidney	kidney
47	chr9:115759400-115762400	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:115759400-115762400	ZNF genes & repeats	Left Ventricle	heart
49	chr9:115759400-115762600	ZNF genes & repeats	Colon Smooth Muscle	Colon
50	chr9:115759400-115764200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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