Variant report

Variant	nsv1032487
Chromosome Location	chr9:3601907-3661151
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:226)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:9)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:226 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr9:3607963-3608436	GM12878	blood:	n/a	n/a
2	ATF2	chr9:3607966-3608348	GM12878	blood:	n/a	n/a
3	BACH1	chr9:3604433-3604472	H1-hESC	embryonic stem cell:	n/a	n/a
4	BATF	chr9:3656318-3656576	GM12878	blood:	n/a	n/a
5	BATF	chr9:3656298-3656558	GM12878	blood:	n/a	n/a
6	BATF	chr9:3631375-3631642	GM12878	blood:	n/a	n/a
7	BATF	chr9:3607987-3608334	GM12878	blood:	n/a	n/a
8	BATF	chr9:3608014-3608345	GM12878	blood:	n/a	n/a
9	BCL11A	chr9:3608133-3608328	GM12878	blood:	n/a	n/a
10	BCL3	chr9:3651345-3651710	GM12878	blood:	n/a	n/a
11	BCLAF1	chr9:3608009-3608344	GM12878	blood:	n/a	n/a
12	BHLHE40	chr9:3651100-3651575	GM12878	blood:	n/a	n/a
13	BHLHE40	chr9:3648954-3649126	K562	blood:	n/a	n/a
14	BHLHE40	chr9:3607905-3608488	GM12878	blood:	n/a	n/a
15	CEBPB	chr9:3651301-3651734	GM12878	blood:	n/a	n/a
16	CEBPB	chr9:3649161-3649459	IMR90	lung:	n/a	chr9:3649331-3649344 chr9:3649332-3649343
17	CEBPB	chr9:3649165-3649500	HepG2	liver:	n/a	chr9:3649331-3649344 chr9:3649332-3649343
18	CEBPB	chr9:3649175-3649477	K562	blood:	n/a	chr9:3649331-3649344 chr9:3649332-3649343
19	CEBPB	chr9:3633690-3633806	K562	blood:	n/a	n/a
20	CEBPB	chr9:3649158-3649446	A549	lung:	n/a	chr9:3649331-3649344 chr9:3649332-3649343
21	CEBPB	chr9:3650762-3650973	HepG2	liver:	n/a	chr9:3650859-3650872 chr9:3650856-3650873 chr9:3650859-3650870
22	CEBPB	chr9:3633564-3633808	HepG2	liver:	n/a	n/a
23	CEBPB	chr9:3642748-3642878	K562	blood:	n/a	chr9:3642822-3642833
24	CEBPB	chr9:3603761-3603960	A549	lung:	n/a	chr9:3603896-3603907 chr9:3603896-3603909 chr9:3603896-3603909 chr9:3603896-3603907 chr9:3603874-3603886
25	CEBPB	chr9:3618064-3618264	HepG2	liver:	n/a	chr9:3618137-3618148
26	CEBPB	chr9:3649628-3649648	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr9:3649224-3649451	Hela-S3	cervix:	n/a	chr9:3649331-3649344 chr9:3649332-3649343
28	CEBPB	chr9:3642733-3642933	HepG2	liver:	n/a	chr9:3642822-3642833
29	CHD1	chr9:3651104-3651525	GM12878	blood:	n/a	n/a
30	CHD2	chr9:3651207-3651583	GM12878	blood:	n/a	n/a
31	CTCF	chr9:3647781-3647916	GM10266	blood:	n/a	n/a
32	CTCF	chr9:3647760-3647910	MCF-7	breast:	n/a	n/a
33	CTCF	chr9:3651540-3651690	GM12878	blood:	n/a	n/a
34	CTCF	chr9:3647805-3647942	GM13977	blood:	n/a	n/a
35	CTCF	chr9:3647818-3647910	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr9:3625940-3626090	WI-38	lung:	n/a	n/a
37	CTCF	chr9:3651560-3651710	GM12871	blood:	n/a	n/a
38	CTCF	chr9:3610960-3611110	HEK293	kidney:	n/a	n/a
39	CTCF	chr9:3647780-3647930	RPTEC	kidney:	n/a	n/a
40	CTCF	chr9:3618279-3618341	GM20000	blood:	n/a	n/a
41	CTCF	chr9:3651540-3651655	GM12878	blood:	n/a	n/a
42	CTCF	chr9:3647754-3647963	LNCaP	prostate:	n/a	n/a
43	CTCF	chr9:3651430-3651766	GM12878	blood:	n/a	n/a
44	CTCF	chr9:3608320-3608470	GM12873	blood:	n/a	n/a
45	CTCF	chr9:3647860-3648010	HAc	cerebellar:	n/a	n/a
46	CTCF	chr9:3647780-3647922	GM12878	blood:	n/a	n/a
47	CTCF	chr9:3608140-3608290	GM12872	blood:	n/a	n/a
48	CTCF	chr9:3647640-3647790	HMEC	breast:	n/a	n/a
49	CTCF	chr9:3647880-3648030	HRPEpiC	eye:	n/a	n/a
50	CTCF	chr9:3647820-3647970	SAEC	small airway:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:3632578..3635092-chr9:3639764..3642505,2	MCF-7	breast:
2	chr9:3525115..3527683-chr9:3647759..3649608,2	MCF-7	breast:
3	chr9:3649975..3652712-chr9:3654160..3655972,2	K562	blood:
4	chr9:3605941..3608408-chr9:3657516..3659534,2	K562	blood:
5	chr9:3655163..3657660-chr9:3672402..3674386,2	K562	blood:
6	chr13:45496976..45497802-chr9:3627604..3628338,2	Hela-S3	cervix:
7	chr9:3649975..3652712-chr9:3654160..3655972,2	K562	blood:
8	chr9:3605941..3608408-chr9:3657516..3659534,2	K562	blood:
9	chr9:3526287..3529194-chr9:3646038..3648964,2	K562	blood:
10	chr9:3594034..3597239-chr9:3602535..3604961,3	K562	blood:
11	chr9:3632578..3635092-chr9:3639764..3642505,2	MCF-7	breast:

(count:9 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC1A1-13	chr9:3637754-3638338	NONHSAT130028
2	lnc-KCNV2-3	chr9:3602523-3602584	ENSG00000232104.2
3	lnc-KCNV2-3	chr9:3606693-3606738	ENSG00000232104
4	lnc-KCNV2-3	chr9:3602535-3602584	ENSG00000232104
5	lnc-SLC1A1-5	chr9:3647335-3647477	ENSG00000237359
6	lnc-SLC1A1-12	chr9:3656974-3658408	l_3729_chr9:3656973-3664950_testes
7	lnc-SLC1A1-5	chr9:3647754-3648338	ENSG00000237359
8	lnc-SLC1A1-13	chr9:3637335-3637477	NONHSAT130028
9	lnc-KCNV2-3	chr9:3606693-3606738	ENSG00000232104.2

No data

Variant related genes	Relation type
ENSG00000237359	TF binding region
ENSG00000232104	chromatin interactions
ENSG00000080298	chromatin interactions

Extended variants
information (count: 2236 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:2236 , 50 per page) page: 1 2 3 4 5 6 7 ... 45

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546418480	chr9:3601998-3601999	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs559518977	chr9:3602010-3602011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs1334069	chr9:3602018-3602019	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs547867320	chr9:3602066-3602067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs561414772	chr9:3602078-3602079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs370765063	chr9:3602115-3602116	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs12346979	chr9:3602137-3602138	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs7852723	chr9:3602147-3602148	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs7867712	chr9:3602170-3602171	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs141977103	chr9:3602176-3602177	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs35884227	chr9:3602196-3602197	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs553652032	chr9:3602207-3602208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs192079446	chr9:3602230-3602231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs76386103	chr9:3602245-3602246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181657937	chr9:3602257-3602258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs73389729	chr9:3602283-3602284	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs537463489	chr9:3602288-3602289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs557069680	chr9:3602312-3602313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs577514702	chr9:3602315-3602316	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs370554643	chr9:3602385-3602386	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs146024060	chr9:3602445-3602446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs559557701	chr9:3602505-3602506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs35852502	chr9:3602506-3602507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs71508575	chr9:3602511-3602512	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs541994163	chr9:3602533-3602534	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs540157442	chr9:3602540-3602541	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs561448296	chr9:3602556-3602557	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs142162313	chr9:3602562-3602563	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs550589211	chr9:3602567-3602568	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs563921590	chr9:3602580-3602581	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs187624736	chr9:3602590-3602591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs546899464	chr9:3602596-3602597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs13293031	chr9:3602614-3602615	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs190769371	chr9:3602630-3602631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs78412394	chr9:3602696-3602697	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs200479452	chr9:3602702-3602703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs201619701	chr9:3602703-3602704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs398068389	chr9:3602704-3602705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs535668215	chr9:3602720-3602721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs182279113	chr9:3602728-3602729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372168416	chr9:3602755-3602756	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs376727187	chr9:3602774-3602775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs10972631	chr9:3602811-3602812	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs544170471	chr9:3602830-3602831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs574882177	chr9:3602870-3602871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs537147679	chr9:3602892-3602893	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs150784068	chr9:3603087-3603088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs562520124	chr9:3603097-3603098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs112455395	chr9:3603104-3603105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186459231	chr9:3603126-3603127	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Gastric cancer	16715143	CNVD
Glioblastoma multiforme	22286061	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Autism	20531469	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21373258	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Autism	20808228	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3600800-3620400	Weak transcription	Ovary	ovary
2	chr9:3603400-3603800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr9:3603400-3603800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:3606400-3640400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:3607800-3608200	Enhancers	Primary B cells from peripheral blood	blood
6	chr9:3607800-3608400	Enhancers	GM12878-XiMat	blood
7	chr9:3610800-3611000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:3611600-3628000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:3611800-3612800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:3612600-3612800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:3612800-3613600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:3613000-3613400	Enhancers	HSMMtube	muscle
13	chr9:3613600-3619600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:3619600-3625600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:3619800-3620000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:3621400-3629600	Weak transcription	Brain Substantia Nigra	brain
17	chr9:3621800-3627800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:3622600-3626200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:3622800-3626000	Weak transcription	Pancreas	Pancrea
20	chr9:3623800-3625800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr9:3624000-3624800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:3624000-3626200	Weak transcription	Spleen	Spleen
23	chr9:3624000-3629800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:3624200-3627000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:3624800-3626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:3625600-3626400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr9:3625800-3626000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr9:3626000-3626800	ZNF genes & repeats	Pancreas	Pancrea
29	chr9:3626000-3629400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:3626200-3626800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:3626200-3626800	ZNF genes & repeats	Spleen	Spleen
32	chr9:3626400-3627200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:3626400-3629400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:3626800-3627600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:3627000-3627400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr9:3627800-3628800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:3627800-3629800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:3628000-3630000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:3628000-3630000	Enhancers	Osteobl	bone
40	chr9:3628200-3629800	Enhancers	Adipose Nuclei	Adipose
41	chr9:3628200-3630000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:3628800-3629200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:3629000-3630000	Enhancers	Stomach Smooth Muscle	stomach
44	chr9:3629200-3629400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:3629400-3629600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr9:3629400-3630000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr9:3629600-3630000	Enhancers	Brain Substantia Nigra	brain
48	chr9:3629800-3630000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:3632200-3633600	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr9:3644400-3644600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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