Variant report

Variant	nsv892277
Chromosome Location	chr9:9785685-9882950
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	chr9:9790306-9790512	HepG2	liver:	n/a	n/a
2	BHLHE40	chr9:9790315-9790593	GM12878	blood:	n/a	n/a
3	BHLHE40	chr9:9847834-9848021	GM12878	blood:	n/a	n/a
4	BRCA1	chr9:9790311-9790476	HepG2	liver:	n/a	n/a
5	CEBPB	chr9:9863586-9863715	A549	lung:	n/a	n/a
6	CEBPB	chr9:9860120-9860628	IMR90	lung:	n/a	chr9:9860493-9860504 chr9:9860133-9860145 chr9:9860492-9860503 chr9:9860492-9860505
7	CEBPB	chr9:9878262-9878354	A549	lung:	n/a	n/a
8	CEBPB	chr9:9831744-9832058	HepG2	liver:	n/a	chr9:9831888-9831899
9	CEBPB	chr9:9831774-9832068	IMR90	lung:	n/a	chr9:9831888-9831899
10	CEBPB	chr9:9860177-9860680	HepG2	liver:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
11	CEBPB	chr9:9824877-9825036	HepG2	liver:	n/a	chr9:9824982-9824993
12	CEBPB	chr9:9831770-9832132	A549	lung:	n/a	chr9:9831888-9831899
13	CEBPB	chr9:9860376-9860648	A549	lung:	n/a	chr9:9860493-9860504 chr9:9860492-9860503 chr9:9860492-9860505
14	CTCF	chr9:9790342-9790449	GM12892	blood:	n/a	n/a
15	CTCF	chr9:9790400-9790550	GM12864	blood:	n/a	chr9:9790450-9790458
16	CTCF	chr9:9791780-9791930	RPTEC	kidney:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
17	CTCF	chr9:9790360-9790510	GM12870	blood:	n/a	chr9:9790450-9790458
18	CTCF	chr9:9790214-9790555	H1-hESC	embryonic stem cell:	n/a	chr9:9790450-9790458
19	CTCF	chr9:9790400-9790550	BE2_C	brain:	n/a	chr9:9790450-9790458
20	CTCF	chr9:9790139-9790154	Spleen_OC	spleen:	n/a	n/a
21	CTCF	chr9:9790372-9790450	NHEK	skin:	n/a	n/a
22	CTCF	chr9:9791828-9791906	GM10266	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
23	CTCF	chr9:9790361-9790525	GM20000	blood:	n/a	chr9:9790450-9790458
24	CTCF	chr9:9791760-9791910	HAc	cerebellar:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
25	CTCF	chr9:9790323-9790494	A549	lung:	n/a	chr9:9790450-9790458
26	CTCF	chr9:9791827-9791882	GM10248	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
27	CTCF	chr9:9790337-9790583	Pancreas_OC	pancreas:	n/a	chr9:9790450-9790458
28	CTCF	chr9:9791820-9791970	HL-60	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
29	CTCF	chr9:9791700-9791850	HRPEpiC	eye:	n/a	n/a
30	CTCF	chr9:9790380-9790530	HFF-Myc	foreskin:	n/a	chr9:9790450-9790458
31	CTCF	chr9:9790340-9790490	HCM	heart:	n/a	chr9:9790450-9790458
32	CTCF	chr9:9790360-9790510	HCT-116	colon:	n/a	chr9:9790450-9790458
33	CTCF	chr9:9790220-9790370	HFF-Myc	foreskin:	n/a	n/a
34	CTCF	chr9:9790329-9790576	GM10266	blood:	n/a	chr9:9790450-9790458
35	CTCF	chr9:9790400-9790550	HEK293	kidney:	n/a	chr9:9790450-9790458
36	CTCF	chr9:9790380-9790530	GM12864	blood:	n/a	chr9:9790450-9790458
37	CTCF	chr9:9790282-9790581	A549	lung:	n/a	chr9:9790450-9790458
38	CTCF	chr9:9790380-9790530	Caco-2	colon:	n/a	chr9:9790450-9790458
39	CTCF	chr9:9790320-9790470	AG09309	skin:	n/a	chr9:9790450-9790458
40	CTCF	chr9:9790400-9790550	HA-sp	spinal cord:	n/a	chr9:9790450-9790458
41	CTCF	chr9:9791740-9791890	HPF	lung:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
42	CTCF	chr9:9791843-9791895	Spleen_OC	spleen:	n/a	chr9:9791844-9791862
43	CTCF	chr9:9790380-9790530	HRPEpiC	eye:	n/a	chr9:9790450-9790458
44	CTCF	chr9:9791740-9791890	NB4	blood:	n/a	chr9:9791839-9791860 chr9:9791844-9791862
45	CTCF	chr9:9790337-9790563	HepG2	liver:	n/a	chr9:9790450-9790458
46	CTCF	chr9:9790400-9790550	AG09319	gingival:	n/a	chr9:9790450-9790458
47	CTCF	chr9:9790141-9790804	SK-N-SH	brain:	n/a	chr9:9790450-9790458
48	CTCF	chr9:9790400-9790550	NHEK	skin:	n/a	chr9:9790450-9790458
49	CTCF	chr9:9790281-9790523	ECC-1	luminal epithelium:	n/a	chr9:9790450-9790458
50	CTCF	chr9:9790265-9790567	SK-N-SH_RA	brain:	n/a	chr9:9790450-9790458

No.	Distal block	Cell Line	Cell type
1	chr9:9606153..9607209-chr9:9791346..9792141,4	MCF-7	breast:
2	chr9:9606507..9607603-chr9:9789935..9790958,7	MCF-7	breast:
3	chr9:9606591..9607143-chr9:9791328..9791942,2	MCF-7	breast:
4	chr9:9606480..9607195-chr9:9789919..9790916,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-10	chr9:9803717-9803784	ENSG00000230920
2	lnc-KDM4C-10	chr9:9800546-9800674	ENSG00000230920
3	lnc-KDM4C-10	chr9:9799423-9799608	ENSG00000230920

Variant related genes	Relation type
ENSG00000230920	TF binding region

Extended variants
information (count: 2221 )
Associated
traits (count: 115 )

Variant overlapped rSNPs/rCNVs (count:2221 , 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	rs2382056	chr9:9785685-9785686	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs374002827	chr9:9785714-9785715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs566020628	chr9:9785731-9785732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs528812944	chr9:9785747-9785748	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530354903	chr9:9785802-9785803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs7874425	chr9:9785805-9785806	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs539477746	chr9:9785809-9785810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs555986283	chr9:9785835-9785836	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs569811039	chr9:9785846-9785847	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs535635808	chr9:9785856-9785857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs560752750	chr9:9785883-9785884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs189901682	chr9:9785884-9785885	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs372124635	chr9:9785905-9785906	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs540988802	chr9:9785915-9785916	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs558094012	chr9:9785916-9785917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs182124410	chr9:9785920-9785921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs16930284	chr9:9785924-9785925	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs541474787	chr9:9785931-9785932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs186223500	chr9:9785988-9785989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs146480530	chr9:9786000-9786001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs190899709	chr9:9786024-9786025	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs571923834	chr9:9786043-9786044	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs77871534	chr9:9786046-9786047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs559545271	chr9:9786051-9786052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs528750618	chr9:9786067-9786068	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs551795533	chr9:9786069-9786070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs570377306	chr9:9786071-9786072	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs114585582	chr9:9786080-9786081	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs78269431	chr9:9786083-9786084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs569752279	chr9:9786122-9786123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs535570592	chr9:9786126-9786127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs564160457	chr9:9786128-9786129	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs531989307	chr9:9786135-9786136	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs565747055	chr9:9786185-9786186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs534872506	chr9:9786196-9786197	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs17232558	chr9:9789202-9789203	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs563094694	chr9:9789203-9789204	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs531408714	chr9:9789252-9789253	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs576437059	chr9:9789259-9789260	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs374149453	chr9:9789301-9789302	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs542219484	chr9:9789307-9789308	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs550942435	chr9:9789321-9789322	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs186328853	chr9:9789334-9789335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs148212941	chr9:9789341-9789342	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs112533381	chr9:9789350-9789351	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs564654771	chr9:9789356-9789357	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs10977977	chr9:9789362-9789363	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs534693095	chr9:9790023-9790024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs146017692	chr9:9790029-9790030	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs118071760	chr9:9790059-9790060	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:115)

Disease	PMID	Source
abnormal development	18461090	CNVD
Disorders of sex development	21048976	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
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21080181	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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Lung cancer	20668451	CNVD
Schizophrenia	20838587	CNVD
Glioblastoma	18772890	CNVD
Glioblastoma multiforme	21390271	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Lung adenocarcinoma	17982442	CNVD
Nasopharyngeal cancer	20548289	CNVD
Breast cancer	21611746	CNVD
Schizophrenia	23813976	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9784600-9786000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:9786000-9786200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr9:9789200-9789400	Enhancers	Liver	Liver
4	chr9:9790000-9790400	Enhancers	Dnd41	blood
5	chr9:9790200-9790400	Enhancers	Liver	Liver
6	chr9:9791400-9793000	Enhancers	Primary B cells from cord blood	blood
7	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells	blood
8	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr9:9792000-9792600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:9792200-9792800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:9799400-9799800	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr9:9799400-9799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr9:9799400-9800800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr9:9799400-9801400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr9:9799600-9799800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr9:9799800-9800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:9799800-9800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:9799800-9801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:9800600-9801600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr9:9800800-9801600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:9801000-9801600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr9:9805200-9806000	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr9:9807800-9808000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr9:9820000-9821000	Enhancers	NH-A	brain
25	chr9:9825200-9825400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:9825400-9825600	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:9832800-9834600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr9:9834200-9834600	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:9845200-9845800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:9845400-9846200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:9845400-9846200	Enhancers	Dnd41	blood
32	chr9:9845800-9846800	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:9845800-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:9845800-9847800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr9:9846200-9847000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:9846200-9847000	Flanking Active TSS	Dnd41	blood
37	chr9:9846600-9847000	Active TSS	GM12878-XiMat	blood
38	chr9:9846800-9847200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:9847000-9848200	Enhancers	Dnd41	blood
40	chr9:9847000-9848400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:9847000-9848600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:9847200-9848400	Enhancers	Primary hematopoietic stem cells	blood
43	chr9:9847600-9847800	Enhancers	GM12878-XiMat	blood
44	chr9:9847600-9848200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:9847600-9848200	Enhancers	Placenta	Placenta
46	chr9:9848200-9855000	Weak transcription	Placenta	Placenta
47	chr9:9848600-9855400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr9:9853600-9853800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:9854000-9855600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:9855000-9855200	Enhancers	Pancreatic Islets	Pancreatic Islet

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