Variant report

Variant	esv1825486
Chromosome Location	chr9:6662795-6672169
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	chr9:6667709-6667966	K562	blood:	n/a	n/a
2	ARID3A	chr9:6664541-6665413	HepG2	liver:	n/a	n/a
3	ARID3A	chr9:6667619-6667991	HepG2	liver:	n/a	n/a
4	ATF3	chr9:6664294-6664873	A549	lung:	n/a	n/a
5	ATF3	chr9:6664488-6664934	A549	lung:	n/a	n/a
6	BACH1	chr9:6667638-6667964	H1-hESC	embryonic stem cell:	n/a	n/a
7	BCL3	chr9:6664480-6665034	A549	lung:	n/a	n/a
8	BCL3	chr9:6664426-6665297	A549	lung:	n/a	chr9:6665033-6665042
9	BCLAF1	chr9:6667616-6668061	GM12878	blood:	n/a	n/a
10	BHLHE40	chr9:6664329-6665171	HepG2	liver:	n/a	n/a
11	BRCA1	chr9:6664596-6664874	Hela-S3	cervix:	n/a	n/a
12	BRCA1	chr9:6664464-6664732	HepG2	liver:	n/a	n/a
13	CEBPB	chr9:6664533-6665234	MCF-7	breast:	n/a	n/a
14	CEBPB	chr9:6664587-6665287	HepG2	liver:	n/a	n/a
15	CEBPB	chr9:6664551-6665250	A549	lung:	n/a	n/a
16	CEBPB	chr9:6664576-6665291	HepG2	liver:	n/a	n/a
17	CEBPB	chr9:6664643-6664861	HepG2	liver:	n/a	n/a
18	CEBPB	chr9:6664583-6664967	MCF-7	breast:	n/a	n/a
19	CEBPB	chr9:6664574-6665059	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr9:6664589-6665192	A549	lung:	n/a	n/a
21	CEBPB	chr9:6664875-6665208	HepG2	liver:	n/a	n/a
22	CEBPB	chr9:6664453-6665284	A549	lung:	n/a	n/a
23	CEBPB	chr9:6664492-6665376	HepG2	liver:	n/a	n/a
24	CEBPD	chr9:6664550-6665175	HepG2	liver:	n/a	n/a
25	CEBPD	chr9:6664675-6665149	HepG2	liver:	n/a	n/a
26	CEBPZ	chr9:6664872-6665103	HepG2	liver:	n/a	n/a
27	CHD2	chr9:6664515-6664915	Hela-S3	cervix:	n/a	n/a
28	CHD2	chr9:6664463-6664849	HepG2	liver:	n/a	n/a
29	CREB1	chr9:6664317-6665332	HepG2	liver:	n/a	n/a
30	CREB1	chr9:6664431-6664819	A549	lung:	n/a	n/a
31	CREB1	chr9:6664175-6665459	HepG2	liver:	n/a	n/a
32	CREB1	chr9:6664582-6664891	A549	lung:	n/a	n/a
33	CTCF	chr9:6667759-6667929	MCF-7	breast:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
34	CTCF	chr9:6667720-6667870	GM12872	blood:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
35	CTCF	chr9:6667800-6667950	AoAF	blood vessel:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
36	CTCF	chr9:6667800-6667950	AG10803	skin:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
37	CTCF	chr9:6667840-6667990	GM12869	blood:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
38	CTCF	chr9:6667780-6667930	HUVEC	blood vessel:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
39	CTCF	chr9:6667815-6667965	GM20000	blood:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
40	CTCF	chr9:6667754-6667907	GM19240	blood:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
41	CTCF	chr9:6667740-6667890	GM12865	blood:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
42	CTCF	chr9:6667780-6667930	Caco-2	colon:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
43	CTCF	chr9:6667760-6667910	Hela-S3	cervix:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
44	CTCF	chr9:6667760-6667910	AG10803	skin:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
45	CTCF	chr9:6667820-6667970	HCM	heart:	n/a	chr9:6667851-6667869 chr9:6667846-6667867
46	CTCF	chr9:6669280-6669430	NB4	blood:	n/a	n/a
47	CTCF	chr9:6670820-6670970	HFF	foreskin:	n/a	n/a
48	CTCF	chr9:6667900-6668050	WI-38	lung:	n/a	n/a
49	CTCF	chr9:6667500-6667730	GM12865	blood:	n/a	n/a
50	CTCF	chr9:6667763-6667764	Kidney_OC	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:6663663..6666675-chr9:6715678..6718421,3	MCF-7	breast:
2	chr9:6662765..6664429-chr9:6666367..6668579,2	MCF-7	breast:
3	chr9:6584834..6585802-chr9:6667386..6668426,5	MCF-7	breast:
4	chr9:6667615..6669315-chr9:6679006..6681464,2	K562	blood:
5	chr9:6654607..6656764-chr9:6663214..6664911,2	K562	blood:
6	chr9:6585232..6587306-chr9:6664888..6666750,2	MCF-7	breast:
7	chr9:6523722..6524445-chr9:6667595..6668159,2	K562	blood:
8	chr9:6644301..6646741-chr9:6667847..6669482,2	MCF-7	breast:
9	chr9:6663029..6667664-chr9:6679639..6683357,9	MCF-7	breast:
10	chr9:6665749..6668244-chr9:6673822..6675444,2	MCF-7	breast:
11	chr9:6656639..6659482-chr9:6662780..6664665,3	MCF-7	breast:
12	chr9:6662765..6664429-chr9:6666367..6668579,2	MCF-7	breast:
13	chr9:6354241..6354767-chr9:6667295..6668097,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-13	chr9:6662424-6662810	NONHSAT130148
2	lnc-KDM4C-13	chr9:6663156-6663366	NONHSAT130148
3	lnc-KDM4C-5	chr9:6669544-6669728	NONHSAT130145
4	lnc-KDM4C-5	chr9:6669544-6669728	ENSG00000236924.1
5	lnc-KDM4C-5	chr9:6670425-6670690	NONHSAT130145
6	lnc-KDM4C-5	chr9:6670425-6670635	ENSG00000236924.1
7	lnc-KDM4C-13	chr9:6663657-6663792	NONHSAT130148

Variant related genes	Relation type
ENSG00000232946	TF binding region
RNF2P1	TF binding region
ENSG00000225489	chromatin interactions
ENSG00000236924	chromatin interactions
ENSG00000232946	chromatin interactions
ENSG00000178445	chromatin interactions

Extended variants
information (count: 499 )
Associated
traits (count: 105 )

Variant overlapped rSNPs/rCNVs (count:499 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142477735	chr9:6662817-6662818	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs189192583	chr9:6662818-6662819	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs71485085	chr9:6662822-6662823	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs13288054	chr9:6662823-6662824	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs193114438	chr9:6662851-6662852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs114491836	chr9:6662861-6662862	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs565222933	chr9:6662869-6662870	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs13286945	chr9:6662875-6662876	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs139923699	chr9:6662884-6662885	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs13288092	chr9:6662898-6662899	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs1755622	chr9:6662915-6662916	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs60788557	chr9:6662982-6662983	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs80050274	chr9:6662984-6662985	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs77919986	chr9:6662985-6662986	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs4008331	chr9:6662997-6662998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs1658966	chr9:6662998-6662999	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs13292350	chr9:6663038-6663039	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs530360115	chr9:6663065-6663066	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs139684544	chr9:6663074-6663075	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs570813510	chr9:6663075-6663076	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs183551976	chr9:6663086-6663087	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs188385807	chr9:6663094-6663095	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs556154701	chr9:6663100-6663101	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs574749329	chr9:6663101-6663102	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs13297574	chr9:6663106-6663107	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs13292494	chr9:6663138-6663139	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs191519499	chr9:6663145-6663146	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs540482673	chr9:6663146-6663147	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs565022935	chr9:6663147-6663148	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs112774989	chr9:6663151-6663152	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs34998284	chr9:6663152-6663153	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs570836394	chr9:6663161-6663162	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs397948640	chr9:6663167-6663168	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs532464536	chr9:6663199-6663200	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs141598751	chr9:6663237-6663238	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs562364976	chr9:6663256-6663257	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs57811849	chr9:6663273-6663274	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs147716404	chr9:6663291-6663292	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs142582931	chr9:6663306-6663307	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs10975721	chr9:6663317-6663318	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs552363650	chr9:6663352-6663353	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs368331774	chr9:6663367-6663368	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs13292868	chr9:6663374-6663375	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs184137065	chr9:6663380-6663381	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs568645895	chr9:6663408-6663409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs13298054	chr9:6663419-6663420	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs117146066	chr9:6663425-6663426	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs572508135	chr9:6663434-6663435	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs539897737	chr9:6663439-6663440	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs3847263	chr9:6663449-6663450	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:105)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Developmental delay	21147756	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
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Metastatic melanoma	18483359	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	16783165	CNVD
Dyslexia	22102821	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Schizophrenia	21346763	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6648200-6670400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:6648400-6669400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:6648400-6680400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:6648600-6677600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:6648600-6680400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:6648800-6680400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:6649800-6664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:6654000-6669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:6657200-6669400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:6657200-6669800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:6657200-6680400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:6657400-6664400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:6657400-6680400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:6657400-6680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:6658600-6667600	Weak transcription	GM12878-XiMat	blood
16	chr9:6659200-6664600	Weak transcription	HUVEC	blood vessel
17	chr9:6660800-6664200	Enhancers	Liver	Liver
18	chr9:6662000-6664200	Enhancers	HepG2	liver
19	chr9:6662600-6662800	Flanking Active TSS	A549	lung
20	chr9:6662800-6664200	Enhancers	A549	lung
21	chr9:6664200-6664600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:6664200-6664800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:6664200-6664800	Flanking Active TSS	Liver	Liver
24	chr9:6664200-6665000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:6664200-6665000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:6664200-6665000	Enhancers	Stomach Mucosa	stomach
27	chr9:6664200-6665200	Enhancers	Placenta	Placenta
28	chr9:6664200-6665200	Enhancers	Gastric	stomach
29	chr9:6664200-6665400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:6664200-6665400	Enhancers	Pancreas	Pancrea
31	chr9:6664200-6665400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr9:6664200-6665800	Enhancers	Hela-S3	cervix
33	chr9:6664200-6665800	Flanking Active TSS	HepG2	liver
34	chr9:6664200-6666000	Enhancers	Fetal Intestine Large	intestine
35	chr9:6664200-6666000	Enhancers	Fetal Intestine Small	intestine
36	chr9:6664200-6666000	Flanking Active TSS	A549	lung
37	chr9:6664400-6664800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr9:6664400-6664800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:6664600-6665000	Enhancers	HUVEC	blood vessel
40	chr9:6664600-6665200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:6664600-6680600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:6664800-6665400	Enhancers	Liver	Liver
43	chr9:6664800-6680000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:6665200-6677800	Weak transcription	Placenta	Placenta
45	chr9:6665400-6665600	Flanking Active TSS	Liver	Liver
46	chr9:6665400-6677800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:6665600-6665800	Enhancers	Liver	Liver
48	chr9:6665800-6666000	Flanking Active TSS	Liver	Liver
49	chr9:6665800-6666600	Enhancers	HepG2	liver
50	chr9:6665800-6667600	Weak transcription	Hela-S3	cervix

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