Variant report

Variant	esv1810687
Chromosome Location	chr9:6729601-6739489
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	chr9:6739329-6739619	HepG2	liver:	n/a	n/a
2	CBX3	chr9:6735364-6735786	K562	blood:	n/a	n/a
3	CTCF	chr9:6739420-6739570	GM12873	blood:	n/a	chr9:6739422-6739430
4	CTCF	chr9:6739336-6739545	Hela-S3	cervix:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
5	CTCF	chr9:6739407-6739495	GM13976	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
6	CTCF	chr9:6739320-6739470	RPTEC	kidney:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
7	CTCF	chr9:6739340-6739490	HEEpiC	esophagus:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
8	CTCF	chr9:6739326-6739564	SK-N-SH_RA	brain:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
9	CTCF	chr9:6739320-6739470	GM12874	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
10	CTCF	chr9:6739360-6739510	GM12871	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
11	CTCF	chr9:6739360-6739510	HFF-Myc	foreskin:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
12	CTCF	chr9:6739340-6739550	GM12869	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
13	CTCF	chr9:6739340-6739490	HCT-116	colon:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
14	CTCF	chr9:6739320-6739470	HRE	kidney:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
15	CTCF	chr9:6739356-6739540	Spleen_OC	spleen:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
16	CTCF	chr9:6739360-6739510	GM12801	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
17	CTCF	chr9:6739400-6739550	HMEC	breast:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
18	CTCF	chr9:6739320-6739470	HBMEC	blood vessel:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
19	CTCF	chr9:6739320-6739470	GM12867	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
20	CTCF	chr9:6739360-6739510	MCF-7	breast:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
21	CTCF	chr9:6739314-6739551	GM12878	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
22	CTCF	chr9:6739380-6739530	HPAF	blood vessel:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
23	CTCF	chr9:6739340-6739490	A549	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
24	CTCF	chr9:6739380-6739530	Hela-S3	cervix:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
25	CTCF	chr9:6739360-6739510	HepG2	liver:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
26	CTCF	chr9:6739343-6739535	HepG2	liver:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
27	CTCF	chr9:6739420-6739570	HEK293	kidney:	n/a	chr9:6739422-6739430
28	CTCF	chr9:6739340-6739490	NHDF-neo	bronchial:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
29	CTCF	chr9:6739321-6739538	MCF-7	breast:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
30	CTCF	chr9:6739240-6739535	H1-hESC	embryonic stem cell:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
31	CTCF	chr9:6739400-6739550	AG09309	skin:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
32	CTCF	chr9:6739380-6739530	HPF	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
33	CTCF	chr9:6739340-6739490	HA-sp	spinal cord:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
34	CTCF	chr9:6739360-6739510	AG04450	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
35	CTCF	chr9:6739250-6739587	MCF-7	breast:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
36	CTCF	chr9:6739360-6739510	HPAF	blood vessel:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
37	CTCF	chr9:6739297-6739566	MCF-7	breast:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
38	CTCF	chr9:6739300-6739450	GM12864	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
39	CTCF	chr9:6739072-6739825	SK-N-SH	brain:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
40	CTCF	chr9:6739355-6739508	LNCaP	prostate:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
41	CTCF	chr9:6739380-6739530	HA-sp	spinal cord:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
42	CTCF	chr9:6739360-6739510	GM12873	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
43	CTCF	chr9:6739400-6739550	AG09319	gingival:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
44	CTCF	chr9:6739259-6739604	A549	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
45	CTCF	chr9:6739380-6739530	HVMF	connective:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
46	CTCF	chr9:6739360-6739510	HPF	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
47	CTCF	chr9:6739340-6739490	SAEC	small airway:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
48	CTCF	chr9:6739380-6739530	HRPEpiC	eye:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
49	CTCF	chr9:6739300-6739450	NHLF	lung:	n/a	chr9:6739412-6739433 chr9:6739422-6739430
50	CTCF	chr9:6739360-6739510	NB4	blood:	n/a	chr9:6739412-6739433 chr9:6739422-6739430

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:6731623-6731673	NT2-D1	testis:	n/a
2	chr9:6731623-6731673	NB4	blood:	n/a
3	chr9:6731623-6731673	AG09319	gingival:	n/a
4	chr9:6731623-6731673	HMEC	breast:	n/a
5	chr9:6731623-6731673	HRCEpiC	kidney:	n/a
6	chr9:6731623-6731673	LNCaP	prostate:	n/a
7	chr9:6731623-6731673	Caco-2	colon:	n/a
8	chr9:6731623-6731673	HEEpiC	esophagus:	n/a
9	chr9:6731623-6731673	SKMC	muscle:	n/a
10	chr9:6731623-6731673	GM12892	blood:	n/a
11	chr9:6731623-6731673	Hela-S3	cervix:	n/a
12	chr9:6731623-6731673	AG10803	skin:	n/a
13	chr9:6731623-6731673	HRPEpiC	eye:	n/a
14	chr9:6731623-6731673	BJ	skin:	n/a
15	chr9:6731623-6731673	HIPEpiC	eye:	n/a
16	chr9:6731623-6731673	AG09309	skin:	n/a
17	chr9:6731623-6731673	SK-N-SH	brain:	n/a
18	chr9:6731623-6731673	IMR90	lung:	fetal
19	chr9:6731623-6731673	HAEpiC	amniotic membrane:	n/a
20	chr9:6731623-6731673	HUVEC	blood vessel:	n/a
21	chr9:6731623-6731673	HEK293	kidney:	embryo
22	chr9:6731623-6731673	NHDF-neo	bronchial:	n/a
23	chr9:6731623-6731673	PANC-1	pancreas:	n/a
24	chr9:6731623-6731673	MCF10A-Er-Src	breast:	n/a
25	chr9:6731623-6731673	GM19239	blood:	n/a
26	chr9:6731623-6731673	HCM	heart:	n/a
27	chr9:6731623-6731673	AoSMC	blood vessel:	n/a
28	chr9:6731623-6731673	GM06990	blood:	n/a
29	chr9:6731623-6731673	Hepatocyte	liver:	n/a
30	chr9:6731623-6731673	ECC-1	luminal epithelium:	n/a
31	chr9:6731623-6731673	U87	brain:	n/a
32	chr9:6731623-6731673	T-47D	breast:	n/a
33	chr9:6731623-6731673	HCPEpiC	choroid plexus:	n/a
34	chr9:6731623-6731673	A549	lung:	n/a
35	chr9:6731623-6731673	HepG2	liver:	n/a
36	chr9:6731623-6731673	RPTEC	kidney:	n/a
37	chr9:6731623-6731673	PFSK-1	brain:	n/a
38	chr9:6731623-6731673	ProgFib	skin:	n/a
39	chr9:6731623-6731673	HRE	kidney:	n/a
40	chr9:6731623-6731673	NH-A	brain:	n/a
41	chr9:6731623-6731673	MCF-7	breast:	n/a
42	chr9:6731623-6731673	HPAEpiC	pulmonary alveolar:	n/a
43	chr9:6731623-6731673	Jurkat	blood:	n/a
44	chr9:6731623-6731673	ovcar-3	ovarian:	n/a
45	chr9:6731623-6731673	PrEC	prostate:	n/a
46	chr9:6731623-6731673	GM12891	blood:	n/a
47	chr9:6731623-6731673	SAEC	small airway:	n/a
48	chr9:6731623-6731673	BE2_C	brain:	n/a
49	chr9:6731623-6731673	HL-60	blood:	n/a
50	chr9:6731623-6731673	K562	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:6679734..6682958-chr9:6730915..6733550,3	MCF-7	breast:
2	chr9:6714855..6717847-chr9:6737862..6741209,3	MCF-7	breast:
3	chr9:6354073..6354743-chr9:6738989..6739892,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNRPEP2-1	chr9:6734598-6735076	NONHSAT130163

Variant related genes	Relation type
ENSG00000231108	TF binding region
ENSG00000231108	CpG island
ENSG00000225489	chromatin interactions

Extended variants
information (count: 616 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:616 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574505649	chr9:6729605-6729606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs185786669	chr9:6729639-6729640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs190686301	chr9:6729644-6729645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs527378894	chr9:6729697-6729698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs150234789	chr9:6729746-6729747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs182497481	chr9:6729768-6729769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs138912450	chr9:6729823-6729824	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs550086213	chr9:6729831-6729832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs62566468	chr9:6729927-6729928	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs552829045	chr9:6729928-6729929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs62566469	chr9:6729930-6729931	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs547759149	chr9:6729949-6729950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs62566470	chr9:6729951-6729952	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs539897965	chr9:6729973-6729974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs558818527	chr9:6730015-6730016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs202182030	chr9:6730118-6730119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs142942724	chr9:6730119-6730120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs577127370	chr9:6730120-6730121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs141853418	chr9:6730187-6730188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs62566471	chr9:6730216-6730217	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs574743914	chr9:6730217-6730218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs185304007	chr9:6730249-6730250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs115619716	chr9:6730274-6730275	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs375798516	chr9:6730275-6730276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs572080791	chr9:6730316-6730317	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs147121766	chr9:6730354-6730355	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs36111586	chr9:6730363-6730364	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs553921543	chr9:6730374-6730375	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs543571165	chr9:6730381-6730382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs367796161	chr9:6730391-6730392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs562086209	chr9:6730403-6730404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs201729418	chr9:6730414-6730415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs35465144	chr9:6730445-6730446	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs544978872	chr9:6730463-6730464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs373818432	chr9:6730470-6730471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs566047709	chr9:6730475-6730476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191432356	chr9:6730476-6730477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs551927234	chr9:6730481-6730482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs34640702	chr9:6730507-6730508	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs538046985	chr9:6730540-6730541	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs556391599	chr9:6730549-6730550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs199525576	chr9:6730551-6730552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs376454998	chr9:6730577-6730578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs34693373	chr9:6730587-6730588	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs535724761	chr9:6730592-6730593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs182450975	chr9:6730602-6730603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs36043237	chr9:6730628-6730629	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs572031778	chr9:6730646-6730647	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs561041650	chr9:6730649-6730650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs187923210	chr9:6730704-6730705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:106)

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
early-passage human iPS cells	21368824	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Schizophrenia	23813976	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6724200-6749200	Weak transcription	Primary B cells from cord blood	blood
2	chr9:6725200-6734600	Weak transcription	GM12878-XiMat	blood
3	chr9:6726800-6737800	Weak transcription	Liver	Liver
4	chr9:6732600-6733800	Enhancers	HepG2	liver
5	chr9:6733200-6734200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr9:6733400-6733600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:6738600-6739800	Enhancers	Primary B cells from peripheral blood	blood

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