Variant report

Variant	nsv1015017
Chromosome Location	chr3:255395-300898
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	chr3:291259-291870	HepG2	liver:	n/a	n/a
2	BACH1	chr3:271174-271333	K562	blood:	n/a	n/a
3	BATF	chr3:259675-259847	GM12878	blood:	n/a	n/a
4	BHLHE40	chr3:260263-260618	GM12878	blood:	n/a	n/a
5	BHLHE40	chr3:260829-261058	GM12878	blood:	n/a	n/a
6	CEBPB	chr3:291612-291803	H1-hESC	embryonic stem cell:	n/a	chr3:291705-291716
7	CEBPB	chr3:279120-279410	A549	lung:	n/a	chr3:279226-279239 chr3:279227-279238
8	CEBPB	chr3:284758-286178	IMR90	lung:	n/a	chr3:284916-284933 chr3:285984-286001 chr3:284887-284900
9	CEBPB	chr3:279116-279413	HepG2	liver:	n/a	chr3:279226-279239 chr3:279227-279238
10	CEBPB	chr3:271018-271333	H1-hESC	embryonic stem cell:	n/a	chr3:271305-271317
11	CEBPB	chr3:291583-291816	HepG2	liver:	n/a	chr3:291705-291716
12	CEBPB	chr3:291542-291836	HepG2	liver:	n/a	chr3:291705-291716
13	CREB1	chr3:299561-299956	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:278940-279009	GM19238	blood:	n/a	n/a
15	CTCF	chr3:287440-287590	GM12869	blood:	n/a	n/a
16	CTCF	chr3:278947-279007	MCF-7	breast:	n/a	n/a
17	CTCF	chr3:266691-266735	GM20000	blood:	n/a	n/a
18	CTCF	chr3:287360-287510	MCF-7	breast:	n/a	n/a
19	E2F4	chr3:298337-298540	MCF10A-Er-Src	breast:	n/a	chr3:298525-298534
20	E2F4	chr3:284901-285229	MCF10A-Er-Src	breast:	n/a	n/a
21	E2F4	chr3:285810-286234	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F6	chr3:299503-299921	H1-hESC	embryonic stem cell:	n/a	n/a
23	EBF1	chr3:280766-280963	GM12878	blood:	n/a	n/a
24	EBF1	chr3:278951-279133	GM12878	blood:	n/a	n/a
25	EBF1	chr3:260927-261165	GM12878	blood:	n/a	chr3:261010-261021
26	EGR1	chr3:260837-260993	GM12878	blood:	n/a	chr3:260903-260917
27	EP300	chr3:260882-260922	GM12878	blood:	n/a	n/a
28	EP300	chr3:299608-299896	H1-hESC	embryonic stem cell:	n/a	n/a
29	FAM48A	chr3:269401-269442	GM12878	blood:	n/a	n/a
30	FOS	chr3:283085-283384	MCF10A-Er-Src	breast:	n/a	n/a
31	FOS	chr3:284903-285477	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr3:284921-285373	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:298246-298527	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr3:285827-286162	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:299894-299996	MCF10A-Er-Src	breast:	n/a	chr3:299957-299965 chr3:299958-299965 chr3:299956-299965
36	FOS	chr3:285774-286081	MCF10A-Er-Src	breast:	n/a	n/a
37	FOS	chr3:285762-286097	MCF10A-Er-Src	breast:	n/a	n/a
38	FOS	chr3:284929-285522	MCF10A-Er-Src	breast:	n/a	n/a
39	FOS	chr3:299826-300140	MCF10A-Er-Src	breast:	n/a	chr3:299957-299965 chr3:299958-299965 chr3:299956-299965
40	FOS	chr3:299860-300099	MCF10A-Er-Src	breast:	n/a	chr3:299957-299965 chr3:299958-299965 chr3:299956-299965
41	FOS	chr3:298227-298598	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr3:285829-286080	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr3:284855-285381	MCF10A-Er-Src	breast:	n/a	chr3:284862-284874
44	FOS	chr3:299885-300144	MCF10A-Er-Src	breast:	n/a	chr3:299957-299965 chr3:299958-299965 chr3:299956-299965
45	FOS	chr3:298221-298528	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr3:298207-298653	MCF10A-Er-Src	breast:	n/a	n/a
47	FOXA1	chr3:291289-291627	HepG2	liver:	n/a	n/a
48	FOXA1	chr3:270033-270288	T-47D	breast:	n/a	chr3:270233-270245
49	FOXA1	chr3:291207-291600	HepG2	liver:	n/a	n/a
50	GATA2	chr3:290698-291090	SH-SY5Y	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:271185-271235	NHBE	bronchial:	n/a
2	chr3:271185-271235	NHBE	bronchial:	n/a
3	chr3:271185-271235	Caco-2	colon:	n/a
4	chr3:271185-271235	AG04450	lung:	fetal
5	chr3:285234-285284	HCPEpiC	choroid plexus:	n/a
6	chr3:285234-285284	GM06990	blood:	n/a
7	chr3:285234-285284	Caco-2	colon:	n/a
8	chr3:285234-285284	U87	brain:	n/a
9	chr3:271185-271235	IMR90	lung:	fetal
10	chr3:285234-285284	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:285234-285284	HUVEC	blood vessel:	n/a
12	chr3:285234-285284	T-47D	breast:	n/a
13	chr3:285234-285284	GM12878	blood:	n/a
14	chr3:285234-285284	NHBE	bronchial:	n/a
15	chr3:271185-271235	HEK293	kidney:	embryo
16	chr3:285234-285284	AoSMC	blood vessel:	n/a
17	chr3:285234-285284	PrEC	prostate:	n/a
18	chr3:285234-285284	RPTEC	kidney:	n/a
19	chr3:271185-271235	GM12891	blood:	n/a
20	chr3:285234-285284	AG10803	skin:	n/a
21	chr3:271185-271235	HRCEpiC	kidney:	n/a
22	chr3:285234-285284	SAEC	small airway:	n/a
23	chr3:271185-271235	AG09309	skin:	n/a
24	chr3:285234-285284	MCF-7	breast:	n/a
25	chr3:271185-271235	SAEC	small airway:	n/a
26	chr3:285234-285284	ovcar-3	ovarian:	n/a
27	chr3:271185-271235	AoSMC	blood vessel:	n/a
28	chr3:285234-285284	IMR90	lung:	fetal
29	chr3:271185-271235	AG09319	gingival:	n/a
30	chr3:271185-271235	HAEpiC	amniotic membrane:	n/a
31	chr3:285234-285284	Hepatocyte	liver:	n/a
32	chr3:285234-285284	HAEpiC	amniotic membrane:	n/a
33	chr3:271185-271235	GM12878	blood:	n/a
34	chr3:285234-285284	SKMC	muscle:	n/a
35	chr3:271185-271235	Hepatocyte	liver:	n/a
36	chr3:271185-271235	HL-60	blood:	n/a
37	chr3:271185-271235	ProgFib	skin:	n/a
38	chr3:285234-285284	PFSK-1	brain:	n/a
39	chr3:271185-271235	BJ	skin:	n/a
40	chr3:271185-271235	U87	brain:	n/a
41	chr3:271185-271235	A549	lung:	n/a
42	chr3:271185-271235	HPAEpiC	pulmonary alveolar:	n/a
43	chr3:285234-285284	SK-N-SH_RA	brain:	n/a
44	chr3:271185-271235	HUVEC	blood vessel:	n/a
45	chr3:271185-271235	PFSK-1	brain:	n/a
46	chr3:285234-285284	HIPEpiC	eye:	n/a
47	chr3:285234-285284	HRCEpiC	kidney:	n/a
48	chr3:285234-285284	LNCaP	prostate:	n/a
49	chr3:285234-285284	SK-N-SH	brain:	n/a
50	chr3:285234-285284	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
2	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
3	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
4	chr3:297411..299702-chr3:300779..302869,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN6-7	chr3:288251-288539	NONHSAT087560
2	lnc-CNTN6-7	chr3:286296-286375	NONHSAT087560
3	lnc-CNTN6-7	chr3:288251-290282	NONHSAT087561
4	lnc-CNTN6-7	chr3:286296-286375	NONHSAT087561

Variant related genes	Relation type
CHL1	TF binding region
CHL1	CpG island

Extended variants
information (count: 2411 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:2411 , 50 per page) page: 1 2 3 4 5 6 7 ... 49

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs331869	chr3:255395-255396	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs559844044	chr3:255396-255397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs530218916	chr3:255407-255408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs75493794	chr3:255424-255425	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs187462832	chr3:255426-255427	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs530765153	chr3:255473-255474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs138608233	chr3:255480-255481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs190697397	chr3:255545-255546	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs534284660	chr3:255550-255551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs546194946	chr3:255554-255555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs115337896	chr3:255557-255558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs199729902	chr3:255581-255582	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs367983888	chr3:255605-255606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs548423001	chr3:255642-255643	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs230821	chr3:255644-255645	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs77724706	chr3:255671-255672	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs143465201	chr3:255672-255673	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs148161518	chr3:255681-255682	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs558951385	chr3:255704-255705	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs577474475	chr3:255721-255722	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs34709116	chr3:255722-255723	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs541389759	chr3:255724-255725	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs556497628	chr3:255738-255739	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs553399488	chr3:255775-255776	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs183269084	chr3:255796-255797	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs112284505	chr3:255846-255847	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs563831279	chr3:255850-255851	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs530588246	chr3:255873-255874	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs79168009	chr3:255878-255879	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs111537942	chr3:255883-255884	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs556945397	chr3:255897-255898	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs564181718	chr3:255907-255908	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs528386027	chr3:255937-255938	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs546533368	chr3:255976-255977	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs567705078	chr3:256011-256012	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs528885938	chr3:256028-256029	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs550233442	chr3:256029-256030	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs188932083	chr3:256049-256050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs530692217	chr3:256102-256103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs57199434	chr3:256110-256111	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs143215422	chr3:256149-256150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs535325691	chr3:256150-256151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs553734096	chr3:256179-256180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs147474353	chr3:256180-256181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs542264411	chr3:256181-256182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs557139239	chr3:256189-256190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs575699106	chr3:256223-256224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs2133402	chr3:256258-256259	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs140014726	chr3:256271-256272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs528307839	chr3:256277-256278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:229 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:246200-258600	Weak transcription	Fetal Brain Female	brain
2	chr3:251600-255400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:252800-256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:253200-258200	Weak transcription	Fetal Brain Male	brain
5	chr3:254400-255400	Weak transcription	GM12878-XiMat	blood
6	chr3:254400-258400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:254600-258400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:255200-258400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:255400-265400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:257000-257200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr3:257200-258200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:258200-258600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr3:258200-259400	Enhancers	Fetal Brain Male	brain
14	chr3:258400-258600	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:258400-258800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:258400-259400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:258400-261400	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:258600-258800	Enhancers	Brain Germinal Matrix	brain
19	chr3:258600-259400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:258600-259400	Enhancers	Fetal Brain Female	brain
21	chr3:258600-259400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:259200-259400	Enhancers	Esophagus	oesophagus
23	chr3:259200-260000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:259200-260000	Weak transcription	GM12878-XiMat	blood
25	chr3:259600-261400	Enhancers	Primary B cells from cord blood	blood
26	chr3:260000-261000	Enhancers	GM12878-XiMat	blood
27	chr3:265400-265800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:265800-267000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:266000-266200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:268200-268400	Enhancers	Ovary	ovary
31	chr3:268400-271000	Weak transcription	Ovary	ovary
32	chr3:269000-269200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr3:269200-270200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:269400-269600	Enhancers	Brain Anterior Caudate	brain
35	chr3:269400-271200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:269600-271000	Weak transcription	Brain Anterior Caudate	brain
37	chr3:270000-271800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:270200-270600	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:270200-272200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr3:270200-272800	Enhancers	Brain Germinal Matrix	brain
41	chr3:270400-271400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:270400-272000	Enhancers	HMEC	breast
43	chr3:270600-270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:270600-271000	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:270600-271000	Enhancers	NHEK	skin
46	chr3:270600-272000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:270800-271400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr3:270800-271800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:270800-272600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:271000-271200	Flanking Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links