Variant report

Variant	nsv3812
Chromosome Location	chr3:49669773-49680587
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	ATF3	chr3:49675948-49676168	K562	blood:	n/a	chr3:49676058-49676072
2	ATF3	chr3:49675821-49676257	K562	blood:	n/a	chr3:49676058-49676072
3	BHLHE40	chr3:49675944-49676366	K562	blood:	n/a	chr3:49676190-49676199 chr3:49676191-49676200 chr3:49676184-49676205 chr3:49676190-49676199
4	BRCA1	chr3:49675906-49676162	Hela-S3	cervix:	n/a	n/a
5	CBX3	chr3:49675774-49676157	K562	blood:	n/a	n/a
6	CEBPB	chr3:49671838-49672044	K562	blood:	n/a	n/a
7	CEBPB	chr3:49675885-49676238	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr3:49671861-49672028	IMR90	lung:	n/a	n/a
9	CEBPB	chr3:49671861-49672036	A549	lung:	n/a	n/a
10	CHD2	chr3:49675874-49676230	Hela-S3	cervix:	n/a	n/a
11	CREB1	chr3:49674327-49674883	GM12878	blood:	n/a	n/a
12	CREB1	chr3:49674227-49674916	GM12878	blood:	n/a	n/a
13	CTCF	chr3:49672263-49672525	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr3:49680479-49680610	MCF-7	breast:	n/a	n/a
15	CTCF	chr3:49672294-49672472	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr3:49672280-49672430	HCT-116	colon:	n/a	n/a
17	CTCF	chr3:49680467-49680620	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:49672260-49672410	Hela-S3	cervix:	n/a	n/a
19	CTCF	chr3:49672260-49672410	HBMEC	blood vessel:	n/a	n/a
20	CTCF	chr3:49670181-49670227	GM13976	blood:	n/a	n/a
21	CTCF	chr3:49672400-49672550	BE2_C	brain:	n/a	n/a
22	CTCF	chr3:49672280-49672430	HCPEpiC	choroid plexus:	n/a	n/a
23	CTCF	chr3:49672320-49672470	HEK293	kidney:	n/a	n/a
24	CTCF	chr3:49672331-49672409	K562	blood:	n/a	n/a
25	CTCF	chr3:49680520-49680589	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:49672261-49672472	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:49672281-49672476	K562	blood:	n/a	n/a
28	CTCF	chr3:49672340-49672490	K562	blood:	n/a	n/a
29	CTCF	chr3:49675145-49675179	GM12878	blood:	n/a	n/a
30	CTCF	chr3:49672380-49672530	GM12873	blood:	n/a	n/a
31	E2F6	chr3:49675819-49676033	K562	blood:	n/a	n/a
32	E2F6	chr3:49676064-49676276	K562	blood:	n/a	n/a
33	ELK1	chr3:49676012-49676081	Hela-S3	cervix:	n/a	n/a
34	EP300	chr3:49675874-49676192	K562	blood:	n/a	chr3:49676063-49676072
35	EP300	chr3:49675924-49676227	Hela-S3	cervix:	n/a	chr3:49676063-49676072
36	FOS	chr3:49674249-49674630	MCF10A-Er-Src	breast:	n/a	chr3:49674404-49674413 chr3:49674404-49674414 chr3:49674404-49674414
37	FOS	chr3:49675876-49676248	Hela-S3	cervix:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
38	FOS	chr3:49674227-49674724	MCF10A-Er-Src	breast:	n/a	chr3:49674404-49674413 chr3:49674404-49674414 chr3:49674404-49674414
39	FOS	chr3:49674228-49674734	MCF10A-Er-Src	breast:	n/a	chr3:49674404-49674413 chr3:49674404-49674414 chr3:49674404-49674414
40	FOS	chr3:49675883-49676287	MCF10A-Er-Src	breast:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
41	FOS	chr3:49674295-49674638	MCF10A-Er-Src	breast:	n/a	chr3:49674404-49674413 chr3:49674404-49674414 chr3:49674404-49674414
42	FOS	chr3:49675890-49676275	MCF10A-Er-Src	breast:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
43	FOS	chr3:49675882-49676310	MCF10A-Er-Src	breast:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
44	FOS	chr3:49675890-49676312	MCF10A-Er-Src	breast:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
45	FOSL1	chr3:49675808-49676563	HCT-116	colon:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676062-49676073 chr3:49676064-49676073 chr3:49676448-49676460
46	FOSL1	chr3:49675781-49676305	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676062-49676073 chr3:49676064-49676073
47	FOSL1	chr3:49675917-49676229	K562	blood:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676062-49676073 chr3:49676064-49676073
48	FOSL2	chr3:49675873-49676265	A549	lung:	n/a	chr3:49676170-49676178 chr3:49676063-49676072 chr3:49676062-49676074 chr3:49676064-49676073
49	FOXM1	chr3:49674286-49674691	GM12878	blood:	n/a	n/a
50	GTF2F1	chr3:49675863-49676248	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49666488..49668184-chr3:49675281..49676977,2	K562	blood:
2	chr3:49663253..49665357-chr3:49680487..49682256,2	K562	blood:
3	chr3:49585320..49587935-chr3:49676099..49678339,2	K562	blood:
4	chr3:49673401..49676066-chr3:49680626..49682586,2	MCF-7	breast:
5	chr3:49654340..49656120-chr3:49672426..49675250,2	K562	blood:
6	chr3:49666595..49669232-chr3:49671512..49673692,2	K562	blood:
7	chr3:49676360..49678118-chr3:49683625..49686002,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MST1-1	chr3:49679053-49679202	ENSG00000235120.1
2	lnc-MST1-1	chr3:49677916-49678226	ENSG00000235120.1

Variant related genes	Relation type
BSN-AS1	TF binding region
BSN	TF binding region

Extended variants
information (count: 310 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:310 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs568416848	chr3:49669790-49669791	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs535495694	chr3:49669791-49669792	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs539048549	chr3:49669824-49669825	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs557615473	chr3:49669934-49669935	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs576033805	chr3:49669941-49669942	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs71324982	chr3:49669948-49669949	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	mRNA abundance
7	rs188940086	chr3:49669963-49669964	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs573486353	chr3:49670015-49670016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78158066	chr3:49670081-49670082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs575596066	chr3:49670098-49670099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12497107	chr3:49670129-49670130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs182737831	chr3:49670145-49670146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs573568198	chr3:49670168-49670169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs187031621	chr3:49670179-49670180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs562439859	chr3:49670190-49670191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs191670331	chr3:49670235-49670236	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs544914593	chr3:49670253-49670254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs76886191	chr3:49670310-49670311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs115324393	chr3:49670351-49670352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs547039560	chr3:49670530-49670531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs568493595	chr3:49670551-49670552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs529263985	chr3:49670580-49670581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs373151449	chr3:49670589-49670590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs550742508	chr3:49670606-49670607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs12497288	chr3:49670650-49670651	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs540098178	chr3:49670727-49670728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs548859335	chr3:49670734-49670735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs75155734	chr3:49670735-49670736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs78690155	chr3:49670737-49670738	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs569125923	chr3:49670862-49670863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs558492240	chr3:49670930-49670931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs567042114	chr3:49670962-49670963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs534142847	chr3:49671027-49671028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73077107	chr3:49671037-49671038	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs139087782	chr3:49671062-49671063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs544187232	chr3:49671085-49671086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs118097861	chr3:49671160-49671161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs577225393	chr3:49671165-49671166	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs35007338	chr3:49671186-49671187	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs1586827	chr3:49671224-49671225	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs533755137	chr3:49671248-49671249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs576892087	chr3:49671361-49671362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs369282747	chr3:49671405-49671406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545767548	chr3:49671414-49671415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs562206645	chr3:49671415-49671416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs184647251	chr3:49671435-49671436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs558191084	chr3:49671444-49671445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs541708708	chr3:49671483-49671484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs551103487	chr3:49671497-49671498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs187548066	chr3:49671500-49671501	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:99)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:140 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49655600-49676200	Weak transcription	HepG2	liver
2	chr3:49657600-49685400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49660800-49682600	Weak transcription	Liver	Liver
4	chr3:49661600-49692400	Weak transcription	Ovary	ovary
5	chr3:49661800-49682200	Weak transcription	Fetal Brain Male	brain
6	chr3:49662800-49685000	Weak transcription	Right Ventricle	heart
7	chr3:49663800-49679600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:49664200-49683200	Weak transcription	Pancreas	Pancrea
9	chr3:49664600-49674000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:49664600-49680000	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:49665000-49672400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:49665600-49673800	Weak transcription	Brain Angular Gyrus	brain
13	chr3:49667200-49674000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:49667600-49679800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:49668000-49673800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:49668800-49670000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:49669400-49670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:49669400-49674200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49669400-49692000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:49669600-49679400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49669600-49679800	Weak transcription	Fetal Brain Female	brain
22	chr3:49669600-49680000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49670000-49680000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:49672200-49673000	Enhancers	K562	blood
25	chr3:49672400-49673000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:49672800-49676000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:49673000-49673400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:49673000-49673400	Weak transcription	K562	blood
29	chr3:49673400-49676000	Enhancers	K562	blood
30	chr3:49673400-49676200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:49673600-49673800	Enhancers	Gastric	stomach
32	chr3:49673600-49674000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:49673600-49675600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:49673800-49674200	Enhancers	GM12878-XiMat	blood
35	chr3:49673800-49675000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:49673800-49675600	Enhancers	Brain Angular Gyrus	brain
37	chr3:49673800-49676400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:49673800-49676600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:49673800-49676800	Enhancers	NHEK	skin
41	chr3:49673800-49692400	Weak transcription	Gastric	stomach
42	chr3:49674000-49674400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:49674000-49674400	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:49674000-49674600	Enhancers	Placenta	Placenta
45	chr3:49674000-49675400	Enhancers	Brain Anterior Caudate	brain
46	chr3:49674000-49676000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:49674000-49676000	Enhancers	Spleen	Spleen
48	chr3:49674000-49676200	Enhancers	Hela-S3	cervix
49	chr3:49674000-49676600	Enhancers	HMEC	breast
50	chr3:49674200-49674400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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