Variant report

Variant	nsv437347
Chromosome Location	chr3:145620810-145665218
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	BATF	chr3:145661502-145661720	GM12878	blood:	n/a	chr3:145661650-145661660 chr3:145661649-145661660
2	CEBPB	chr3:145654854-145655147	HepG2	liver:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
3	CEBPB	chr3:145643113-145643361	A549	lung:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
4	CEBPB	chr3:145654848-145655110	A549	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
5	CEBPB	chr3:145627344-145627617	Hela-S3	cervix:	n/a	chr3:145627469-145627480
6	CEBPB	chr3:145627381-145627633	A549	lung:	n/a	chr3:145627469-145627480
7	CEBPB	chr3:145627345-145627654	HepG2	liver:	n/a	chr3:145627469-145627480
8	CEBPB	chr3:145627345-145627605	IMR90	lung:	n/a	chr3:145627469-145627480
9	CEBPB	chr3:145643100-145643364	HepG2	liver:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
10	CEBPB	chr3:145654814-145655116	IMR90	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
11	CHD2	chr3:145657978-145657991	HepG2	liver:	n/a	n/a
12	CTCF	chr3:145633840-145633990	NHDF-neo	bronchial:	n/a	n/a
13	CTCF	chr3:145633597-145634009	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
14	CTCF	chr3:145633680-145633830	GM06990	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
15	CTCF	chr3:145633740-145633890	HCT-116	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
16	CTCF	chr3:145633760-145633910	HEEpiC	esophagus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
17	CTCF	chr3:145633660-145633810	Caco-2	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
18	CTCF	chr3:145633741-145633819	HUVEC	blood vessel:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
19	CTCF	chr3:145633760-145633910	HFF	foreskin:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
20	CTCF	chr3:145633704-145633867	Hela-S3	cervix:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
21	CTCF	chr3:145633600-145633750	HBMEC	blood vessel:	n/a	n/a
22	CTCF	chr3:145633620-145633770	HMEC	breast:	n/a	n/a
23	CTCF	chr3:145633780-145633930	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr3:145633740-145633890	HMF	breast:	n/a	chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784 chr3:145633771-145633784
25	CTCF	chr3:145633793-145633809	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:145633660-145633810	GM06990	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
27	CTCF	chr3:145633740-145633890	HEEpiC	esophagus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
28	CTCF	chr3:145633700-145633850	SAEC	small airway:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
29	CTCF	chr3:145633740-145633890	GM12867	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
30	CTCF	chr3:145633660-145633810	HEK293	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
31	CTCF	chr3:145633620-145633770	BE2_C	brain:	n/a	n/a
32	CTCF	chr3:145633710-145633889	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
33	CTCF	chr3:145655045-145655063	Kidney_OC	kidney:	n/a	n/a
34	CTCF	chr3:145633740-145633890	HRPEpiC	eye:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
35	CTCF	chr3:145633689-145633849	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
36	CTCF	chr3:145633639-145633942	GM12878	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
37	CTCF	chr3:145633660-145633810	HMF	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
38	CTCF	chr3:145633700-145633850	WERI-Rb-1	eye:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
39	CTCF	chr3:145633720-145633870	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
40	CTCF	chr3:145633680-145633830	NHEK	skin:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
41	CTCF	chr3:145633860-145634010	A549	lung:	n/a	n/a
42	CTCF	chr3:145633680-145633830	GM12873	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
43	CTCF	chr3:145633680-145633830	Hela-S3	cervix:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
44	CTCF	chr3:145622335-145622443	GM10248	blood:	n/a	n/a
45	CTCF	chr3:145633751-145633795	GM12878	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
46	CTCF	chr3:145633760-145633910	HBMEC	blood vessel:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
47	CTCF	chr3:145633700-145633850	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
48	CTCF	chr3:145633660-145633810	RPTEC	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
49	CTCF	chr3:145633680-145633930	GM12872	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
50	CTCF	chr3:145633720-145633870	GM12871	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:
2	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC107021.1-3	chr3:145657699-145657941	XLOC_002852
2	lnc-AC107021.1-3	chr3:145664191-145664408	XLOC_002852
3	lnc-AC107021.1-3	chr3:145657755-145657941	XLOC_002852

Variant related genes	Relation type
ENSG00000244358	TF binding region
TWSG1	miRNA target sites

Extended variants
information (count: 626 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:626 , 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	rs9853304	chr3:145620810-145620811	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs574246200	chr3:145620820-145620821	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs544857325	chr3:145620850-145620851	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs541634326	chr3:145620892-145620893	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs1967207	chr3:145620906-145620907	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs578016273	chr3:145620915-145620916	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs545517932	chr3:145621023-145621024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs185837504	chr3:145621063-145621064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs563497738	chr3:145621069-145621070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs530954001	chr3:145621122-145621123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs386666760	chr3:145621150-145621151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs548957447	chr3:145621197-145621198	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs548405481	chr3:145621210-145621211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs534512706	chr3:145621232-145621233	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs560841594	chr3:145621274-145621275	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs6769191	chr3:145621327-145621328	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs189773822	chr3:145621337-145621338	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs145793237	chr3:145621358-145621359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs571145670	chr3:145621408-145621409	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs538321337	chr3:145621423-145621424	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs6805174	chr3:145621439-145621440	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs369009317	chr3:145621474-145621475	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs35225711	chr3:145621477-145621478	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs7651211	chr3:145621478-145621479	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs113476373	chr3:145621488-145621489	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs6440400	chr3:145621532-145621533	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs9820635	chr3:145621555-145621556	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs535366106	chr3:145621589-145621590	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs553587715	chr3:145621597-145621598	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs578133587	chr3:145621675-145621676	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs7628962	chr3:145621691-145621692	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs183181004	chr3:145621759-145621760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs575506602	chr3:145621822-145621823	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs186372821	chr3:145621829-145621830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs190476752	chr3:145621868-145621869	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs528356891	chr3:145621888-145621889	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs36093559	chr3:145621901-145621902	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs564904272	chr3:145621934-145621935	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs116679133	chr3:145621997-145621998	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs550363556	chr3:145622006-145622007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs62270848	chr3:145622021-145622022	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs529797580	chr3:145622072-145622073	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs548187252	chr3:145622089-145622090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs566506469	chr3:145622090-145622091	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs535300501	chr3:145622172-145622173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs553723405	chr3:145622192-145622193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs571700682	chr3:145622250-145622251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs62270849	chr3:145622271-145622272	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs557321415	chr3:145622277-145622278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs62270850	chr3:145622278-145622279	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Autism	18923514	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Autism	21956041	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	21509527	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145615000-145621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:145616600-145621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:145617400-145621000	Weak transcription	HSMMtube	muscle
4	chr3:145619800-145621000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:145620800-145621200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:145620800-145621400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:145621000-145621400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:145621000-145621400	Enhancers	HSMMtube	muscle
9	chr3:145621000-145621600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:145621200-145621600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:145621200-145621600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:145621400-145622200	Enhancers	Fetal Muscle Trunk	muscle
13	chr3:145621400-145622200	Enhancers	Fetal Muscle Leg	muscle
14	chr3:145621400-145623400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:145621600-145622800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:145622800-145623000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:145622800-145623200	ZNF genes & repeats	Pancreas	Pancrea
18	chr3:145623800-145624800	Enhancers	Fetal Brain Female	brain
19	chr3:145624200-145625200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:145624400-145624800	Enhancers	Fetal Brain Male	brain
21	chr3:145643400-145644200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:145643800-145644200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:145643800-145644200	Active TSS	Aorta	Aorta
24	chr3:145651800-145653200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:145652600-145653000	Enhancers	HepG2	liver
26	chr3:145653200-145654400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:145654200-145654400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:145654200-145654800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:145654400-145654800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:145654400-145654800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:145654400-145654800	Enhancers	NHDF-Ad	bronchial
32	chr3:145654400-145655200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:145654400-145655400	Enhancers	Osteobl	bone
34	chr3:145654800-145655200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:145655200-145656600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:145655200-145659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:145655400-145659600	Weak transcription	Osteobl	bone
38	chr3:145655800-145657000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:145657000-145657200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr3:145657200-145658400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:145657600-145658000	Enhancers	Esophagus	oesophagus
42	chr3:145658000-145659800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:145658400-145659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:145659200-145659600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:145659600-145660000	Enhancers	HMEC	breast
46	chr3:145659600-145660200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:145659600-145660400	Enhancers	Osteobl	bone
48	chr3:145659600-145662600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr3:145659800-145660200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:145659800-145660200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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