Variant report

Variant	nsv523075
Chromosome Location	chr3:145387917-145482086
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	BRCA1	chr3:145477935-145478012	Hela-S3	cervix:	n/a	n/a
2	CCNT2	chr3:145410614-145410809	K562	blood:	n/a	n/a
3	CEBPB	chr3:145453343-145453829	MCF-7	breast:	n/a	n/a
4	CEBPB	chr3:145412696-145412767	HepG2	liver:	n/a	chr3:145412717-145412728
5	CEBPB	chr3:145455783-145456111	IMR90	lung:	n/a	chr3:145455933-145455946 chr3:145455933-145455944 chr3:145455933-145455946 chr3:145455935-145455946
6	CEBPB	chr3:145455799-145456091	K562	blood:	n/a	chr3:145455933-145455946 chr3:145455933-145455944 chr3:145455933-145455946 chr3:145455935-145455946
7	CEBPB	chr3:145479861-145479895	HepG2	liver:	n/a	n/a
8	CEBPB	chr3:145479900-145479932	H1-hESC	embryonic stem cell:	n/a	n/a
9	CEBPB	chr3:145396239-145396517	HepG2	liver:	n/a	chr3:145396391-145396402
10	CEBPB	chr3:145455775-145456115	HepG2	liver:	n/a	chr3:145455933-145455946 chr3:145455933-145455944 chr3:145455933-145455946 chr3:145455935-145455946
11	CEBPB	chr3:145453348-145453857	MCF-7	breast:	n/a	n/a
12	CEBPB	chr3:145455772-145456084	A549	lung:	n/a	chr3:145455933-145455946 chr3:145455933-145455944 chr3:145455933-145455946 chr3:145455935-145455946
13	CEBPB	chr3:145455860-145456099	H1-hESC	embryonic stem cell:	n/a	chr3:145455933-145455946 chr3:145455933-145455944 chr3:145455933-145455946 chr3:145455935-145455946
14	CTCF	chr3:145405577-145405678	MCF-7	breast:	n/a	chr3:145405619-145405637
15	CTCF	chr3:145405530-145405714	H1-hESC	embryonic stem cell:	n/a	chr3:145405619-145405637
16	CTCF	chr3:145424860-145425010	HMF	breast:	n/a	n/a
17	CTCF	chr3:145416700-145416850	HRPEpiC	eye:	n/a	n/a
18	CTCF	chr3:145416726-145416744	LNCaP	prostate:	n/a	n/a
19	CTCF	chr3:145439800-145439950	HPF	lung:	n/a	n/a
20	CTCF	chr3:145416680-145416830	WERI-Rb-1	eye:	n/a	n/a
21	CTCF	chr3:145416593-145416884	GM12878	blood:	n/a	n/a
22	CTCF	chr3:145416677-145416814	MCF-7	breast:	n/a	n/a
23	CTCF	chr3:145416703-145416800	HUVEC	blood vessel:	n/a	n/a
24	CTCF	chr3:145416640-145416790	WERI-Rb-1	eye:	n/a	n/a
25	CTCF	chr3:145416666-145416793	HepG2	liver:	n/a	n/a
26	CTCF	chr3:145416600-145416750	RPTEC	kidney:	n/a	n/a
27	CTCF	chr3:145405520-145405670	GM06990	blood:	n/a	chr3:145405619-145405637
28	CTCF	chr3:145416580-145416730	BE2_C	brain:	n/a	n/a
29	CTCF	chr3:145416738-145416766	NHEK	skin:	n/a	n/a
30	CTCF	chr3:145416637-145416798	Medullo	brain:	n/a	n/a
31	CTCF	chr3:145416696-145416789	GM13977	blood:	n/a	n/a
32	CTCF	chr3:145416640-145416790	HepG2	liver:	n/a	n/a
33	CTCF	chr3:145416707-145416826	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:145416640-145416790	HEEpiC	esophagus:	n/a	n/a
35	CUX1	chr3:145450688-145450695	GM12878	blood:	n/a	n/a
36	E2F4	chr3:145476115-145476451	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr3:145396192-145396492	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F4	chr3:145390504-145390784	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr3:145408262-145408413	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr3:145416173-145416373	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr3:145452946-145453138	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr3:145421601-145421801	MCF10A-Er-Src	breast:	n/a	n/a
43	EP300	chr3:145436888-145437261	H1-hESC	embryonic stem cell:	n/a	n/a
44	ESR1	chr3:145461052-145461511	ECC-1	luminal epithelium:	n/a	n/a
45	ESR1	chr3:145461055-145461450	ECC-1	luminal epithelium:	n/a	n/a
46	ESR1	chr3:145461008-145461447	ECC-1	luminal epithelium:	n/a	n/a
47	ESR1	chr3:145457671-145458162	ECC-1	luminal epithelium:	n/a	n/a
48	ESR1	chr3:145457681-145458106	ECC-1	luminal epithelium:	n/a	n/a
49	ESR1	chr3:145461159-145461454	ECC-1	luminal epithelium:	n/a	n/a
50	ESR1	chr3:145457743-145457988	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:144984029..144984834-chr3:145416240..145416755,2	MCF-7	breast:

Variant related genes	Relation type
GM2AP1	TF binding region

Extended variants
information (count: 2296 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:2296 , 50 per page) page: 1 2 3 4 5 6 7 ... 46

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1609195	chr3:145387917-145387918	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs564127302	chr3:145387951-145387952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs6808237	chr3:145387960-145387961	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs1609194	chr3:145387999-145388000	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs531740511	chr3:145388110-145388111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs550115363	chr3:145388175-145388176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs568384900	chr3:145388203-145388204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529545239	chr3:145388223-145388224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs183524594	chr3:145388240-145388241	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs187960284	chr3:145388244-145388245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs7652097	chr3:145388304-145388305	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs115575234	chr3:145388339-145388340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs566074040	chr3:145388378-145388379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs539644840	chr3:145388452-145388453	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs557822236	chr3:145388491-145388492	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs146927636	chr3:145388539-145388540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs570515389	chr3:145388568-145388569	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs192052098	chr3:145388691-145388692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs537016674	chr3:145388699-145388700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs537557081	chr3:145388709-145388710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs556093725	chr3:145388723-145388724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs576600609	chr3:145388732-145388733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs574351566	chr3:145388757-145388758	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs536501633	chr3:145388767-145388768	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs573639441	chr3:145388769-145388770	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs542060922	chr3:145388783-145388784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554340076	chr3:145388797-145388798	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150965685	chr3:145388811-145388812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs546069968	chr3:145388836-145388837	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs183055011	chr3:145388906-145388907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs78311832	chr3:145388921-145388922	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs554097304	chr3:145388988-145388989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs201677661	chr3:145389011-145389012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs562046480	chr3:145389017-145389018	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs140776636	chr3:145389062-145389063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs78335752	chr3:145389079-145389080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs559483695	chr3:145389098-145389099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs549398384	chr3:145389158-145389159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs376252567	chr3:145389215-145389216	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs533293537	chr3:145389241-145389242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs572415113	chr3:145389251-145389252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs188110874	chr3:145389264-145389265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs537051454	chr3:145389299-145389300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545999131	chr3:145389313-145389314	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs192792459	chr3:145389315-145389316	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs184358766	chr3:145389331-145389332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs150151721	chr3:145389333-145389334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs534706333	chr3:145389337-145389338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs575380290	chr3:145389338-145389339	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs369353837	chr3:145389358-145389359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

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
Breast cancer	22522925	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145386600-145390400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:145386800-145390800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:145390400-145390800	Enhancers	HUVEC	blood vessel
4	chr3:145390400-145391600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:145390800-145392000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:145391600-145392000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:145391600-145392000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:145391600-145392000	Enhancers	Fetal Brain Male	brain
9	chr3:145392000-145396000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:145392000-145396200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:145394800-145398400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:145396000-145396400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:145396200-145396600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:145396400-145398400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:145396600-145397600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:145397600-145398000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:145398000-145399000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:145398400-145399400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:145398600-145399400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr3:145399000-145399400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:145399000-145399400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr3:145399200-145399600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:145402200-145404800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:145404800-145405600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:145404800-145405600	Enhancers	Stomach Mucosa	stomach
26	chr3:145405000-145405600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:145408800-145410000	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:145410200-145410600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:145410200-145411800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:145411200-145411600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr3:145411200-145412600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:145411400-145411800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:145411400-145411800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:145412200-145412800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:145412200-145412800	Enhancers	Brain Substantia Nigra	brain
36	chr3:145412800-145415800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:145415600-145415800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:145415600-145415800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:145415600-145415800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:145415800-145416000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:145415800-145416200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:145415800-145416200	Active TSS	Esophagus	oesophagus
43	chr3:145415800-145416200	Enhancers	NHEK	skin
44	chr3:145415800-145416400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:145415800-145416400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:145415800-145416400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:145415800-145416400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:145416000-145416200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:145416000-145416200	Enhancers	Stomach Mucosa	stomach
50	chr3:145416000-145416400	Enhancers	Adipose Nuclei	Adipose

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