Variant report

Variant	nsv877627
Chromosome Location	chr3:146628382-146700377
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	CBX3	chr3:146685849-146686581	HCT-116	colon:	n/a	n/a
2	CBX3	chr3:146685751-146686637	HCT-116	colon:	n/a	n/a
3	CEBPB	chr3:146637236-146637407	Hela-S3	cervix:	n/a	chr3:146637326-146637337
4	CEBPB	chr3:146666856-146667157	MCF-7	breast:	n/a	chr3:146666948-146666959
5	CEBPB	chr3:146666824-146667006	HepG2	liver:	n/a	chr3:146666948-146666959
6	CEBPB	chr3:146666792-146667139	A549	lung:	n/a	chr3:146666948-146666959
7	CEBPB	chr3:146666764-146667147	H1-hESC	embryonic stem cell:	n/a	chr3:146666948-146666959
8	CEBPB	chr3:146637291-146637349	K562	blood:	n/a	chr3:146637326-146637337
9	CEBPB	chr3:146686339-146686461	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr3:146687962-146688145	HepG2	liver:	n/a	n/a
11	CEBPB	chr3:146666869-146667104	A549	lung:	n/a	chr3:146666948-146666959
12	CEBPB	chr3:146685521-146686346	HCT-116	colon:	n/a	n/a
13	CEBPB	chr3:146666865-146667078	ECC-1	luminal epithelium:	n/a	chr3:146666948-146666959
14	CEBPB	chr3:146666769-146667143	HepG2	liver:	n/a	chr3:146666948-146666959
15	CEBPB	chr3:146666799-146667103	ECC-1	luminal epithelium:	n/a	chr3:146666948-146666959
16	CEBPB	chr3:146637289-146637433	H1-hESC	embryonic stem cell:	n/a	chr3:146637326-146637337
17	CEBPB	chr3:146687179-146687451	IMR90	lung:	n/a	n/a
18	CEBPB	chr3:146666770-146667146	IMR90	lung:	n/a	chr3:146666948-146666959
19	CEBPB	chr3:146685570-146686464	HCT-116	colon:	n/a	n/a
20	CEBPB	chr3:146666777-146667143	K562	blood:	n/a	chr3:146666948-146666959
21	CEBPB	chr3:146685262-146686134	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr3:146685602-146686183	IMR90	lung:	n/a	n/a
23	CEBPB	chr3:146666800-146667132	Hela-S3	cervix:	n/a	chr3:146666948-146666959
24	CEBPB	chr3:146637184-146637457	HepG2	liver:	n/a	chr3:146637326-146637337
25	CEBPB	chr3:146666819-146667156	MCF-7	breast:	n/a	chr3:146666948-146666959
26	CEBPB	chr3:146694613-146694842	HepG2	liver:	n/a	chr3:146694708-146694719 chr3:146694708-146694721
27	CTCF	chr3:146646593-146646700	MCF-7	breast:	n/a	n/a
28	CTCF	chr3:146655760-146655910	HepG2	liver:	n/a	n/a
29	CTCF	chr3:146646520-146646670	HL-60	blood:	n/a	n/a
30	CTCF	chr3:146679757-146679825	Lung_OC	lung:	n/a	n/a
31	CTCF	chr3:146646580-146646730	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr3:146646600-146646750	MCF-7	breast:	n/a	n/a
33	CTCF	chr3:146646701-146646703	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:146646620-146646770	WERI-Rb-1	eye:	n/a	n/a
35	CTCF	chr3:146646640-146646790	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:146646520-146646670	HBMEC	blood vessel:	n/a	n/a
37	CTCF	chr3:146646563-146646697	MCF-7	breast:	n/a	n/a
38	CTCF	chr3:146646500-146646650	WERI-Rb-1	eye:	n/a	n/a
39	CTCF	chr3:146646582-146646709	MCF-7	breast:	n/a	n/a
40	E2F4	chr3:146649596-146649642	MCF10A-Er-Src	breast:	n/a	chr3:146649611-146649628
41	E2F4	chr3:146653076-146653276	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F4	chr3:146637329-146637367	MCF10A-Er-Src	breast:	n/a	n/a
43	E2F4	chr3:146686402-146686720	MCF10A-Er-Src	breast:	n/a	n/a
44	E2F4	chr3:146637847-146637936	MCF10A-Er-Src	breast:	n/a	n/a
45	EBF1	chr3:146634328-146634651	GM12878	blood:	n/a	chr3:146634488-146634499
46	EP300	chr3:146685598-146686610	Hela-S3	cervix:	n/a	n/a
47	EP300	chr3:146696425-146696455	GM12878	blood:	n/a	n/a
48	EP300	chr3:146685946-146686506	SK-N-SH_RA	brain:	n/a	n/a
49	EP300	chr3:146685660-146686751	SK-N-SH	brain:	n/a	n/a
50	EP300	chr3:146685914-146686514	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:146636773..146638616-chr3:146643446..146646080,2	K562	blood:
2	chr3:146698311..146701060-chr3:146701293..146703528,2	MCF-7	breast:
3	chr3:146636773..146638616-chr3:146643446..146646080,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZIC1-4	chr3:146641389-146641628	XLOC_002856
2	lnc-ZIC4-3	chr3:146636855-146636972	ENSG00000243620.1
3	lnc-ZIC1-4	chr3:146641389-146643005	XLOC_002856
4	lnc-ZIC1-4	chr3:146641088-146641111	XLOC_002856
5	lnc-ZIC1-4	chr3:146639750-146639961	XLOC_002856
6	lnc-ZIC1-4	chr3:146639710-146639961	XLOC_002856
7	lnc-ZIC4-3	chr3:146644242-146644437	ENSG00000243620.1

Variant related genes	Relation type
ENSG00000251800	TF binding region
ENSG00000242671	TF binding region
PHF19	miRNA target sites

Extended variants
information (count: 1329 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:1329 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1357130	chr3:146628382-146628383	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs571508633	chr3:146628425-146628426	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs1357129	chr3:146628469-146628470	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs550923134	chr3:146628512-146628513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs140633790	chr3:146628553-146628554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs79555233	chr3:146628556-146628557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs553343545	chr3:146628607-146628608	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs563936412	chr3:146628608-146628609	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs73865887	chr3:146628642-146628643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs558709324	chr3:146628655-146628656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs188021472	chr3:146628659-146628660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs544421288	chr3:146628663-146628664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs144375880	chr3:146628664-146628665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs575086495	chr3:146628688-146628689	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs565158519	chr3:146628691-146628692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs191585817	chr3:146628714-146628715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs559345653	chr3:146628743-146628744	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs528186831	chr3:146628756-146628757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs76715296	chr3:146628776-146628777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs569379349	chr3:146628777-146628778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs146997310	chr3:146628833-146628834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs565052042	chr3:146628863-146628864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs111473608	chr3:146628867-146628868	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs34159404	chr3:146628874-146628875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs374310508	chr3:146628877-146628878	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs7640356	chr3:146628893-146628894	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs567411060	chr3:146628902-146628903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs530007089	chr3:146628936-146628937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs147820473	chr3:146628940-146628941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs566890607	chr3:146628954-146628955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs372310247	chr3:146628972-146628973	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs116115988	chr3:146628988-146628989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs569025143	chr3:146628994-146628995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs538008798	chr3:146628996-146628997	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs534173504	chr3:146629012-146629013	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs79879702	chr3:146629033-146629034	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs11408285	chr3:146629046-146629047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs397828870	chr3:146629051-146629052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs575028541	chr3:146629076-146629077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs540963892	chr3:146629102-146629103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs552680007	chr3:146629106-146629107	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs140329432	chr3:146629124-146629125	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs560873382	chr3:146629141-146629142	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs545043977	chr3:146629142-146629143	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs73162890	chr3:146629165-146629166	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs371693396	chr3:146629196-146629197	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs542139942	chr3:146629202-146629203	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs530634968	chr3:146629208-146629209	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs544032454	chr3:146629239-146629240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs561184854	chr3:146629257-146629258	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
Chordoma	21215367	CNVD

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146623000-146629000	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:146627800-146629000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:146629000-146629800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:146629000-146631000	Enhancers	Colon Smooth Muscle	Colon
5	chr3:146629600-146631000	Enhancers	Fetal Lung	lung
6	chr3:146629800-146630000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:146629800-146631000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:146630000-146630800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:146630000-146630800	Active TSS	Osteobl	bone
10	chr3:146630200-146631200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:146630400-146630800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:146630400-146630800	Active TSS	Brain Anterior Caudate	brain
13	chr3:146630400-146631000	Enhancers	Brain Hippocampus Middle	brain
14	chr3:146630400-146631200	Enhancers	Dnd41	blood
15	chr3:146630800-146631200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:146631000-146631800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:146646200-146646600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:146646400-146647200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:146647800-146648200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:146650800-146651400	Enhancers	Dnd41	blood
21	chr3:146651400-146653000	Weak transcription	Dnd41	blood
22	chr3:146653000-146654200	Enhancers	Dnd41	blood
23	chr3:146666000-146666600	Enhancers	Dnd41	blood
24	chr3:146666400-146666600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:146670800-146671200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:146671000-146671200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:146671200-146671400	Flanking Active TSS	Osteobl	bone
28	chr3:146671200-146671600	Enhancers	NH-A	brain
29	chr3:146671200-146671800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:146671200-146671800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:146671200-146671800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:146671200-146671800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:146671200-146671800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:146671200-146671800	Enhancers	Fetal Brain Male	brain
35	chr3:146671200-146671800	Enhancers	NHDF-Ad	bronchial
36	chr3:146671200-146672000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:146671200-146672000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:146671200-146672000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:146671200-146672200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:146671400-146672000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:146671400-146672000	Enhancers	Fetal Lung	lung
42	chr3:146671400-146672200	Enhancers	Osteobl	bone
43	chr3:146671600-146671800	Flanking Active TSS	NH-A	brain
44	chr3:146671800-146672000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:146671800-146672000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:146671800-146672200	Enhancers	NH-A	brain
47	chr3:146671800-146674400	Weak transcription	Fetal Brain Male	brain
48	chr3:146671800-146684800	Weak transcription	NHDF-Ad	bronchial
49	chr3:146672000-146672200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:146672000-146675800	Weak transcription	Fetal Lung	lung

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