Variant report

Variant	nsv999378
Chromosome Location	chr3:146578693-146682581
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	chr3:146614791-146614794	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:146666800-146667132	Hela-S3	cervix:	n/a	chr3:146666948-146666959
3	CEBPB	chr3:146592582-146592634	HepG2	liver:	n/a	chr3:146592596-146592607
4	CEBPB	chr3:146666824-146667006	HepG2	liver:	n/a	chr3:146666948-146666959
5	CEBPB	chr3:146619744-146619883	HepG2	liver:	n/a	chr3:146619796-146619807 chr3:146619794-146619811 chr3:146619795-146619808 chr3:146619795-146619808
6	CEBPB	chr3:146637184-146637457	HepG2	liver:	n/a	chr3:146637326-146637337
7	CEBPB	chr3:146666777-146667143	K562	blood:	n/a	chr3:146666948-146666959
8	CEBPB	chr3:146626801-146627083	HepG2	liver:	n/a	chr3:146626928-146626939 chr3:146626929-146626938 chr3:146626927-146626938
9	CEBPB	chr3:146666792-146667139	A549	lung:	n/a	chr3:146666948-146666959
10	CEBPB	chr3:146605165-146605465	HepG2	liver:	n/a	chr3:146605290-146605301
11	CEBPB	chr3:146666769-146667143	HepG2	liver:	n/a	chr3:146666948-146666959
12	CEBPB	chr3:146666819-146667156	MCF-7	breast:	n/a	chr3:146666948-146666959
13	CEBPB	chr3:146607077-146607216	H1-hESC	embryonic stem cell:	n/a	chr3:146607178-146607189
14	CEBPB	chr3:146605363-146605409	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr3:146666865-146667078	ECC-1	luminal epithelium:	n/a	chr3:146666948-146666959
16	CEBPB	chr3:146605148-146605460	IMR90	lung:	n/a	chr3:146605290-146605301
17	CEBPB	chr3:146666764-146667147	H1-hESC	embryonic stem cell:	n/a	chr3:146666948-146666959
18	CEBPB	chr3:146619668-146619908	IMR90	lung:	n/a	chr3:146619796-146619807 chr3:146619794-146619811 chr3:146619795-146619808 chr3:146619795-146619808
19	CEBPB	chr3:146607048-146607271	HepG2	liver:	n/a	chr3:146607178-146607189
20	CEBPB	chr3:146666799-146667103	ECC-1	luminal epithelium:	n/a	chr3:146666948-146666959
21	CEBPB	chr3:146626783-146627078	IMR90	lung:	n/a	chr3:146626928-146626939 chr3:146626929-146626938 chr3:146626927-146626938
22	CEBPB	chr3:146666856-146667157	MCF-7	breast:	n/a	chr3:146666948-146666959
23	CEBPB	chr3:146605252-146605373	K562	blood:	n/a	chr3:146605290-146605301
24	CEBPB	chr3:146614578-146614858	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr3:146666869-146667104	A549	lung:	n/a	chr3:146666948-146666959
26	CEBPB	chr3:146637236-146637407	Hela-S3	cervix:	n/a	chr3:146637326-146637337
27	CEBPB	chr3:146637291-146637349	K562	blood:	n/a	chr3:146637326-146637337
28	CEBPB	chr3:146666770-146667146	IMR90	lung:	n/a	chr3:146666948-146666959
29	CEBPB	chr3:146637289-146637433	H1-hESC	embryonic stem cell:	n/a	chr3:146637326-146637337
30	CEBPB	chr3:146607136-146607259	K562	blood:	n/a	chr3:146607178-146607189
31	CTCF	chr3:146646520-146646670	HBMEC	blood vessel:	n/a	n/a
32	CTCF	chr3:146655760-146655910	HepG2	liver:	n/a	n/a
33	CTCF	chr3:146646520-146646670	HL-60	blood:	n/a	n/a
34	CTCF	chr3:146646600-146646750	MCF-7	breast:	n/a	n/a
35	CTCF	chr3:146646640-146646790	MCF-7	breast:	n/a	n/a
36	CTCF	chr3:146601200-146601350	MCF-7	breast:	n/a	n/a
37	CTCF	chr3:146679757-146679825	Lung_OC	lung:	n/a	n/a
38	CTCF	chr3:146646620-146646770	WERI-Rb-1	eye:	n/a	n/a
39	CTCF	chr3:146646701-146646703	MCF-7	breast:	n/a	n/a
40	CTCF	chr3:146599315-146599409	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:146593693-146593738	Fibrobl	skin:	n/a	n/a
42	CTCF	chr3:146599312-146599381	Fibrobl	skin:	n/a	n/a
43	CTCF	chr3:146646563-146646697	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:146646593-146646700	MCF-7	breast:	n/a	n/a
45	CTCF	chr3:146646500-146646650	WERI-Rb-1	eye:	n/a	n/a
46	CTCF	chr3:146646580-146646730	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr3:146593480-146593630	GM12866	blood:	n/a	n/a
48	CTCF	chr3:146646582-146646709	MCF-7	breast:	n/a	n/a
49	E2F4	chr3:146653076-146653276	MCF10A-Er-Src	breast:	n/a	n/a
50	E2F4	chr3:146637847-146637936	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:146636773..146638616-chr3:146643446..146646080,2	K562	blood:
2	chr3:146636773..146638616-chr3:146643446..146646080,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZIC1-4	chr3:146639750-146639961	XLOC_002856
2	lnc-ZIC4-3	chr3:146644242-146644437	ENSG00000243620.1
3	lnc-ZIC1-4	chr3:146641389-146641628	XLOC_002856
4	lnc-ZIC1-4	chr3:146641389-146643005	XLOC_002856
5	lnc-ZIC4-3	chr3:146636855-146636972	ENSG00000243620.1
6	lnc-ZIC4-3	chr3:146627472-146627498	ENSG00000243620.1
7	lnc-ZIC1-4	chr3:146639710-146639961	XLOC_002856
8	lnc-ZIC1-4	chr3:146641088-146641111	XLOC_002856

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

Extended variants
information (count: 2062 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:2062 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529597451	chr3:146578838-146578839	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs141729551	chr3:146578852-146578853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs374668708	chr3:146578860-146578861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs115804447	chr3:146578877-146578878	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs575655569	chr3:146578901-146578902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs35263996	chr3:146578947-146578948	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs560033034	chr3:146578962-146578963	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs532346816	chr3:146578969-146578970	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs546025853	chr3:146578976-146578977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs147020906	chr3:146579025-146579026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs549321062	chr3:146579035-146579036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs562072603	chr3:146579041-146579042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs562736526	chr3:146579043-146579044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs116213795	chr3:146579065-146579066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs77039696	chr3:146579074-146579075	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548213890	chr3:146579109-146579110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs143686287	chr3:146579187-146579188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs543155356	chr3:146579192-146579193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs150141622	chr3:146579213-146579214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs1521586	chr3:146579248-146579249	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs527725808	chr3:146579255-146579256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs199753943	chr3:146579270-146579271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs200727176	chr3:146579272-146579273	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs565599838	chr3:146579376-146579377	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs547865925	chr3:146579378-146579379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs372593528	chr3:146579389-146579390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs532820961	chr3:146579405-146579406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs570613401	chr3:146579415-146579416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs184972468	chr3:146579442-146579443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs534626485	chr3:146579454-146579455	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs189353645	chr3:146579494-146579495	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs569986915	chr3:146579581-146579582	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs536124475	chr3:146579653-146579654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs193156645	chr3:146579655-146579656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs370018324	chr3:146579675-146579676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs574367073	chr3:146579684-146579685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs112754939	chr3:146579692-146579693	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs143127415	chr3:146579722-146579723	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs554339069	chr3:146579728-146579729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs34709512	chr3:146579731-146579732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs190195871	chr3:146579732-146579733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs181443991	chr3:146579775-146579776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs79281595	chr3:146579776-146579777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs373511498	chr3:146579784-146579785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs576336361	chr3:146579831-146579832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs574477611	chr3:146579857-146579858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs561880251	chr3:146579862-146579863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs17438440	chr3:146579888-146579889	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs567232029	chr3:146579904-146579905	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs6785051	chr3:146579970-146579971	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:55)

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
Non-syndromic sensorineural hearing loss	22037309	CNVD
Chordoma	21215367	CNVD

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146572600-146580400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:146580400-146580600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:146580600-146581000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:146580600-146583600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:146581000-146581200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:146581200-146582400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:146582200-146583400	Enhancers	Fetal Heart	heart
8	chr3:146582200-146583600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:146582400-146583200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:146582600-146583400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:146583000-146583400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:146583200-146583600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:146594200-146594600	Active TSS	Gastric	stomach
14	chr3:146599200-146599400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:146599400-146599800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:146599400-146599800	Enhancers	NHDF-Ad	bronchial
17	chr3:146599800-146600200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:146599800-146601800	Weak transcription	NHDF-Ad	bronchial
19	chr3:146600200-146600400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:146600200-146601800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr3:146600200-146602800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:146600400-146602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:146601200-146601800	Enhancers	Dnd41	blood
24	chr3:146601800-146602000	Enhancers	Brain Substantia Nigra	brain
25	chr3:146601800-146602400	Enhancers	NHDF-Ad	bronchial
26	chr3:146601800-146606200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:146602400-146603200	Weak transcription	NHDF-Ad	bronchial
28	chr3:146602400-146603600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:146602800-146605600	Weak transcription	Fetal Lung	lung
30	chr3:146603200-146603400	Enhancers	NHDF-Ad	bronchial
31	chr3:146603600-146605800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:146605600-146606200	Enhancers	Fetal Lung	lung
33	chr3:146605800-146606400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:146606200-146606600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr3:146606400-146607000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:146607000-146608400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:146608400-146611800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:146611600-146613800	Enhancers	NHDF-Ad	bronchial
39	chr3:146611600-146614600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:146611800-146612200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:146611800-146612400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:146611800-146613600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:146611800-146613600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr3:146611800-146614000	Enhancers	Osteobl	bone
45	chr3:146612000-146613400	Enhancers	HSMM	muscle
46	chr3:146612000-146613800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:146612200-146614800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:146612400-146613400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:146613000-146613800	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:146613200-146613400	Enhancers	NH-A	brain

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