Variant report

Variant	nsv877628
Chromosome Location	chr3:146964828-147058367
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:324)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:324 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr3:147016198-147016843	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:147016337-147016774	A549	lung:	n/a	n/a
3	CEBPB	chr3:147016381-147016644	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr3:147016462-147016664	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:147016290-147016779	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr3:147015660-147015810	MCF-7	breast:	n/a	n/a
7	CTCF	chr3:147034957-147035049	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr3:147043660-147043810	MCF-7	breast:	n/a	n/a
9	CTCF	chr3:147035003-147035052	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:147015600-147015750	A549	lung:	n/a	n/a
11	CTCF	chr3:147029020-147029170	HMF	breast:	n/a	n/a
12	CTCF	chr3:147015560-147015710	HAc	cerebellar:	n/a	n/a
13	CTCF	chr3:147015620-147015770	HPF	lung:	n/a	n/a
14	CTCF	chr3:147034999-147035179	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:147035005-147035074	MCF-7	breast:	n/a	n/a
16	CTCF	chr3:147034981-147035127	MCF-7	breast:	n/a	n/a
17	CTCF	chr3:146987820-146987970	GM12864	blood:	n/a	n/a
18	CTCF	chr3:147015660-147015810	AG04450	lung:	n/a	n/a
19	CTCF	chr3:147029071-147029122	LNCaP	prostate:	n/a	n/a
20	CTCF	chr3:147043680-147043830	MCF-7	breast:	n/a	n/a
21	CTCF	chr3:147043736-147043813	LNCaP	prostate:	n/a	n/a
22	CTCF	chr3:146987820-146987970	GM12873	blood:	n/a	n/a
23	CTCF	chr3:147015580-147015730	HAc	cerebellar:	n/a	n/a
24	CTCF	chr3:147034920-147035070	A549	lung:	n/a	n/a
25	CTCF	chr3:146987820-146987970	MCF-7	breast:	n/a	n/a
26	CTCF	chr3:146987800-146987950	GM12872	blood:	n/a	n/a
27	CTCF	chr3:147028945-147029228	IMR90	lung:	n/a	n/a
28	CTCF	chr3:147034940-147035090	HBMEC	blood vessel:	n/a	n/a
29	CTCF	chr3:147015666-147015723	GM10266	blood:	n/a	n/a
30	CTCF	chr3:147015840-147015990	AG10803	skin:	n/a	n/a
31	CTCF	chr3:147034752-147034825	GM10248	blood:	n/a	n/a
32	CTCF	chr3:146988579-146988601	Kidney_OC	kidney:	n/a	n/a
33	CTCF	chr3:147043660-147043810	A549	lung:	n/a	n/a
34	CTCF	chr3:146987920-146988070	GM12869	blood:	n/a	n/a
35	CTCF	chr3:147037833-147037890	GM13976	blood:	n/a	n/a
36	CTCF	chr3:147043719-147043944	GM12878	blood:	n/a	n/a
37	CTCF	chr3:146987780-146987930	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr3:147045723-147045746	Lung_OC	lung:	n/a	n/a
39	CTCF	chr3:147034900-147035050	HCT-116	colon:	n/a	n/a
40	CTCF	chr3:147034987-147035074	MCF-7	breast:	n/a	n/a
41	CTCF	chr3:146987880-146988030	MCF-7	breast:	n/a	n/a
42	CTCF	chr3:146994304-146994311	GM13976	blood:	n/a	n/a
43	CTCF	chr3:147027434-147027471	Fibrobl	skin:	n/a	n/a
44	CTCF	chr3:146987778-146987981	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr3:147034940-147035090	GM12866	blood:	n/a	n/a
46	CTCF	chr3:147015860-147016010	MCF-7	breast:	n/a	n/a
47	CTCF	chr3:147015640-147015790	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr3:147053869-147053895	GM13976	blood:	n/a	n/a
49	CTCF	chr3:147004167-147004251	GM13976	blood:	n/a	n/a
50	CTCF	chr3:147043719-147043853	LNCaP	prostate:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:146964907-146964957	RPTEC	kidney:	n/a
2	chr3:147016780-147016830	ProgFib	skin:	n/a
3	chr3:146964907-146964957	HNPCEpiC	eye:	n/a
4	chr3:146964907-146964957	HEK293	kidney:	embryo
5	chr3:146964907-146964957	Jurkat	blood:	n/a
6	chr3:146964907-146964957	IMR90	lung:	fetal
7	chr3:146964907-146964957	HUVEC	blood vessel:	n/a
8	chr3:147016780-147016830	HPAEpiC	pulmonary alveolar:	n/a
9	chr3:146964907-146964957	ovcar-3	ovarian:	n/a
10	chr3:146964907-146964957	ProgFib	skin:	n/a
11	chr3:147016780-147016830	PrEC	prostate:	n/a
12	chr3:147016780-147016830	BJ	skin:	n/a
13	chr3:147016780-147016830	K562	blood:	n/a
14	chr3:146964907-146964957	NHDF-neo	bronchial:	n/a
15	chr3:147016780-147016830	Hela-S3	cervix:	n/a
16	chr3:147016780-147016830	NHDF-neo	bronchial:	n/a
17	chr3:146964907-146964957	NB4	blood:	n/a
18	chr3:147016780-147016830	AG09319	gingival:	n/a
19	chr3:146964907-146964957	HPAEpiC	pulmonary alveolar:	n/a
20	chr3:146964907-146964957	GM06990	blood:	n/a
21	chr3:147016780-147016830	SKMC	muscle:	n/a
22	chr3:147016780-147016830	HRE	kidney:	n/a
23	chr3:146964907-146964957	SKMC	muscle:	n/a
24	chr3:146964907-146964957	AG04450	lung:	fetal
25	chr3:146964907-146964957	HCM	heart:	n/a
26	chr3:147016780-147016830	SAEC	small airway:	n/a
27	chr3:147016780-147016830	SK-N-SH_RA	brain:	n/a
28	chr3:146964907-146964957	NHBE	bronchial:	n/a
29	chr3:147016780-147016830	IMR90	lung:	fetal
30	chr3:147016780-147016830	AoSMC	blood vessel:	n/a
31	chr3:146964907-146964957	AG10803	skin:	n/a
32	chr3:147016780-147016830	GM12891	blood:	n/a
33	chr3:147016780-147016830	HepG2	liver:	n/a
34	chr3:146964907-146964957	SK-N-MC	brain:	n/a
35	chr3:147016780-147016830	NT2-D1	testis:	n/a
36	chr3:147016780-147016830	SK-N-MC	brain:	n/a
37	chr3:146964907-146964957	GM12892	blood:	n/a
38	chr3:146964907-146964957	HepG2	liver:	n/a
39	chr3:147016780-147016830	GM12892	blood:	n/a
40	chr3:146964907-146964957	CMK	blood:	n/a
41	chr3:147016780-147016830	RPTEC	kidney:	n/a
42	chr3:146964907-146964957	HCPEpiC	choroid plexus:	n/a
43	chr3:146964907-146964957	SK-N-SH_RA	brain:	n/a
44	chr3:147016780-147016830	H1-hESC	embryonic stem cell:	embryo
45	chr3:147016780-147016830	GM06990	blood:	n/a
46	chr3:147016780-147016830	LNCaP	prostate:	n/a
47	chr3:147016780-147016830	NHBE	bronchial:	n/a
48	chr3:146964907-146964957	HCF	heart:	n/a
49	chr3:146964907-146964957	AoSMC	blood vessel:	n/a
50	chr3:147016780-147016830	T-47D	breast:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:146961674..146963696-chr3:146964903..146966637,2	K562	blood:
2	chr3:147024132..147026356-chr3:147029104..147031588,2	K562	blood:
3	chr3:147009121..147010965-chr3:147109797..147111774,2	MCF-7	breast:
4	chr3:147013273..147015507-chr3:147016010..147018534,2	K562	blood:
5	chr3:147024132..147026356-chr3:147029104..147031588,2	K562	blood:
6	chr3:147013273..147015507-chr3:147016010..147018534,2	K562	blood:
7	chr3:147042796..147043515-chrX:22603585..22604371,2	MCF-7	breast:
8	chr11:67350476..67351889-chr3:147038109..147038629,4	HCT-116	colon:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZIC1-7	chr3:146994555-146994774	NONHSAT092574
2	lnc-ZIC1-7	chr3:146994801-146995039	NONHSAT092574

No data

Variant related genes	Relation type
RPL21P71	TF binding region
RPL21P71	CpG island
ENSG00000174963	chromatin interactions
ENSG00000084207	chromatin interactions
ENSG00000152977	chromatin interactions

Extended variants
information (count: 1111 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:1111 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12496794	chr3:146964828-146964829	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs559221010	chr3:146964860-146964861	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs79475141	chr3:146964863-146964864	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs187930530	chr3:146964907-146964908	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs72450722	chr3:146964917-146964918	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs35433571	chr3:146964920-146964921	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs567849930	chr3:146985004-146985005	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs560582418	chr3:146985006-146985007	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs570039692	chr3:146985041-146985042	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs74649747	chr3:146985063-146985064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs549531621	chr3:146985077-146985078	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs566030706	chr3:146985089-146985090	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs527819498	chr3:146985281-146985282	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs78948440	chr3:146985307-146985308	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs7625116	chr3:146985355-146985356	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs571917321	chr3:146985378-146985379	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs115957270	chr3:146990632-146990633	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs547435557	chr3:146990639-146990640	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs9854570	chr3:146990672-146990673	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs539913312	chr3:146990685-146990686	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs2318778	chr3:146990692-146990693	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs367612041	chr3:146990696-146990697	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs9816787	chr3:146990730-146990731	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs375591688	chr3:146990745-146990746	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs141275576	chr3:146990746-146990747	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs112716548	chr3:146994556-146994557	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs542663248	chr3:146994558-146994559	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs116910632	chr3:146994560-146994561	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs566402594	chr3:146994567-146994568	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs573021717	chr3:146994602-146994603	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs545132396	chr3:146994627-146994628	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs373682697	chr3:146994651-146994652	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs531057704	chr3:146994662-146994663	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs544746542	chr3:146994689-146994690	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs151270651	chr3:146994715-146994716	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs77063902	chr3:146994732-146994733	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs80115753	chr3:146994755-146994756	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs559325379	chr3:146994766-146994767	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs551540477	chr3:146994810-146994811	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs149982831	chr3:146994862-146994863	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs537244605	chr3:146994863-146994864	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs145196553	chr3:146994868-146994869	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs544794868	chr3:146994955-146994956	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs567464808	chr3:146994973-146994974	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs536518300	chr3:146995024-146995025	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs552976727	chr3:146995039-146995040	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs545822912	chr3:147005439-147005440	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs181454569	chr3:147005440-147005441	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs377149435	chr3:147005444-147005445	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs542205738	chr3:147005473-147005474	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

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

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146964200-146965000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:146964400-146965000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:146964600-146965000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:146985000-146985400	Enhancers	Osteobl	bone
5	chr3:147005400-147005800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:147005800-147009600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:147009600-147010000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:147009600-147010200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:147009800-147010200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:147010000-147012400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:147010200-147015800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:147012400-147012600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:147014400-147015600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:147015200-147016000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:147015600-147015800	Enhancers	NH-A	brain
16	chr3:147015600-147016000	Enhancers	Osteobl	bone
17	chr3:147015600-147016200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:147015600-147016600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:147015600-147016800	Enhancers	Brain Germinal Matrix	brain
20	chr3:147015600-147017000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:147015600-147017200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:147015600-147017200	Enhancers	NHLF	lung
23	chr3:147015600-147017600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr3:147015600-147017800	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:147015600-147018000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:147015800-147016000	Enhancers	NHDF-Ad	bronchial
27	chr3:147015800-147016200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:147015800-147016200	Enhancers	Fetal Lung	lung
29	chr3:147015800-147016200	Enhancers	Hela-S3	cervix
30	chr3:147015800-147016400	Flanking Active TSS	NH-A	brain
31	chr3:147015800-147016800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:147015800-147016800	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr3:147015800-147016800	Enhancers	Fetal Stomach	stomach
34	chr3:147015800-147017000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:147015800-147017600	Enhancers	Colon Smooth Muscle	Colon
36	chr3:147015800-147017800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:147015800-147017800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:147015800-147018400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:147016000-147016400	Flanking Active TSS	NHDF-Ad	bronchial
40	chr3:147016000-147016400	Flanking Active TSS	Osteobl	bone
41	chr3:147016000-147016600	Enhancers	H9 Cell Line	embryonic stem cell
42	chr3:147016000-147016600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:147016000-147016800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:147016000-147016800	Enhancers	HUVEC	blood vessel
45	chr3:147016000-147017000	Enhancers	Fetal Brain Male	brain
46	chr3:147016200-147016400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:147016200-147016400	Enhancers	Stomach Smooth Muscle	stomach
48	chr3:147016200-147016600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:147016200-147016800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:147016200-147016800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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