Variant report

Variant	nsv1008719
Chromosome Location	chr3:60333-107035
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	ARID3A	chr3:86873-86900	HepG2	liver:	n/a	n/a
2	ARID3A	chr3:104725-105176	HepG2	liver:	n/a	n/a
3	ARID3A	chr3:84683-85432	HepG2	liver:	n/a	n/a
4	BHLHE40	chr3:84678-84869	GM12878	blood:	n/a	n/a
5	BRCA1	chr3:85112-85127	Hela-S3	cervix:	n/a	n/a
6	BRCA1	chr3:84696-84876	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr3:86185-86385	IMR90	lung:	n/a	n/a
8	CEBPB	chr3:86201-86402	HepG2	liver:	n/a	n/a
9	CEBPB	chr3:85095-85318	HepG2	liver:	n/a	chr3:85237-85250 chr3:85237-85248
10	CEBPB	chr3:99754-100055	HepG2	liver:	n/a	n/a
11	CEBPB	chr3:74958-75169	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr3:104930-105426	HepG2	liver:	n/a	chr3:105311-105324
13	CEBPB	chr3:85080-85291	HepG2	liver:	n/a	chr3:85237-85250 chr3:85237-85248 chr3:85092-85105
14	CEBPB	chr3:88330-88522	HepG2	liver:	n/a	chr3:88338-88349 chr3:88336-88349 chr3:88336-88347
15	CEBPB	chr3:85051-85419	HepG2	liver:	n/a	chr3:85237-85250 chr3:85237-85248 chr3:85092-85105
16	CEBPB	chr3:62164-62476	IMR90	lung:	n/a	n/a
17	CEBPB	chr3:99766-99979	H1-hESC	embryonic stem cell:	n/a	n/a
18	CEBPD	chr3:85139-85291	HepG2	liver:	n/a	chr3:85238-85249
19	CHD2	chr3:105065-105090	HepG2	liver:	n/a	n/a
20	CTCF	chr3:96060-96210	HMF	breast:	n/a	n/a
21	CTCF	chr3:97159-97300	MCF-7	breast:	n/a	n/a
22	CTCF	chr3:84700-84850	HMEC	breast:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
23	CTCF	chr3:84600-84750	Caco-2	colon:	n/a	n/a
24	CTCF	chr3:84720-84870	AG10803	skin:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
25	CTCF	chr3:96060-96210	GM12866	blood:	n/a	n/a
26	CTCF	chr3:84660-84810	RPTEC	kidney:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
27	CTCF	chr3:96040-96190	RPTEC	kidney:	n/a	n/a
28	CTCF	chr3:96100-96250	HMEC	breast:	n/a	n/a
29	CTCF	chr3:84720-84870	HBMEC	blood vessel:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
30	CTCF	chr3:96080-96230	MCF-7	breast:	n/a	n/a
31	CTCF	chr3:84655-84849	Hela-S3	cervix:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
32	CTCF	chr3:87304-87397	Lung_OC	lung:	n/a	n/a
33	CTCF	chr3:96040-96160	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:84660-84810	GM12865	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
35	CTCF	chr3:82180-82305	Medullo	brain:	n/a	n/a
36	CTCF	chr3:84680-84830	GM12871	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
37	CTCF	chr3:82220-82271	Spleen_OC	spleen:	n/a	n/a
38	CTCF	chr3:96040-96190	Caco-2	colon:	n/a	n/a
39	CTCF	chr3:84554-84973	GM12878	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
40	CTCF	chr3:82180-82330	RPTEC	kidney:	n/a	n/a
41	CTCF	chr3:84640-84790	WERI-Rb-1	eye:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
42	CTCF	chr3:84640-84790	HCFaa	heart:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
43	CTCF	chr3:96060-96210	WERI-Rb-1	eye:	n/a	n/a
44	CTCF	chr3:84642-84859	GM13977	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
45	CTCF	chr3:82200-82350	GM12874	blood:	n/a	n/a
46	CTCF	chr3:84640-84790	GM12872	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
47	CTCF	chr3:84660-84810	HA-sp	spinal cord:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
48	CTCF	chr3:84700-84850	HMF	breast:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
49	CTCF	chr3:84543-84909	HepG2	liver:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756
50	CTCF	chr3:84620-84770	GM12871	blood:	n/a	chr3:84742-84763 chr3:84740-84758 chr3:84743-84756

No.	Distal block	Cell Line	Cell type
1	chr3:84468..85168-chr3:395782..396503,2	MCF-7	breast:
2	chr3:84682..85249-chr3:418773..419384,2	MCF-7	breast:
3	chr3:84119..86199-chr3:87586..89599,2	K562	blood:
4	chr3:84540..85233-chr3:395143..396665,5	MCF-7	breast:
5	chr3:86365..87356-chr3:395941..396726,2	MCF-7	breast:
6	chr14:56081549..56082133-chr3:97763..98653,2	MCF-7	breast:
7	chr3:84119..86199-chr3:87586..89599,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHL1-1	chr3:95888-96275	XLOC_002563
2	lnc-IL5RA-7	chr3:95976-96029	XLOC_003014
3	lnc-IL5RA-7	chr3:95031-95375	XLOC_003014
4	lnc-CHL1-4	chr3:84310-84695	l_2300_chr3:84309-87048_testes
5	lnc-CHL1-2	chr3:65642-66175	XLOC_002562
6	lnc-CHL1-2	chr3:65431-65486	XLOC_002562
7	lnc-CHL1-4	chr3:86531-87048	l_2300_chr3:84309-87048_testes
8	lnc-CHL1-1	chr3:95888-96275	XLOC_002563

Variant related genes	Relation type
ENSG00000224918	TF binding region
ENSG00000223587	TF binding region

Extended variants
information (count: 1166 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:1166 , 50 per page) page: 1 2 3 4 5 6 7 ... 24

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183190499	chr3:60676-60677	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs376763689	chr3:60686-60687	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs188073721	chr3:60687-60688	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs192023809	chr3:60688-60689	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs143697718	chr3:60759-60760	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs531816158	chr3:60768-60769	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs13081384	chr3:61466-61467	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs13060385	chr3:61495-61496	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs541152469	chr3:61553-61554	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs559726984	chr3:61589-61590	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs13067440	chr3:61591-61592	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs145505212	chr3:61642-61643	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs184742076	chr3:61657-61658	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs73009205	chr3:61662-61663	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs139163391	chr3:61694-61695	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs368368123	chr3:61702-61703	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs13067752	chr3:61705-61706	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs374428640	chr3:61710-61711	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs189600515	chr3:61711-61712	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs144053997	chr3:61733-61734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs369665104	chr3:61748-61749	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs62240674	chr3:61762-61763	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs367643930	chr3:62113-62114	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs556974490	chr3:62120-62121	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs143391690	chr3:62168-62169	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs187331111	chr3:62179-62180	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs539425352	chr3:62214-62215	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs528665990	chr3:62219-62220	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs9799162	chr3:62226-62227	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs568016892	chr3:62232-62233	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs190928083	chr3:62236-62237	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs550559966	chr3:62254-62255	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs535291411	chr3:62266-62267	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs9681823	chr3:62309-62310	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs151333018	chr3:62324-62325	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs558082390	chr3:62328-62329	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs180933565	chr3:62337-62338	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs73009208	chr3:62425-62426	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs9682412	chr3:62437-62438	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs533112258	chr3:62464-62465	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs186343931	chr3:62481-62482	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs190261893	chr3:62508-62509	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs140541705	chr3:62521-62522	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs566612695	chr3:62537-62538	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs534081286	chr3:62546-62547	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs375808044	chr3:62603-62604	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs9799274	chr3:62614-62615	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs369716732	chr3:62680-62681	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs150446262	chr3:62689-62690	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs540443415	chr3:62696-62697	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
Ependymoma	20639864	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61600-61800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:62200-62800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:62400-62800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:74400-74800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:75200-75800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:84000-84400	Enhancers	Fetal Brain Male	brain
7	chr3:84200-84600	Enhancers	Fetal Brain Female	brain
8	chr3:84400-85400	Weak transcription	Fetal Brain Male	brain
9	chr3:84800-85200	Enhancers	Brain Germinal Matrix	brain
10	chr3:84800-85200	Active TSS	Fetal Brain Female	brain
11	chr3:84800-85400	Enhancers	Liver	Liver
12	chr3:85200-85800	Enhancers	Fetal Brain Female	brain
13	chr3:85200-85800	Enhancers	HepG2	liver
14	chr3:85400-86000	Flanking Active TSS	Liver	Liver
15	chr3:85400-86200	Enhancers	Fetal Brain Male	brain
16	chr3:85600-85800	Flanking Active TSS	Gastric	stomach
17	chr3:85600-86000	Bivalent Enhancer	Fetal Kidney	kidney
18	chr3:85800-86000	ZNF genes & repeats	Gastric	stomach
19	chr3:85800-86200	Flanking Active TSS	HepG2	liver
20	chr3:86000-86800	Enhancers	Liver	Liver
21	chr3:86200-86800	Enhancers	HepG2	liver
22	chr3:86800-87800	Weak transcription	HepG2	liver
23	chr3:88000-88200	Enhancers	HepG2	liver
24	chr3:88000-89000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:88000-90400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:88200-89800	Enhancers	Adipose Nuclei	Adipose
27	chr3:95000-95600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:95000-96600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:95600-104600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:97400-97600	Enhancers	Brain Hippocampus Middle	brain
31	chr3:97600-98000	Enhancers	Fetal Brain Male	brain
32	chr3:97800-98200	Active TSS	Fetal Brain Female	brain
33	chr3:98000-98600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:98000-104800	Weak transcription	Fetal Brain Male	brain
35	chr3:98200-98600	Enhancers	Fetal Brain Female	brain
36	chr3:103600-104400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:103800-104200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:104200-104400	Enhancers	Gastric	stomach
39	chr3:104400-104800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:104400-105000	Weak transcription	Gastric	stomach
41	chr3:104400-105400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:104400-105400	Enhancers	HepG2	liver
43	chr3:104400-105600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:104600-104800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:104600-104800	Enhancers	Adipose Nuclei	Adipose
46	chr3:104600-104800	Enhancers	Brain Substantia Nigra	brain
47	chr3:104600-105600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:104600-105600	Enhancers	Fetal Lung	lung
49	chr3:104800-105000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:104800-105000	Active TSS	Brain Germinal Matrix	brain

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