Variant report

Variant	nsv1012874
Chromosome Location	chr3:145631140-145662154
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	BATF	chr3:145661502-145661720	GM12878	blood:	n/a	chr3:145661650-145661660 chr3:145661649-145661660
2	CEBPB	chr3:145654814-145655116	IMR90	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
3	CEBPB	chr3:145654854-145655147	HepG2	liver:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
4	CEBPB	chr3:145643100-145643364	HepG2	liver:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
5	CEBPB	chr3:145654848-145655110	A549	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
6	CEBPB	chr3:145643113-145643361	A549	lung:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
7	CHD2	chr3:145657978-145657991	HepG2	liver:	n/a	n/a
8	CTCF	chr3:145633720-145633870	HMEC	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
9	CTCF	chr3:145633680-145633830	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
10	CTCF	chr3:145633680-145633830	Hela-S3	cervix:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
11	CTCF	chr3:145633780-145633930	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr3:145633680-145633830	NHEK	skin:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
13	CTCF	chr3:145633760-145633910	HFF	foreskin:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
14	CTCF	chr3:145633700-145633850	HRE	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
15	CTCF	chr3:145633597-145634009	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
16	CTCF	chr3:145633710-145633889	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
17	CTCF	chr3:145633720-145633870	Caco-2	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
18	CTCF	chr3:145635708-145635840	GM20000	blood:	n/a	n/a
19	CTCF	chr3:145633760-145633910	HBMEC	blood vessel:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
20	CTCF	chr3:145633689-145633849	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
21	CTCF	chr3:145633760-145633910	GM12865	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
22	CTCF	chr3:145633740-145633890	HEEpiC	esophagus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
23	CTCF	chr3:145633680-145633830	GM06990	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
24	CTCF	chr3:145633738-145633867	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
25	CTCF	chr3:145633580-145633730	NHDF-neo	bronchial:	n/a	n/a
26	CTCF	chr3:145633840-145633990	NHDF-neo	bronchial:	n/a	n/a
27	CTCF	chr3:145633740-145633890	HCT-116	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
28	CTCF	chr3:145633680-145633930	GM12872	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
29	CTCF	chr3:145633760-145633910	HEEpiC	esophagus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
30	CTCF	chr3:145633640-145633790	GM12872	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
31	CTCF	chr3:145655045-145655063	Kidney_OC	kidney:	n/a	n/a
32	CTCF	chr3:145633620-145633770	BE2_C	brain:	n/a	n/a
33	CTCF	chr3:145633740-145633890	HMF	breast:	n/a	chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784 chr3:145633771-145633784
34	CTCF	chr3:145633660-145633810	GM06990	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
35	CTCF	chr3:145633600-145633750	HBMEC	blood vessel:	n/a	n/a
36	CTCF	chr3:145633660-145633810	Caco-2	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
37	CTCF	chr3:145633740-145633890	GM12867	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
38	CTCF	chr3:145633640-145633790	HCT-116	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
39	CTCF	chr3:145633700-145633850	HCPEpiC	choroid plexus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
40	CTCF	chr3:145633720-145633870	A549	lung:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
41	CTCF	chr3:145633793-145633809	MCF-7	breast:	n/a	n/a
42	CTCF	chr3:145633740-145633890	BE2_C	brain:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
43	CTCF	chr3:145633660-145633810	HEK293	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
44	CTCF	chr3:145633620-145633770	HMEC	breast:	n/a	n/a
45	CTCF	chr3:145633660-145633810	HRPEpiC	eye:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
46	CTCF	chr3:145633700-145633850	WERI-Rb-1	eye:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
47	CTCF	chr3:145633764-145633787	Gliobla	brain:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
48	CTCF	chr3:145633660-145633810	RPTEC	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
49	CTCF	chr3:145633704-145633867	Hela-S3	cervix:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
50	CTCF	chr3:145633720-145633870	GM12871	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC107021.1-3	chr3:145657699-145657941	XLOC_002852
2	lnc-AC107021.1-3	chr3:145657755-145657941	XLOC_002852

Variant related genes	Relation type
ENSG00000244358	TF binding region
TWSG1	miRNA target sites

Extended variants
information (count: 427 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:427 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558820687	chr3:145643430-145643431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs577493403	chr3:145643433-145643434	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375736526	chr3:145643437-145643438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs112709079	chr3:145643501-145643502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs369879779	chr3:145643514-145643515	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs200185879	chr3:145643611-145643612	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs371249840	chr3:145643644-145643645	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs544773688	chr3:145643646-145643647	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs560951908	chr3:145643650-145643651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs556494051	chr3:145643676-145643677	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs114590419	chr3:145643686-145643687	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs185086128	chr3:145643829-145643830	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs560480986	chr3:145643847-145643848	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs6762748	chr3:145643853-145643854	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs546268249	chr3:145643871-145643872	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs144207252	chr3:145643875-145643876	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs1398780	chr3:145643928-145643929	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs146536363	chr3:145643931-145643932	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs190067947	chr3:145643940-145643941	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs528915497	chr3:145643960-145643961	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs369929948	chr3:145644007-145644008	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs181143292	chr3:145644013-145644014	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs960451	chr3:145644014-145644015	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs141002264	chr3:145644041-145644042	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs551122704	chr3:145644062-145644063	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs571088023	chr3:145644121-145644122	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs572857635	chr3:145651820-145651821	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs370199895	chr3:145651895-145651896	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs146249341	chr3:145651928-145651929	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs60285559	chr3:145651929-145651930	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs376058023	chr3:145651936-145651937	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs183473279	chr3:145651942-145651943	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs78373005	chr3:145651962-145651963	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs370496576	chr3:145651980-145651981	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs559165855	chr3:145651988-145651989	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs533061651	chr3:145652050-145652051	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs142697215	chr3:145652078-145652079	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs113614349	chr3:145652082-145652083	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs532004668	chr3:145652099-145652100	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs550488672	chr3:145652104-145652105	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs115393198	chr3:145652118-145652119	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs531992148	chr3:145652130-145652131	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs529488938	chr3:145652151-145652152	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs11709175	chr3:145652158-145652159	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs566007529	chr3:145652175-145652176	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs370620049	chr3:145652209-145652210	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs200668568	chr3:145652239-145652240	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs57797792	chr3:145652240-145652241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs201395470	chr3:145652241-145652242	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs56039931	chr3:145652242-145652243	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
Bipolar disorder	19114987	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145643400-145644200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:145643800-145644200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:145643800-145644200	Active TSS	Aorta	Aorta
4	chr3:145651800-145653200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:145652600-145653000	Enhancers	HepG2	liver
6	chr3:145653200-145654400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:145654200-145654400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:145654200-145654800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:145654400-145654800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:145654400-145654800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:145654400-145654800	Enhancers	NHDF-Ad	bronchial
12	chr3:145654400-145655200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:145654400-145655400	Enhancers	Osteobl	bone
14	chr3:145654800-145655200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:145655200-145656600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:145655200-145659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:145655400-145659600	Weak transcription	Osteobl	bone
18	chr3:145655800-145657000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr3:145657000-145657200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:145657200-145658400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:145657600-145658000	Enhancers	Esophagus	oesophagus
22	chr3:145658000-145659800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:145658400-145659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:145659200-145659600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:145659600-145660000	Enhancers	HMEC	breast
26	chr3:145659600-145660200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:145659600-145660400	Enhancers	Osteobl	bone
28	chr3:145659600-145662600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr3:145659800-145660200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:145659800-145660200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:145659800-145660400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:145660000-145661800	Weak transcription	HMEC	breast
33	chr3:145660200-145661400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:145660200-145661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:145661400-145662000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:145661400-145662000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:145661600-145662000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:145661800-145662000	Enhancers	HMEC	breast

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