Variant report

Variant	nsv10293
Chromosome Location	chr3:98936979-98950897
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	CEBPB	chr3:98945624-98945864	HepG2	liver:	n/a	chr3:98945722-98945733
2	CTCF	chr3:98937480-98937630	A549	lung:	n/a	n/a
3	CTCF	chr3:98937400-98937550	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr3:98937448-98937572	NHEK	skin:	n/a	n/a
5	CTCF	chr3:98937475-98937542	HepG2	liver:	n/a	n/a
6	CTCF	chr3:98943170-98943206	Spleen_OC	spleen:	n/a	n/a
7	CTCF	chr3:98937376-98937607	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:98937440-98937590	HCT-116	colon:	n/a	n/a
9	CTCF	chr3:98937500-98937650	HVMF	connective:	n/a	n/a
10	CTCF	chr3:98937409-98937688	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr3:98937460-98937610	RPTEC	kidney:	n/a	n/a
12	CTCF	chr3:98937520-98937670	HCT-116	colon:	n/a	n/a
13	CTCF	chr3:98937500-98937650	HMEC	breast:	n/a	n/a
14	E2F4	chr3:98937115-98937150	MCF10A-Er-Src	breast:	n/a	n/a
15	FAM48A	chr3:98939502-98939597	GM12878	blood:	n/a	n/a
16	MAFF	chr3:98945658-98945713	K562	blood:	n/a	n/a
17	MYC	chr3:98940915-98940924	H1-hESC	embryonic stem cell:	n/a	n/a
18	RAD21	chr3:98937266-98937737	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr3:98937312-98937696	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr3:98937329-98937669	H1-hESC	embryonic stem cell:	n/a	n/a
21	RAD21	chr3:98937321-98937733	H1-hESC	embryonic stem cell:	n/a	n/a
22	SETDB1	chr3:98937742-98938197	U2OS	brain:	n/a	n/a
23	STAT3	chr3:98939265-98939457	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ACTG1P13	TF binding region

Extended variants
information (count: 215 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:215 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139103564	chr3:98937021-98937022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs552463369	chr3:98937039-98937040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs190903050	chr3:98937050-98937051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs530229530	chr3:98937051-98937052	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530077731	chr3:98937057-98937058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs73859874	chr3:98937081-98937082	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs149895150	chr3:98937097-98937098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs371588336	chr3:98937155-98937156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs570054529	chr3:98937226-98937227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs538671874	chr3:98937252-98937253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs558886253	chr3:98937254-98937255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs569256444	chr3:98937263-98937264	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs538178513	chr3:98937276-98937277	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs114738808	chr3:98937343-98937344	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs182770797	chr3:98937350-98937351	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs540373264	chr3:98937352-98937353	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs550016286	chr3:98937398-98937399	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs11344312	chr3:98937399-98937400	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs571502366	chr3:98937432-98937433	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs144937844	chr3:98937439-98937440	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs560786191	chr3:98937456-98937457	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs140326195	chr3:98937464-98937465	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs75709535	chr3:98937527-98937528	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs188141626	chr3:98937556-98937557	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs531191984	chr3:98937567-98937568	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs544553022	chr3:98937568-98937569	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs371823428	chr3:98937592-98937593	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs530242232	chr3:98937608-98937609	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs554156652	chr3:98937617-98937618	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs566876760	chr3:98937636-98937637	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs532669300	chr3:98937658-98937659	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs552691104	chr3:98937752-98937753	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs569317235	chr3:98937766-98937767	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs538238067	chr3:98937768-98937769	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs144198669	chr3:98937773-98937774	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs554903828	chr3:98937776-98937777	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs34204175	chr3:98937791-98937792	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs112040185	chr3:98937799-98937800	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs568318965	chr3:98937803-98937804	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs375754968	chr3:98937809-98937810	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs572296055	chr3:98937816-98937817	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs533761010	chr3:98937950-98937951	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs553902628	chr3:98938003-98938004	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs576938560	chr3:98938005-98938006	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs190096544	chr3:98938023-98938024	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs555830144	chr3:98938030-98938031	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs575635893	chr3:98938035-98938036	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs182380072	chr3:98938044-98938045	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs561262621	chr3:98938057-98938058	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs535881395	chr3:98938083-98938084	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98925800-98939600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98945400-98945600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr3:98945400-98946600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:98945600-98945800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:98945600-98946200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:98945600-98946800	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:98945600-98946800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr3:98945800-98946000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr3:98945800-98946400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:98945800-98946600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:98945800-98946800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:98946000-98946200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:98946000-98946600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:98946000-98946800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:98946200-98946800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:98946800-98947800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:98947800-98948000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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