Variant report

Variant	nsv1002549
Chromosome Location	chr3:145226633-145255828
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	chr3:145236420-145236719	HepG2	liver:	n/a	n/a
2	CEBPB	chr3:145236438-145236739	HepG2	liver:	n/a	n/a
3	CEBPB	chr3:145236506-145236645	HepG2	liver:	n/a	n/a
4	CEBPB	chr3:145240424-145240661	HepG2	liver:	n/a	chr3:145240578-145240589
5	CEBPB	chr3:145237238-145237758	HepG2	liver:	n/a	chr3:145237493-145237504 chr3:145237666-145237677
6	CEBPB	chr3:145237587-145237775	H1-hESC	embryonic stem cell:	n/a	chr3:145237666-145237677
7	CTCF	chr3:145253080-145253230	HCPEpiC	choroid plexus:	n/a	n/a
8	E2F4	chr3:145248621-145248900	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F4	chr3:145249268-145249468	MCF10A-Er-Src	breast:	n/a	n/a
10	E2F4	chr3:145253129-145253270	MCF10A-Er-Src	breast:	n/a	n/a
11	ELF1	chr3:145236494-145236755	HepG2	liver:	n/a	n/a
12	ELF1	chr3:145236461-145236796	HepG2	liver:	n/a	n/a
13	EP300	chr3:145236443-145236791	HepG2	liver:	n/a	n/a
14	EP300	chr3:145236518-145236661	HepG2	liver:	n/a	n/a
15	EP300	chr3:145228255-145228361	K562	blood:	n/a	n/a
16	EP300	chr3:145236433-145236796	HepG2	liver:	n/a	n/a
17	FOS	chr3:145246251-145246333	MCF10A-Er-Src	breast:	n/a	n/a
18	FOXA1	chr3:145236422-145236773	HepG2	liver:	n/a	n/a
19	FOXA1	chr3:145235252-145235576	HepG2	liver:	n/a	n/a
20	FOXA1	chr3:145236282-145236822	HepG2	liver:	n/a	n/a
21	FOXA1	chr3:145235231-145235605	HepG2	liver:	n/a	n/a
22	FOXA1	chr3:145236346-145236824	HepG2	liver:	n/a	n/a
23	FOXA1	chr3:145235138-145235628	HepG2	liver:	n/a	n/a
24	FOXA1	chr3:145235252-145235635	HepG2	liver:	n/a	n/a
25	FOXA1	chr3:145236391-145236793	HepG2	liver:	n/a	n/a
26	FOXA2	chr3:145235219-145235545	HepG2	liver:	n/a	n/a
27	FOXA2	chr3:145236463-145236750	HepG2	liver:	n/a	n/a
28	FOXA2	chr3:145236172-145237160	HepG2	liver:	n/a	chr3:145237067-145237079
29	FOXP2	chr3:145237283-145237849	SK-N-MC	brain:	n/a	n/a
30	FOXP2	chr3:145237497-145237798	SK-N-MC	brain:	n/a	n/a
31	HDAC2	chr3:145236425-145236717	HepG2	liver:	n/a	chr3:145236492-145236500
32	HNF4A	chr3:145236425-145236818	HepG2	liver:	n/a	chr3:145236641-145236656 chr3:145236642-145236650 chr3:145236642-145236654 chr3:145236641-145236656 chr3:145236487-145236499 chr3:145236642-145236654 chr3:145236487-145236500 chr3:145236640-145236655 chr3:145236487-145236499 chr3:145236641-145236655 chr3:145236571-145236583 chr3:145236487-145236500
33	HNF4A	chr3:145236466-145236855	HepG2	liver:	n/a	chr3:145236641-145236656 chr3:145236642-145236650 chr3:145236642-145236654 chr3:145236641-145236656 chr3:145236487-145236499 chr3:145236642-145236654 chr3:145236487-145236500 chr3:145236640-145236655 chr3:145236487-145236499 chr3:145236641-145236655 chr3:145236571-145236583 chr3:145236487-145236500
34	HNF4A	chr3:145236451-145236819	HepG2	liver:	n/a	chr3:145236641-145236656 chr3:145236642-145236650 chr3:145236642-145236654 chr3:145236641-145236656 chr3:145236487-145236499 chr3:145236642-145236654 chr3:145236487-145236500 chr3:145236640-145236655 chr3:145236487-145236499 chr3:145236641-145236655 chr3:145236571-145236583 chr3:145236487-145236500
35	HNF4G	chr3:145236432-145236820	HepG2	liver:	n/a	chr3:145236641-145236656 chr3:145236642-145236650 chr3:145236642-145236654 chr3:145236641-145236656 chr3:145236487-145236499 chr3:145236642-145236654 chr3:145236487-145236500 chr3:145236487-145236499 chr3:145236641-145236655 chr3:145236571-145236583 chr3:145236487-145236500
36	HNF4G	chr3:145236400-145236805	HepG2	liver:	n/a	chr3:145236641-145236656 chr3:145236642-145236650 chr3:145236642-145236654 chr3:145236641-145236656 chr3:145236487-145236499 chr3:145236642-145236654 chr3:145236487-145236500 chr3:145236487-145236499 chr3:145236641-145236655 chr3:145236571-145236583 chr3:145236487-145236500
37	IRF3	chr3:145232096-145232139	GM12878	blood:	n/a	n/a
38	MAFK	chr3:145232724-145232801	HepG2	liver:	n/a	n/a
39	MAFK	chr3:145236395-145236778	HepG2	liver:	n/a	n/a
40	MAFK	chr3:145236547-145236782	HepG2	liver:	n/a	n/a
41	MAFK	chr3:145232737-145232813	HepG2	liver:	n/a	n/a
42	MAFK	chr3:145243981-145244016	HepG2	liver:	n/a	n/a
43	MAFK	chr3:145255615-145255744	HepG2	liver:	n/a	n/a
44	MBD4	chr3:145236471-145236841	HepG2	liver:	n/a	n/a
45	MYBL2	chr3:145236343-145236931	HepG2	liver:	n/a	n/a
46	MYBL2	chr3:145236362-145236861	HepG2	liver:	n/a	n/a
47	MYC	chr3:145231672-145231760	H1-hESC	embryonic stem cell:	n/a	n/a
48	NFIC	chr3:145236347-145236858	HepG2	liver:	n/a	n/a
49	NR2F2	chr3:145236256-145236834	HepG2	liver:	n/a	n/a
50	NR2F2	chr3:145236319-145236838	MCF-7	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC107021.1-8	chr3:145241325-145242202	NONHSAT092538

Variant related genes	Relation type
ENSG00000244024	TF binding region

Extended variants
information (count: 1124 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:1124 , 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	rs564071791	chr3:145226647-145226648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs554217958	chr3:145226655-145226656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs67334933	chr3:145226656-145226657	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs73011209	chr3:145226660-145226661	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs73872234	chr3:145226662-145226663	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs113160020	chr3:145226667-145226668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs527652036	chr3:145226687-145226688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs531698209	chr3:145226714-145226715	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs190281623	chr3:145226729-145226730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs58350199	chr3:145226742-145226743	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs59063793	chr3:145226745-145226746	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs547239288	chr3:145226762-145226763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs76258932	chr3:145226854-145226855	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs532802510	chr3:145226859-145226860	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs113919099	chr3:145226906-145226907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs569759395	chr3:145226925-145226926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs76020009	chr3:145226968-145226969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs34145534	chr3:145226984-145226985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs536713507	chr3:145227025-145227026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs550371852	chr3:145227043-145227044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs145052577	chr3:145227100-145227101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs536164276	chr3:145227174-145227175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs493455	chr3:145227185-145227186	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs11706843	chr3:145227217-145227218	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs11718337	chr3:145227218-145227219	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs11710470	chr3:145227230-145227231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs11706844	chr3:145227237-145227238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs11718314	chr3:145227248-145227249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs11710490	chr3:145227249-145227250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs558166126	chr3:145227251-145227252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs9869971	chr3:145227273-145227274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533407081	chr3:145227275-145227276	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs576493471	chr3:145227276-145227277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs11706872	chr3:145227301-145227302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs11706873	chr3:145227302-145227303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs552080990	chr3:145227324-145227325	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs543508618	chr3:145227395-145227396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs62271778	chr3:145227413-145227414	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs537618509	chr3:145227415-145227416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs555692732	chr3:145227420-145227421	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs573797160	chr3:145227438-145227439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs540825949	chr3:145227447-145227448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs184387260	chr3:145227459-145227460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs73872235	chr3:145227519-145227520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs568102656	chr3:145227544-145227545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs550978164	chr3:145227560-145227561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs114729779	chr3:145227596-145227597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs79713637	chr3:145227616-145227617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs150442897	chr3:145227622-145227623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs567344471	chr3:145227644-145227645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145224600-145237400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:145231600-145231800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:145231600-145232400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:145231800-145232400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:145232400-145232600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:145232600-145236200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:145235200-145237800	Enhancers	HepG2	liver
8	chr3:145236200-145236800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:145236200-145236800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:145236200-145237200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:145236200-145237800	Enhancers	Liver	Liver
12	chr3:145236400-145237000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:145236400-145237000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:145236400-145237200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:145236400-145237200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:145236400-145237800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:145236400-145237800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:145236400-145238000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:145236800-145237600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:145236800-145237800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:145237200-145237800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:145237200-145237800	Enhancers	Brain Germinal Matrix	brain
23	chr3:145237400-145237600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr3:145237800-145238200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:145237800-145238600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:145237800-145239400	Weak transcription	HepG2	liver
27	chr3:145237800-145240600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:145239400-145240000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:145239400-145240200	Enhancers	HepG2	liver
30	chr3:145240000-145240200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:145240000-145240400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:145240000-145241000	Enhancers	Right Ventricle	heart
33	chr3:145240000-145241200	Enhancers	Left Ventricle	heart
34	chr3:145240200-145240800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:145240800-145241000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:145240800-145241200	Enhancers	Lung	lung
37	chr3:145244400-145254600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:145249600-145252200	Enhancers	Fetal Heart	heart
39	chr3:145251800-145252400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr3:145254200-145255800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:145254800-145255200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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