Variant report

Variant	nsv590156
Chromosome Location	chr3:43327924-43328588
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	chr3:43327734-43328196	HepG2	liver:	n/a	n/a
2	ARID3A	chr3:43328109-43328122	K562	blood:	n/a	n/a
3	ATF1	chr3:43327620-43328180	K562	blood:	n/a	n/a
4	ATF3	chr3:43327879-43328116	K562	blood:	n/a	chr3:43327994-43328009 chr3:43327998-43328008 chr3:43327995-43328008 chr3:43327995-43328005 chr3:43327998-43328005 chr3:43327995-43328006 chr3:43327996-43328007 chr3:43327998-43328006 chr3:43327996-43328007 chr3:43327995-43328008 chr3:43327995-43328005 chr3:43327994-43328007 chr3:43327998-43328008
5	BHLHE40	chr3:43327317-43327927	HepG2	liver:	n/a	n/a
6	BHLHE40	chr3:43327568-43328118	K562	blood:	n/a	chr3:43328051-43328067 chr3:43328052-43328068
7	BHLHE40	chr3:43327636-43328158	GM12878	blood:	n/a	chr3:43328124-43328140 chr3:43328135-43328151 chr3:43328051-43328067 chr3:43328127-43328143 chr3:43328126-43328142 chr3:43328052-43328068
8	BRCA1	chr3:43327625-43328173	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr3:43328162-43328165	HepG2	liver:	n/a	n/a
10	BRCA1	chr3:43327652-43328018	H1-hESC	embryonic stem cell:	n/a	n/a
11	CBX3	chr3:43327511-43327953	K562	blood:	n/a	n/a
12	CCNT2	chr3:43327739-43328725	K562	blood:	n/a	n/a
13	CEBPB	chr3:43327764-43328102	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr3:43328384-43328614	HepG2	liver:	n/a	n/a
15	CEBPB	chr3:43328472-43328608	K562	blood:	n/a	n/a
16	CEBPD	chr3:43327798-43328232	HepG2	liver:	n/a	n/a
17	CHD1	chr3:43328042-43328280	GM12878	blood:	n/a	n/a
18	CHD2	chr3:43327719-43328208	K562	blood:	n/a	chr3:43327825-43327835
19	CHD2	chr3:43327330-43328199	Hela-S3	cervix:	n/a	chr3:43327825-43327835
20	CHD2	chr3:43327658-43328189	GM12878	blood:	n/a	chr3:43327825-43327835
21	CHD2	chr3:43327720-43328117	HepG2	liver:	n/a	chr3:43327825-43327835
22	CREB1	chr3:43327461-43328353	K562	blood:	n/a	chr3:43327995-43328008
23	CREB1	chr3:43327639-43328294	H1-hESC	embryonic stem cell:	n/a	chr3:43327995-43328008
24	CREB1	chr3:43327614-43328307	HepG2	liver:	n/a	chr3:43327995-43328008
25	CREB1	chr3:43327820-43328186	A549	lung:	n/a	chr3:43327995-43328008
26	CREB1	chr3:43327641-43328303	K562	blood:	n/a	chr3:43327995-43328008
27	CREB1	chr3:43327816-43328162	ECC-1	luminal epithelium:	n/a	chr3:43327995-43328008
28	CREB1	chr3:43327634-43328339	GM12878	blood:	n/a	chr3:43327995-43328008
29	CREB1	chr3:43327583-43328333	HepG2	liver:	n/a	chr3:43327995-43328008
30	CREB1	chr3:43327804-43328145	ECC-1	luminal epithelium:	n/a	chr3:43327995-43328008
31	CREB1	chr3:43327526-43328311	GM12878	blood:	n/a	chr3:43327995-43328008
32	CREB1	chr3:43327620-43328342	A549	lung:	n/a	chr3:43327995-43328008
33	CREB1	chr3:43327555-43328312	H1-hESC	embryonic stem cell:	n/a	chr3:43327995-43328008
34	CTCF	chr3:43328160-43328310	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr3:43328219-43328315	GM19240	blood:	n/a	n/a
36	CTCF	chr3:43327563-43328484	K562	blood:	n/a	chr3:43327712-43327725
37	CTCF	chr3:43327874-43327931	Kidney_OC	kidney:	n/a	n/a
38	CTCF	chr3:43327646-43328159	Spleen_OC	spleen:	n/a	chr3:43327712-43327725
39	CTCF	chr3:43327558-43328348	GM12878	blood:	n/a	chr3:43327712-43327725
40	CTCF	chr3:43328160-43328450	GM12870	blood:	n/a	n/a
41	CTCF	chr3:43328380-43328530	GM12864	blood:	n/a	n/a
42	CTCF	chr3:43328251-43328280	K562	blood:	n/a	n/a
43	CTCF	chr3:43328025-43328175	Kidney_OC	kidney:	n/a	n/a
44	CTCF	chr3:43328220-43328370	GM12869	blood:	n/a	n/a
45	CTCF	chr3:43328059-43328349	K562	blood:	n/a	n/a
46	CTCF	chr3:43328461-43328483	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr3:43328180-43328330	GM12871	blood:	n/a	n/a
48	CTCF	chr3:43328440-43328590	GM12873	blood:	n/a	n/a
49	CTCF	chr3:43328211-43328331	GM12892	blood:	n/a	n/a
50	CTCF	chr3:43328240-43328390	GM12866	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:43327880-43327930	ECC-1	luminal epithelium:	n/a
2	chr3:43327880-43327930	ECC-1	luminal epithelium:	n/a
3	chr3:43328001-43328051	A549	lung:	n/a
4	chr3:43327880-43327930	K562	blood:	n/a
5	chr3:43328001-43328051	T-47D	breast:	n/a
6	chr3:43328001-43328051	HCPEpiC	choroid plexus:	n/a
7	chr3:43327880-43327930	HRE	kidney:	n/a
8	chr3:43327880-43327930	Jurkat	blood:	n/a
9	chr3:43328001-43328051	Caco-2	colon:	n/a
10	chr3:43328001-43328051	AG09319	gingival:	n/a
11	chr3:43327880-43327930	HCPEpiC	choroid plexus:	n/a
12	chr3:43327880-43327930	NHDF-neo	bronchial:	n/a
13	chr3:43328001-43328051	HMEC	breast:	n/a
14	chr3:43327880-43327930	NB4	blood:	n/a
15	chr3:43328001-43328051	SKMC	muscle:	n/a
16	chr3:43328001-43328051	SK-N-SH	brain:	n/a
17	chr3:43328001-43328051	U87	brain:	n/a
18	chr3:43328001-43328051	PFSK-1	brain:	n/a
19	chr3:43327880-43327930	AG09319	gingival:	n/a
20	chr3:43327880-43327930	HCF	heart:	n/a
21	chr3:43327880-43327930	HIPEpiC	eye:	n/a
22	chr3:43328001-43328051	HCF	heart:	n/a
23	chr3:43328001-43328051	GM19239	blood:	n/a
24	chr3:43328001-43328051	SAEC	small airway:	n/a
25	chr3:43327880-43327930	HCM	heart:	n/a
26	chr3:43327880-43327930	HRCEpiC	kidney:	n/a
27	chr3:43327880-43327930	H1-hESC	embryonic stem cell:	embryo
28	chr3:43328001-43328051	GM12891	blood:	n/a
29	chr3:43327880-43327930	SK-N-MC	brain:	n/a
30	chr3:43327880-43327930	AG10803	skin:	n/a
31	chr3:43328001-43328051	HCM	heart:	n/a
32	chr3:43327880-43327930	BE2_C	brain:	n/a
33	chr3:43328001-43328051	PANC-1	pancreas:	n/a
34	chr3:43328001-43328051	PrEC	prostate:	n/a
35	chr3:43327880-43327930	ProgFib	skin:	n/a
36	chr3:43328001-43328051	ovcar-3	ovarian:	n/a
37	chr3:43328001-43328051	HEEpiC	esophagus:	n/a
38	chr3:43328001-43328051	SK-N-MC	brain:	n/a
39	chr3:43327880-43327930	GM06990	blood:	n/a
40	chr3:43328001-43328051	AG04449	skin:	fetal
41	chr3:43327880-43327930	HEK293	kidney:	embryo
42	chr3:43328001-43328051	NHBE	bronchial:	n/a
43	chr3:43327880-43327930	AG09309	skin:	n/a
44	chr3:43328001-43328051	ECC-1	luminal epithelium:	n/a
45	chr3:43327880-43327930	HL-60	blood:	n/a
46	chr3:43327880-43327930	NT2-D1	testis:	n/a
47	chr3:43328001-43328051	BJ	skin:	n/a
48	chr3:43327880-43327930	NHBE	bronchial:	n/a
49	chr3:43328001-43328051	AG09309	skin:	n/a
50	chr3:43327880-43327930	HepG2	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43328259..43329793-chr3:43345734..43348023,2	K562	blood:
2	chr20:30192245..30193126-chr3:43327692..43328283,2	Hela-S3	cervix:
3	chr3:43328082..43330424-chr3:43353703..43355564,2	K562	blood:
4	chr3:43328576..43330209-chr3:43363736..43365348,2	K562	blood:
5	chr14:103988769..103989622-chr3:43327887..43328473,2	HCT-116	colon:
6	chr3:43327783..43328333-chr5:32173796..32174464,2	Hela-S3	cervix:
7	chr3:43328459..43331117-chr3:43356191..43358697,2	K562	blood:
8	chr2:208394589..208395128-chr3:43327696..43328487,2	Hela-S3	cervix:
9	chr3:43327640..43330625-chr3:43731199..43733951,3	K562	blood:
10	chr10:98346013..98346591-chr3:43327414..43328126,2	Hela-S3	cervix:
11	chr19:1249504..1250049-chr3:43327521..43328330,2	Hela-S3	cervix:
12	chr3:43305979..43308043-chr3:43325669..43327950,2	MCF-7	breast:

Variant related genes	Relation type
SNRK	TF binding region
SNRK	CpG island
ENSG00000241939	chromatin interactions
ENSG00000160746	chromatin interactions
ENSG00000077147	chromatin interactions
ENSG00000125968	chromatin interactions
ENSG00000166165	chromatin interactions
ENSG00000011198	chromatin interactions
ENSG00000113384	chromatin interactions
ENSG00000167470	chromatin interactions
ENSG00000118260	chromatin interactions

Extended variants
information (count: 15 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs552336473	chr3:43327943-43327944	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
2	rs569206949	chr3:43327944-43327945	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
3	rs538118772	chr3:43327994-43327995	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
4	rs554630421	chr3:43327995-43327996	Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
5	rs568026651	chr3:43328014-43328015	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
6	rs148185233	chr3:43328044-43328045	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
7	rs553541262	chr3:43328057-43328058	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
8	rs372569196	chr3:43328064-43328065	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
9	rs545317748	chr3:43328082-43328083	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
10	rs559092205	chr3:43328085-43328086	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
11	rs141210890	chr3:43328116-43328117	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
12	rs113426625	chr3:43328138-43328139	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
13	rs35392864	chr3:43328219-43328220	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
14	rs544469305	chr3:43328239-43328240	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
15	rs560955633	chr3:43328289-43328290	Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43327200-43328800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:43327200-43328800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:43327200-43328800	Active TSS	Brain Germinal Matrix	brain
4	chr3:43327200-43328800	Active TSS	Brain Hippocampus Middle	brain
5	chr3:43327200-43329000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:43327200-43329000	Active TSS	Fetal Brain Female	brain
7	chr3:43327200-43329200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:43327200-43329200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:43327400-43328000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr3:43327400-43328000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:43327400-43328600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:43327400-43328600	Active TSS	HepG2	liver
13	chr3:43327400-43328800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:43327400-43328800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43327400-43328800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:43327400-43328800	Active TSS	Muscle Satellite Cultured Cells	--
17	chr3:43327400-43328800	Active TSS	Fetal Lung	lung
18	chr3:43327400-43329000	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:43327400-43329000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:43327400-43329200	Active TSS	Lung	lung
21	chr3:43327400-43329400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr3:43327400-43329800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:43327400-43330200	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:43327400-43330600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:43327400-43332000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr3:43327600-43328000	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:43327600-43328600	Active TSS	Brain Substantia Nigra	brain
28	chr3:43327600-43328600	Weak transcription	Stomach Mucosa	stomach
29	chr3:43327600-43328600	Active TSS	K562	blood
30	chr3:43327600-43328800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:43327600-43328800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:43327600-43328800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:43327600-43328800	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:43327600-43328800	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr3:43327600-43328800	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr3:43327600-43328800	Active TSS	Brain Angular Gyrus	brain
37	chr3:43327600-43328800	Active TSS	Brain Cingulate Gyrus	brain
38	chr3:43327600-43328800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr3:43327600-43328800	Active TSS	Fetal Kidney	kidney
40	chr3:43327600-43328800	Active TSS	HSMMtube	muscle
41	chr3:43327600-43328800	Active TSS	NH-A	brain
42	chr3:43327600-43328800	Active TSS	Osteobl	bone
43	chr3:43327600-43329000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr3:43327600-43329000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:43327600-43329000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:43327600-43329000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:43327600-43329000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:43327600-43329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:43327600-43329000	Active TSS	Brain Anterior Caudate	brain
50	chr3:43327600-43329000	Active TSS	Brain Inferior Temporal Lobe	brain

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