Variant report

Variant	nsv979827
Chromosome Location	chr3:45924432-45925432
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	FOXM1	chr3:45925059-45925841	GM12878	blood:	n/a	n/a
2	MTA3	chr3:45924851-45926904	GM12878	blood:	n/a	n/a
3	NFATC1	chr3:45924804-45926829	GM12878	blood:	n/a	n/a
4	NFIC	chr3:45925190-45927089	GM12878	blood:	n/a	n/a
5	PML	chr3:45924828-45927210	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:45925150-45925653	GM12878	blood:	n/a	n/a
7	RUNX3	chr3:45925219-45925766	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45922108..45924975-chr3:45933515..45935925,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FYCO1-3	chr3:45925132-45925605	NONHSAT089420

Variant related genes	Relation type
CCR9	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535747958	chr3:45924434-45924435	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs368882773	chr3:45924435-45924436	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs183022170	chr3:45924500-45924501	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs539524120	chr3:45924512-45924513	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs557863678	chr3:45924694-45924695	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs187541113	chr3:45924701-45924702	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs548902838	chr3:45924713-45924714	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs540276316	chr3:45924778-45924779	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs6441929	chr3:45924791-45924792	Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs574216792	chr3:45924816-45924817	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs544912195	chr3:45924819-45924820	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs562919713	chr3:45924823-45924824	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs533603876	chr3:45924833-45924834	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs141942877	chr3:45924851-45924852	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs576701738	chr3:45924879-45924880	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs12631321	chr3:45924897-45924898	Weak transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs150667470	chr3:45924901-45924902	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs546235960	chr3:45924910-45924911	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs6441930	chr3:45924953-45924954	Weak transcription Genic enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs535357656	chr3:45924964-45924965	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs192546544	chr3:45924994-45924995	Weak transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs138421181	chr3:45925170-45925171	Bivalent Enhancer Weak transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs539286981	chr3:45925173-45925174	Bivalent Enhancer Weak transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs142760055	chr3:45925178-45925179	Bivalent Enhancer Weak transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs555662782	chr3:45925270-45925271	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs534316485	chr3:45925290-45925291	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs555447822	chr3:45925322-45925323	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs574009126	chr3:45925345-45925346	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs115004584	chr3:45925363-45925364	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs114039636	chr3:45925382-45925383	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:103)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	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
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45916600-45925200	Genic enhancers	Dnd41	blood
2	chr3:45918400-45926000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:45923200-45928000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:45923400-45930000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:45923400-45932000	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:45923400-45948200	Weak transcription	Right Atrium	heart
7	chr3:45923600-45930200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:45924000-45925200	Weak transcription	Thymus	Thymus
9	chr3:45924000-45925200	Weak transcription	K562	blood
10	chr3:45924000-45925400	Weak transcription	GM12878-XiMat	blood
11	chr3:45924200-45925000	Weak transcription	Fetal Thymus	thymus
12	chr3:45924200-45927400	Weak transcription	Primary T cells from cord blood	blood
13	chr3:45925000-45925400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:45925000-45927400	Genic enhancers	Fetal Thymus	thymus
15	chr3:45925200-45925400	Enhancers	K562	blood
16	chr3:45925200-45925600	Transcr. at gene 5' and 3'	Dnd41	blood
17	chr3:45925200-45926000	Enhancers	Thymus	Thymus
18	chr3:45925200-45949600	Weak transcription	Pancreas	Pancrea
19	chr3:45925400-45925800	Weak transcription	K562	blood
20	chr3:45925400-45926400	Enhancers	GM12878-XiMat	blood

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