Variant report

Variant	nsv523473
Chromosome Location	chr3:54010039-54033865
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53749411..53751208-chr3:54008710..54010882,2	K562	blood:
2	chr3:54027788..54029869-chr3:54035000..54037440,2	K562	blood:
3	chr3:54026756..54029485-chr3:54031370..54034068,2	K562	blood:
4	chr3:54026756..54029485-chr3:54031370..54034068,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-884K10.5.1-2	chr3:54018250-54018322	l_2370_chr3:53996726-54040496_testes

Extended variants
information (count: 761 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:761 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9876934	chr3:54010039-54010040	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs148342379	chr3:54010050-54010051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs114199961	chr3:54010085-54010086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs142128234	chr3:54010088-54010089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs78198695	chr3:54010110-54010111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs527932277	chr3:54010119-54010120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs547751369	chr3:54010120-54010121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs561278772	chr3:54010130-54010131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs146401586	chr3:54010222-54010223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs549782373	chr3:54010237-54010238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs138478489	chr3:54010270-54010271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs538750199	chr3:54010280-54010281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs552689325	chr3:54010295-54010296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs373710478	chr3:54010300-54010301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs543480996	chr3:54010306-54010307	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs373422135	chr3:54010339-54010340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs73841254	chr3:54010388-54010389	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs571334423	chr3:54010402-54010403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs368128122	chr3:54010417-54010418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs534028503	chr3:54010495-54010496	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs112773846	chr3:54010512-54010513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs554074657	chr3:54010515-54010516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs142810102	chr3:54010532-54010533	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs56394075	chr3:54010548-54010549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs189891528	chr3:54010560-54010561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs367586121	chr3:54010619-54010620	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs536207838	chr3:54010653-54010654	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs79333730	chr3:54010671-54010672	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs76935397	chr3:54010672-54010673	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs148716506	chr3:54010696-54010697	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs556204324	chr3:54010770-54010771	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs576027300	chr3:54010782-54010783	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs562145674	chr3:54010830-54010831	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs544774019	chr3:54010877-54010878	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs565019647	chr3:54010895-54010896	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs537467576	chr3:54010934-54010935	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541238118	chr3:54010935-54010936	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs561217261	chr3:54010941-54010942	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs555454502	chr3:54010957-54010958	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs371166703	chr3:54011005-54011006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs7623521	chr3:54011061-54011062	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs55644014	chr3:54011088-54011089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs563340383	chr3:54011134-54011135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs368370768	chr3:54011143-54011144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs532569802	chr3:54011164-54011165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs372356537	chr3:54011174-54011175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs530790317	chr3:54011175-54011176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs566180845	chr3:54011178-54011179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs62253027	chr3:54011209-54011210	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs547617416	chr3:54011235-54011236	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
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	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
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	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
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54008200-54012600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:54010400-54010600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:54010600-54010800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
4	chr3:54010600-54011000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
5	chr3:54010800-54012400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:54011000-54014200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:54011200-54011800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:54011800-54012200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:54012200-54013000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:54012400-54012800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:54012400-54012800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:54012400-54013000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:54012400-54013000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:54012400-54013000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr3:54012400-54013000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:54012600-54013000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr3:54012600-54013000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:54012600-54013200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:54012800-54013000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:54012800-54016000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:54013000-54014000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:54013000-54014200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:54013000-54014200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:54013000-54014200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:54013000-54014400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:54013000-54014400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:54013000-54014800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:54013200-54014400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:54013800-54014000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:54014000-54014200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:54014000-54015600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:54014200-54014400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:54014200-54015600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:54014200-54015600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:54014200-54019400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:54014400-54014600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:54014400-54014600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr3:54014400-54015200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:54014400-54015200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr3:54014600-54014800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:54014600-54014800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:54014600-54014800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:54014600-54014800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr3:54014600-54015200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:54014800-54015200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:54019400-54019600	Enhancers	Fetal Brain Female	brain
47	chr3:54019600-54020200	Enhancers	Brain Germinal Matrix	brain
48	chr3:54020200-54024000	Weak transcription	Brain Germinal Matrix	brain
49	chr3:54020400-54020600	Enhancers	Fetal Brain Female	brain
50	chr3:54024000-54024400	Enhancers	Brain Germinal Matrix	brain

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