Variant report

Variant	esv3442008
Chromosome Location	chr4:3600635-3600951
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRPAP1-5	chr4:3600324-3600789	NONHSAT094890
2	lnc-LRPAP1-5	chr4:3600844-3601755	NONHSAT094890

Extended variants
information (count: 50 )
Associated
traits (count: 57 )

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539982587	chr4:3600644-3600645	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs559802736	chr4:3600645-3600646	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs111161829	chr4:3600649-3600650	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs532748916	chr4:3600650-3600651	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs111161830	chr4:3600656-3600657	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs555543548	chr4:3600661-3600662	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs552441233	chr4:3600664-3600665	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs111065371	chr4:3600676-3600677	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs62644711	chr4:3600679-3600680	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs111203524	chr4:3600698-3600699	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs548887073	chr4:3600700-3600701	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs111066707	chr4:3600709-3600710	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs568495313	chr4:3600712-3600713	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs534182297	chr4:3600713-3600714	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs575281293	chr4:3600715-3600716	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs62644712	chr4:3600723-3600724	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs544188772	chr4:3600732-3600733	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs111161240	chr4:3600739-3600740	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs538847603	chr4:3600751-3600752	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs111161241	chr4:3600753-3600754	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs374100665	chr4:3600761-3600762	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs200965174	chr4:3600762-3600763	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs377748692	chr4:3600776-3600777	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs111161242	chr4:3600782-3600783	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs371013042	chr4:3600786-3600787	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs556645708	chr4:3600788-3600789	ZNF genes & repeats Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs537777618	chr4:3600790-3600791	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs114286739	chr4:3600793-3600794	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs554437616	chr4:3600801-3600802	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs79060974	chr4:3600804-3600805	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs76330108	chr4:3600812-3600813	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs574133400	chr4:3600820-3600821	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs201165559	chr4:3600837-3600838	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs539801283	chr4:3600839-3600840	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs559816738	chr4:3600855-3600856	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs576837798	chr4:3600861-3600862	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs111203528	chr4:3600884-3600885	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs546395677	chr4:3600901-3600902	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs111161243	chr4:3600902-3600903	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs377140763	chr4:3600906-3600907	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs62636036	chr4:3600908-3600909	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs62636037	chr4:3600912-3600913	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs369992945	chr4:3600914-3600915	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs118192386	chr4:3600916-3600917	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs62636038	chr4:3600919-3600920	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs531914654	chr4:3600926-3600927	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs144646523	chr4:3600936-3600937	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs548947672	chr4:3600938-3600939	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs375609128	chr4:3600945-3600946	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs200710652	chr4:3600946-3600947	ZNF genes & repeats Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Ependymoma	20639864	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Lung cancer	18438408	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3595800-3603400	Weak transcription	Right Atrium	heart
2	chr4:3597000-3604200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:3597000-3608000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:3597400-3601200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
5	chr4:3598600-3607600	ZNF genes & repeats	Fetal Stomach	stomach
6	chr4:3598800-3601000	ZNF genes & repeats	Spleen	Spleen
7	chr4:3599400-3601000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:3599600-3601000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:3599800-3601800	ZNF genes & repeats	Fetal Brain Male	brain
10	chr4:3600000-3600800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr4:3600000-3601600	ZNF genes & repeats	Fetal Lung	lung
12	chr4:3600000-3604200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:3600200-3600800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr4:3600200-3601000	ZNF genes & repeats	Gastric	stomach
15	chr4:3600200-3601400	ZNF genes & repeats	Esophagus	oesophagus
16	chr4:3600200-3601600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:3600200-3601600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:3600200-3602200	ZNF genes & repeats	Pancreas	Pancrea
19	chr4:3600400-3601000	ZNF genes & repeats	Fetal Kidney	kidney
20	chr4:3600400-3601600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
21	chr4:3600600-3601400	Weak transcription	Fetal Brain Female	brain
22	chr4:3600800-3601000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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