Variant report

Variant	nsv4325
Chromosome Location	chr4:47142343-47187026
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP10D-2	chr4:47164263-47164397	l_2639_chr4:47160564-47167245_testes
2	lnc-ATP10D-2	chr4:47165941-47166102	l_2639_chr4:47160564-47167245_testes
3	lnc-ATP10D-2	chr4:47166847-47167245	l_2639_chr4:47160564-47167245_testes
4	lnc-ATP10D-2	chr4:47160565-47160809	l_2639_chr4:47160564-47167245_testes

Extended variants
information (count: 1240 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1240 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4463042	chr4:47143805-47143806	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs558601423	chr4:47143837-47143838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs181023917	chr4:47143870-47143871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs577167626	chr4:47143921-47143922	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs374359599	chr4:47143925-47143926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs146498268	chr4:47143941-47143942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs185002567	chr4:47143946-47143947	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs1442101	chr4:47143957-47143958	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs74989815	chr4:47143976-47143977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs555278144	chr4:47143993-47143994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs116574182	chr4:47143994-47143995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs373989084	chr4:47144004-47144005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs10938472	chr4:47144042-47144043	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs573017472	chr4:47144072-47144073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs188009163	chr4:47144100-47144101	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs112356772	chr4:47144110-47144111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs181946689	chr4:47144114-47144115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs551032927	chr4:47144124-47144125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs145493122	chr4:47144126-47144127	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs578018323	chr4:47144173-47144174	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs545206216	chr4:47144210-47144211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs113040399	chr4:47144212-47144213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs148858594	chr4:47144266-47144267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs563487851	chr4:47144322-47144323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs566536468	chr4:47144355-47144356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs540056928	chr4:47144374-47144375	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs113628431	chr4:47144386-47144387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs186064876	chr4:47144400-47144401	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs367727266	chr4:47144442-47144443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs552154372	chr4:47144463-47144464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs145220216	chr4:47144521-47144522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs538128489	chr4:47144542-47144543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs113098421	chr4:47144546-47144547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs556213171	chr4:47144596-47144597	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs137909747	chr4:47144667-47144668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs141106587	chr4:47144670-47144671	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs553944743	chr4:47144697-47144698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs575381755	chr4:47144751-47144752	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs144843048	chr4:47144754-47144755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs191898068	chr4:47144768-47144769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs183389295	chr4:47144771-47144772	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs138761785	chr4:47144794-47144795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs542360270	chr4:47144878-47144879	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs141243260	chr4:47144901-47144902	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs116892927	chr4:47144907-47144908	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs12509369	chr4:47144918-47144919	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs548452267	chr4:47144919-47144920	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs111608182	chr4:47144975-47144976	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs376924957	chr4:47145022-47145023	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs12640095	chr4:47145034-47145035	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:65)

Disease	PMID	Source
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Olfactory neuroblastoma	18408657	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	16616336	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Renal cell carcinoma	18765545	CNVD
Gastric cancer	16891809	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47143800-47146800	Weak transcription	Fetal Heart	heart
2	chr4:47144800-47145600	Enhancers	GM12878-XiMat	blood
3	chr4:47145200-47145400	Enhancers	Brain Anterior Caudate	brain
4	chr4:47145600-47147000	Weak transcription	GM12878-XiMat	blood
5	chr4:47146000-47147000	Weak transcription	Brain Anterior Caudate	brain
6	chr4:47146800-47148000	Enhancers	Fetal Heart	heart
7	chr4:47147000-47147400	Enhancers	GM12878-XiMat	blood
8	chr4:47147000-47147800	Enhancers	Brain Anterior Caudate	brain
9	chr4:47147000-47148600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:47147200-47149200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:47147400-47147600	Flanking Active TSS	GM12878-XiMat	blood
12	chr4:47147400-47148000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr4:47147400-47148400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:47147400-47148800	Enhancers	Fetal Brain Male	brain
15	chr4:47147600-47148000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:47147600-47148000	Active TSS	GM12878-XiMat	blood
17	chr4:47147600-47148600	Enhancers	NH-A	brain
18	chr4:47147800-47148200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:47147800-47148200	Enhancers	Osteobl	bone
20	chr4:47147800-47148400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:47147800-47154800	Weak transcription	Brain Anterior Caudate	brain
22	chr4:47148000-47148200	Enhancers	Left Ventricle	heart
23	chr4:47148000-47148800	Enhancers	GM12878-XiMat	blood
24	chr4:47148400-47149400	Weak transcription	Left Ventricle	heart
25	chr4:47148800-47152000	Weak transcription	Fetal Brain Male	brain
26	chr4:47149400-47149800	Enhancers	Left Ventricle	heart
27	chr4:47152000-47152400	Enhancers	Fetal Brain Male	brain
28	chr4:47154600-47155000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:47154800-47155000	Enhancers	Brain Anterior Caudate	brain
30	chr4:47155000-47156600	Weak transcription	Brain Anterior Caudate	brain
31	chr4:47156600-47157000	Enhancers	Brain Anterior Caudate	brain
32	chr4:47156600-47157800	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:47156800-47157200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:47156800-47157200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:47157000-47157200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr4:47157000-47157400	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr4:47158200-47158600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr4:47158400-47158600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr4:47158600-47161800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:47158800-47161200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr4:47159600-47159800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr4:47160000-47161200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:47161200-47162000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr4:47161200-47163200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr4:47161800-47162400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr4:47161800-47163000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:47162000-47162200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr4:47162200-47162400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr4:47162400-47162600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr4:47168800-47169600	Enhancers	Fetal Brain Female	brain

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