Variant report

Variant	esv3405268
Chromosome Location	chr4:118241604-118245502
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAM1L1-1	chr4:118242468-118242519	XLOC_004051

Variant related genes	Relation type
NCKAP1	miRNA target sites

Extended variants
information (count: 87 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:87 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532648508	chr4:118242474-118242475	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs142583958	chr4:118242510-118242511	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs558399863	chr4:118242864-118242865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs530429483	chr4:118242937-118242938	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs75764198	chr4:118243005-118243006	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs187768847	chr4:118243033-118243034	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs554900096	chr4:118243038-118243039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs574055252	chr4:118243042-118243043	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs543800813	chr4:118243144-118243145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs141508521	chr4:118243160-118243161	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs143667958	chr4:118243189-118243190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs546255044	chr4:118243254-118243255	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs559625176	chr4:118243278-118243279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs72914171	chr4:118243299-118243300	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs575421597	chr4:118243300-118243301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548417653	chr4:118243343-118243344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs191416684	chr4:118243361-118243362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs531118282	chr4:118243399-118243400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs539253439	chr4:118243404-118243405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs182490726	chr4:118243409-118243410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs141886203	chr4:118243410-118243411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs538292314	chr4:118243446-118243447	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs558613120	chr4:118243461-118243462	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs565686344	chr4:118243592-118243593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs187180851	chr4:118243606-118243607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs554813191	chr4:118243654-118243655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs191882413	chr4:118243658-118243659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs546801430	chr4:118243662-118243663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs543762658	chr4:118243689-118243690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs557320365	chr4:118243767-118243768	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs577152338	chr4:118243786-118243787	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs373645812	chr4:118243872-118243873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs545917288	chr4:118243890-118243891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73856314	chr4:118243897-118243898	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs185351701	chr4:118243919-118243920	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs111761564	chr4:118243950-118243951	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs150652239	chr4:118243954-118243955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs561959698	chr4:118243990-118243991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs531039513	chr4:118244029-118244030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs79083056	chr4:118244031-118244032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs564669948	chr4:118244062-118244063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs532132568	chr4:118244077-118244078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs36042452	chr4:118244113-118244114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs5861341	chr4:118244114-118244115	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs398051261	chr4:118244134-118244135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs200075824	chr4:118244180-118244181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188667954	chr4:118244205-118244206	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs76161349	chr4:118244232-118244233	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs534725175	chr4:118244291-118244292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs548378842	chr4:118244383-118244384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Esophageal cancer	21851588	CNVD
Melanoma	20688739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Colorectal cancer	16272173	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	21899760	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18194544	CNVD
Autism	19246517	CNVD
Bipolar disorder	19114987	CNVD

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:118242800-118245000	Weak transcription	HSMM	muscle
2	chr4:118244800-118245800	Enhancers	HMEC	breast
3	chr4:118245000-118247600	Enhancers	HSMM	muscle
4	chr4:118245400-118245800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:118245400-118246600	Enhancers	NH-A	brain

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