Variant report

Variant	esv2763823
Chromosome Location	chr4:86097221-86120444
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86100478..86103305-chr4:86104929..86106522,2	K562	blood:
2	chr4:86100478..86103305-chr4:86104929..86106522,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGAP24-3	chr4:86106995-86107304	ucscGeneNc_uc003hpg_2
2	lnc-ARHGAP24-3	chr4:86109902-86110053	ucscGeneNc_uc003hpg_2

Extended variants
information (count: 110 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:110 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs116765568	chr4:86101609-86101610	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs376857889	chr4:86101660-86101661	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs556673427	chr4:86101690-86101691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs575331249	chr4:86101712-86101713	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs149291073	chr4:86101733-86101734	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs540227209	chr4:86101740-86101741	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs558350364	chr4:86101751-86101752	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs6822829	chr4:86101771-86101772	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs540532110	chr4:86101786-86101787	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs79220845	chr4:86101820-86101821	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs7666169	chr4:86101835-86101836	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs544630017	chr4:86101867-86101868	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs115469812	chr4:86101875-86101876	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs533490522	chr4:86101878-86101879	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs547883020	chr4:86101938-86101939	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs7666556	chr4:86101944-86101945	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs564316060	chr4:86102074-86102075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs528249250	chr4:86102083-86102084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs546813431	chr4:86102180-86102181	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs373208139	chr4:86102194-86102195	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs369860712	chr4:86107036-86107037	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs558603752	chr4:86107049-86107050	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs149021408	chr4:86107177-86107178	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs4361379	chr4:86107220-86107221	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs568217679	chr4:86107249-86107250	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs17009586	chr4:86107271-86107272	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs143092349	chr4:86107275-86107276	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs77210073	chr4:86107276-86107277	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs200947068	chr4:86109906-86109907	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs567895282	chr4:86109911-86109912	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs538504762	chr4:86109924-86109925	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs148751399	chr4:86109958-86109959	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs202245963	chr4:86109985-86109986	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs114751995	chr4:86110011-86110012	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs575285120	chr4:86117061-86117062	Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs185140319	chr4:86117062-86117063	Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs189854900	chr4:86117079-86117080	Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs7663029	chr4:86117082-86117083	Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs114177443	chr4:86117090-86117091	Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs11734764	chr4:86117097-86117098	Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs113213566	chr4:86117155-86117156	Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs13133618	chr4:86117173-86117174	Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs180765583	chr4:86117174-86117175	Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs149373067	chr4:86117179-86117180	Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs55916595	chr4:86117258-86117259	ZNF genes & repeats Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs186422276	chr4:86117260-86117261	ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs112683592	chr4:86117281-86117282	ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs534682290	chr4:86117282-86117283	ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs553301758	chr4:86117305-86117306	ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs113828331	chr4:86117328-86117329	ZNF genes & repeats Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
lymphocytic leukemia	21291569	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
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	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
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
primary effusion lymphomas	17116491	CNVD
Prostate cancer	16573809	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86101600-86102200	Enhancers	NHEK	skin
2	chr4:86117000-86118000	Active TSS	A549	lung
3	chr4:86117200-86117600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:86118000-86118200	Enhancers	A549	lung
5	chr4:86120200-86120400	Enhancers	HMEC	breast
6	chr4:86120200-86121800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:86120400-86121000	Weak transcription	HMEC	breast

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