Variant report

Variant	esv3473993
Chromosome Location	chr6:53924727-53934903
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	chr6:53857425..53857943-chr6:53933277..53933955,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-10	chr6:53927754-53927853	NONHSAT113220
2	lnc-KLHL31-10	chr6:53927195-53927695	NONHSAT113220

Extended variants
information (count: 286 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:286 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370666455	chr6:53924730-53924731	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs530244885	chr6:53924788-53924789	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs200117342	chr6:53924806-53924807	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs200900368	chr6:53924807-53924808	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs201562784	chr6:53924808-53924809	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs374308453	chr6:53924820-53924821	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs549172354	chr6:53924838-53924839	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs565779606	chr6:53924845-53924846	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs35147820	chr6:53924942-53924943	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs187860633	chr6:53925051-53925052	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs569823106	chr6:53925179-53925180	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs547514901	chr6:53925181-53925182	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs570498580	chr6:53925187-53925188	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs539464555	chr6:53925210-53925211	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs193150650	chr6:53925216-53925217	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs34757544	chr6:53925257-53925258	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs570331232	chr6:53925274-53925275	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs538847890	chr6:53925359-53925360	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555917486	chr6:53925392-53925393	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs572596518	chr6:53925417-53925418	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs184267995	chr6:53925428-53925429	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs552469544	chr6:53925430-53925431	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs189217116	chr6:53925435-53925436	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs565988888	chr6:53925472-53925473	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs577674902	chr6:53925523-53925524	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs192849580	chr6:53925632-53925633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs114018072	chr6:53925727-53925728	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs201017189	chr6:53925783-53925784	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs78569538	chr6:53925796-53925797	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs547238429	chr6:53925801-53925802	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs61008480	chr6:53925808-53925809	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs542605619	chr6:53925870-53925871	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs559479537	chr6:53925887-53925888	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs528311436	chr6:53925888-53925889	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs184079517	chr6:53925913-53925914	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs570634942	chr6:53925925-53925926	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs74361017	chr6:53925957-53925958	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs115003769	chr6:53925962-53925963	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs569991398	chr6:53926007-53926008	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs559458370	chr6:53926018-53926019	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs188668871	chr6:53926023-53926024	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs574441047	chr6:53926026-53926027	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs555813042	chr6:53926032-53926033	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528231093	chr6:53926073-53926074	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs76425820	chr6:53926090-53926091	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs557855198	chr6:53926158-53926159	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs577824950	chr6:53926197-53926198	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs563515048	chr6:53926221-53926222	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs556639634	chr6:53926259-53926260	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs113877413	chr6:53926289-53926290	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:171 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53913600-53926000	Weak transcription	Left Ventricle	heart
2	chr6:53918800-53925200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:53919400-53928200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:53919600-53928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:53919600-53928400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:53919600-53928400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:53919800-53925000	Weak transcription	HSMM	muscle
8	chr6:53921400-53926000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:53921600-53936600	Weak transcription	Right Ventricle	heart
10	chr6:53922200-53928000	Weak transcription	Adipose Nuclei	Adipose
11	chr6:53923800-53927600	Enhancers	Fetal Heart	heart
12	chr6:53924000-53924800	Enhancers	Colon Smooth Muscle	Colon
13	chr6:53924000-53925400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:53924000-53935200	Weak transcription	Psoas Muscle	Psoas
15	chr6:53924200-53925200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr6:53924200-53925400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:53924200-53925800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:53924200-53926000	Weak transcription	Small Intestine	intestine
19	chr6:53924400-53924800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr6:53924400-53924800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:53924400-53925000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:53924400-53925000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr6:53924400-53925000	Flanking Active TSS	HUVEC	blood vessel
24	chr6:53924600-53925000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:53924600-53925000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:53924600-53925000	Active TSS	Right Atrium	heart
27	chr6:53924600-53925000	Active TSS	Stomach Mucosa	stomach
28	chr6:53924600-53925000	Active TSS	NHDF-Ad	bronchial
29	chr6:53924600-53925000	Flanking Active TSS	NHLF	lung
30	chr6:53924600-53925000	Flanking Active TSS	Osteobl	bone
31	chr6:53924600-53925200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:53924600-53925400	Enhancers	Fetal Lung	lung
33	chr6:53924600-53925400	Enhancers	Hela-S3	cervix
34	chr6:53924600-53925800	Weak transcription	Liver	Liver
35	chr6:53924800-53925600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr6:53924800-53926000	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:53924800-53926600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:53924800-53927200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr6:53925000-53925400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:53925000-53925400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:53925000-53925400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr6:53925000-53925400	Enhancers	Right Atrium	heart
43	chr6:53925000-53925400	Enhancers	HSMM	muscle
44	chr6:53925000-53925400	Enhancers	NHDF-Ad	bronchial
45	chr6:53925000-53925400	Enhancers	NHLF	lung
46	chr6:53925000-53925600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:53925000-53925800	Weak transcription	Stomach Mucosa	stomach
48	chr6:53925000-53925800	Enhancers	Osteobl	bone
49	chr6:53925000-53926000	Enhancers	HUVEC	blood vessel
50	chr6:53925200-53925400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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