Variant report

Variant	esv3471826
Chromosome Location	chr6:53926793-53936791
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: 283 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:283 , 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	rs372018081	chr6:53926799-53926800	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs566263057	chr6:53926800-53926801	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs137857809	chr6:53926835-53926836	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs116141335	chr6:53926837-53926838	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs561373268	chr6:53926845-53926846	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs571918515	chr6:53926861-53926862	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs9283918	chr6:53926867-53926868	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs142362056	chr6:53926887-53926888	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs55736417	chr6:53926907-53926908	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs201279091	chr6:53926986-53926987	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs535891949	chr6:53927051-53927052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs550563718	chr6:53927083-53927084	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs372257012	chr6:53927084-53927085	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs80190992	chr6:53927147-53927148	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs369908505	chr6:53927152-53927153	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs572811818	chr6:53927156-53927157	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs375147005	chr6:53927199-53927200	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs539210217	chr6:53927207-53927208	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs9357786	chr6:53927238-53927239	Weak transcription Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs190439447	chr6:53927315-53927316	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs572977746	chr6:53927318-53927319	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs4715439	chr6:53927326-53927327	Weak transcription Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs575122804	chr6:53927346-53927347	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs534823352	chr6:53927350-53927351	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs112604366	chr6:53927534-53927535	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs563644766	chr6:53927539-53927540	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs141251232	chr6:53927550-53927551	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs150782574	chr6:53927639-53927640	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs373136051	chr6:53927687-53927688	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs555722522	chr6:53927695-53927696	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs551876409	chr6:53927712-53927713	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs182157340	chr6:53927729-53927730	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs185942421	chr6:53927766-53927767	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs190862957	chr6:53927767-53927768	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs140813825	chr6:53927791-53927792	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs537657983	chr6:53927803-53927804	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs550623566	chr6:53927805-53927806	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs567252593	chr6:53927845-53927846	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs536204601	chr6:53927852-53927853	Weak transcription Active TSS Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs965315	chr6:53927860-53927861	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs566177622	chr6:53927861-53927862	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs143061138	chr6:53927873-53927874	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs115100041	chr6:53927878-53927879	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs182397143	chr6:53927893-53927894	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs544095564	chr6:53927916-53927917	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557376250	chr6:53927926-53927927	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs115934201	chr6:53927981-53927982	Weak transcription Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs5876352	chr6:53928003-53928004	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs76120989	chr6:53928029-53928030	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs113352220	chr6:53928084-53928085	Weak transcription Enhancers Active TSS	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:174 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53919400-53928200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:53919600-53928200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:53919600-53928400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr6:53919600-53928400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:53921600-53936600	Weak transcription	Right Ventricle	heart
6	chr6:53922200-53928000	Weak transcription	Adipose Nuclei	Adipose
7	chr6:53923800-53927600	Enhancers	Fetal Heart	heart
8	chr6:53924000-53935200	Weak transcription	Psoas Muscle	Psoas
9	chr6:53924800-53927200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:53925400-53928200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:53925400-53928200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:53925400-53928200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:53925400-53928400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:53925400-53928400	Weak transcription	Fetal Lung	lung
15	chr6:53925400-53928400	Weak transcription	Right Atrium	heart
16	chr6:53925600-53928200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:53925800-53927000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:53925800-53927200	Enhancers	Liver	Liver
19	chr6:53925800-53928200	Weak transcription	Osteobl	bone
20	chr6:53926200-53927600	Weak transcription	Left Ventricle	heart
21	chr6:53926200-53928200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:53926400-53927200	Weak transcription	Stomach Mucosa	stomach
23	chr6:53926400-53928200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:53926400-53934800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr6:53926600-53928200	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:53927200-53927600	Active TSS	Liver	Liver
27	chr6:53927200-53927800	Enhancers	Stomach Mucosa	stomach
28	chr6:53927200-53934800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:53927600-53927800	Flanking Active TSS	Liver	Liver
30	chr6:53927600-53928000	Weak transcription	Fetal Heart	heart
31	chr6:53927600-53928000	Enhancers	Left Ventricle	heart
32	chr6:53927800-53929000	Active TSS	Liver	Liver
33	chr6:53927800-53930000	Weak transcription	Stomach Mucosa	stomach
34	chr6:53928000-53928400	Enhancers	Adipose Nuclei	Adipose
35	chr6:53928000-53928600	Enhancers	Fetal Heart	heart
36	chr6:53928000-53939000	Weak transcription	Left Ventricle	heart
37	chr6:53928200-53928400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:53928200-53928400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53928200-53928400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr6:53928200-53928400	Flanking Active TSS	Osteobl	bone
41	chr6:53928200-53928600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:53928200-53928600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:53928200-53928600	Active TSS	Colon Smooth Muscle	Colon
44	chr6:53928200-53928600	Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:53928200-53928800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr6:53928200-53928800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr6:53928200-53928800	Active TSS	Stomach Smooth Muscle	stomach
48	chr6:53928400-53928600	Flanking Active TSS	Fetal Lung	lung
49	chr6:53928400-53928800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:53928400-53928800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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