Variant report

Variant	esv3403446
Chromosome Location	chr13:110417051-110420149
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	chr13:110417399..110417917-chr13:110760942..110761494,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL4A1-5	chr13:110419156-110419178	NONHSAT035118
2	lnc-COL4A1-5	chr13:110417658-110418068	NONHSAT035118
3	lnc-COL4A1-5	chr13:110418461-110418469	NONHSAT035118

Extended variants
information (count: 174 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:174 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149372140	chr13:110417055-110417056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs568392123	chr13:110417084-110417085	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs2026816	chr13:110417108-110417109	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs556749718	chr13:110417150-110417151	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs568608860	chr13:110417164-110417165	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs553260445	chr13:110417169-110417170	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs188609424	chr13:110417206-110417207	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs144812781	chr13:110417223-110417224	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs553804445	chr13:110417227-110417228	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs544096980	chr13:110417242-110417243	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs570659940	chr13:110417310-110417311	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs192840253	chr13:110417364-110417365	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs142012206	chr13:110417407-110417408	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs574717366	chr13:110417413-110417414	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs150680301	chr13:110417414-110417415	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs530426913	chr13:110417512-110417513	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs184974009	chr13:110417524-110417525	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs113937915	chr13:110417532-110417533	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs532783167	chr13:110417621-110417622	Weak transcription Enhancers Flanking Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs191320727	chr13:110417711-110417712	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs566205354	chr13:110417745-110417746	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs1755722	chr13:110417746-110417747	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs528475750	chr13:110417757-110417758	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs201348926	chr13:110417778-110417779	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs1755723	chr13:110417779-110417780	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548569557	chr13:110417785-110417786	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs1655953	chr13:110417788-110417789	Weak transcription Enhancers Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs113341861	chr13:110417818-110417819	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs61962697	chr13:110417834-110417835	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs1755724	chr13:110417837-110417838	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs1755725	chr13:110417842-110417843	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs536965904	chr13:110417855-110417856	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs368604448	chr13:110417867-110417868	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs4773083	chr13:110417877-110417878	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs4773084	chr13:110417883-110417884	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs4773085	chr13:110417886-110417887	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs61135282	chr13:110417926-110417927	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs56860385	chr13:110417932-110417933	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs59877324	chr13:110417935-110417936	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs112078854	chr13:110417936-110417937	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs75296047	chr13:110417940-110417941	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs143930484	chr13:110417975-110417976	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs75453923	chr13:110418023-110418024	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs74723876	chr13:110418024-110418025	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs77998677	chr13:110418030-110418031	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs77740516	chr13:110418033-110418034	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs570294888	chr13:110418044-110418045	Weak transcription Enhancers Genic enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs77441592	chr13:110418078-110418079	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs539286703	chr13:110418100-110418101	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs75858903	chr13:110418122-110418123	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Cancer	20164919	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Myoepithelioma	18604193	CNVD
Breast cancer	17133270	CNVD
Prostate cancer	18632612	CNVD
Melanoma	18172304	CNVD
Prostate cancer	16573809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	17053054	CNVD
Gastric cancer	17908304	CNVD
Liposarcoma	21253554	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	22032731	CNVD
Wilms tumour	21544195	CNVD
Thyroid cancer	19087340	CNVD
abortions and stillbirths	19751515	CNVD
Acute myeloid leukemia	21251322	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Burkitt''s lymphoma	20823134	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Burkitt''s lymphoma	19759907	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Medulloblastoma	19270706	CNVD
Mental retardation	17124404	CNVD
Leukemia	18688285	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21858162	CNVD
Melanoma	17363583	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	21645411	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Breast cancer	16608533	CNVD
Glioblastoma multiforme	22286061	CNVD
Follicular lymphoma	20505157	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
abnormal development	18461090	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Malignant glioma	17146433	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Glioma	17123091	CNVD
Sudden cardiac death	19188705	CNVD
Breast cancer	20409316	CNVD
Central neurocytomas	17123091	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Neurocytoma	17123091	CNVD
Mantle cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:303 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110397000-110428800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr13:110397200-110430400	Weak transcription	NHLF	lung
3	chr13:110397400-110419400	Weak transcription	Lung	lung
4	chr13:110401800-110430800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:110403200-110430600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:110406200-110429400	Weak transcription	Primary B cells from cord blood	blood
7	chr13:110407400-110423400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:110408600-110417200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:110408600-110417400	Weak transcription	Fetal Stomach	stomach
10	chr13:110408600-110421600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:110408600-110422800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:110408600-110423800	Weak transcription	Placenta	Placenta
13	chr13:110408600-110424400	Weak transcription	Spleen	Spleen
14	chr13:110408600-110430400	Weak transcription	Colonic Mucosa	Colon
15	chr13:110408800-110420800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:110408800-110421400	Weak transcription	Fetal Intestine Large	intestine
17	chr13:110408800-110421800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr13:110408800-110422800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr13:110408800-110423600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr13:110409000-110422600	Weak transcription	Fetal Lung	lung
21	chr13:110409000-110431200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:110409200-110422200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:110409200-110422600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr13:110409200-110423000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr13:110409400-110429800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr13:110409400-110430200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr13:110411200-110417800	Enhancers	Fetal Brain Male	brain
28	chr13:110411400-110417400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr13:110411400-110417600	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr13:110411600-110417200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:110411600-110422600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:110411800-110420800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr13:110411800-110421800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr13:110412200-110422400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:110412400-110417200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:110412600-110418000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:110413200-110418200	Genic enhancers	HSMM	muscle
38	chr13:110413200-110419200	Weak transcription	Gastric	stomach
39	chr13:110413400-110430400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr13:110413600-110417800	Enhancers	NHEK	skin
41	chr13:110413600-110419200	Weak transcription	Pancreas	Pancrea
42	chr13:110413600-110430800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr13:110414000-110424400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr13:110414400-110418000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr13:110414400-110428800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:110415000-110417200	Weak transcription	Brain Germinal Matrix	brain
47	chr13:110415000-110417600	Strong transcription	Hela-S3	cervix
48	chr13:110415000-110428800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:110415200-110417200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr13:110415200-110417800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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