Variant report

Variant	esv3510341
Chromosome Location	chr13:49141769-49142303
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:49141688..49143234-chr13:49148647..49150198,2	MCF-7	breast:
2	chr13:49115025..49117372-chr13:49140241..49143183,2	MCF-7	breast:
3	chr13:49106056..49107969-chr13:49140390..49142172,2	MCF-7	breast:
4	chr13:49142248..49144143-chr13:49147250..49149323,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RCBTB2-1	chr13:49142298-49142483	XLOC_010605

Variant related genes	Relation type
ENSG00000136161	chromatin interactions
ENSG00000233456	chromatin interactions
RNF145	miRNA target sites

Extended variants
information (count: 19 )
Associated
traits (count: 120 )

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372128052	chr13:49141773-49141774	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs540033129	chr13:49141776-49141777	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs538620124	chr13:49141783-49141784	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs73489037	chr13:49141793-49141794	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs73489039	chr13:49141852-49141853	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs557689410	chr13:49141905-49141906	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs141493866	chr13:49141906-49141907	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs575866254	chr13:49141936-49141937	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs147675435	chr13:49141938-49141939	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs558914825	chr13:49141941-49141942	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs386770814	chr13:49141943-49141944	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs564148178	chr13:49141951-49141952	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs577821262	chr13:49141991-49141992	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs528208632	chr13:49142015-49142016	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs7332631	chr13:49142069-49142070	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs138383372	chr13:49142099-49142100	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs562821526	chr13:49142169-49142170	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs561576347	chr13:49142209-49142210	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs34270259	chr13:49142212-49142213	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:120)

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
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	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
Squamous cell cancer	20885788	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Thyroid cancer	19087340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	17899364	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	16774939	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Trisomy	24170809	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Alveolar rhabdomyosarcoma	16790082	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Prostate cancer	19242612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	17245344	CNVD
Colorectal cancer	21586687	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Retinoblastoma	19183342	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Retinoblastoma	21504564	CNVD
Chronic lymphocytic leukemia	21795749	CNVD
Chronic lymphocytic leukemia	17805327	CNVD
Mental retardation	17502991	CNVD
Retinoblastoma	17502991	CNVD
Bipolar disorder	18458673	CNVD
Liposarcoma	21253554	CNVD
T-cell lymphomas	19863542	CNVD
Cervical cancer	21062161	CNVD
microdeletion syndrome	19284877	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Multiple myeloma	19135901	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Prostate cancer	16461572	CNVD
Merkel cell carcinoma	19020549	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
lymphocytic leukemia	21291569	CNVD
Multiple myeloma	17550852	CNVD
Glioblastoma multiforme	19435819	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Breast cancer	21858162	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	17237825	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Myelofibrosis	22110671	CNVD
Hereditary prostate cancer	22028916	CNVD
Glioblastoma multiforme	22286061	CNVD
Chronic lymphocytic leukemia	21049055	CNVD
Prostate cancer	17217626	CNVD
Ovarian cancer	21781307	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	21922591	CNVD
Metanephric adenoma	20802469	CNVD
Chronic myeloid leukemia	21384125	CNVD
Sezary syndrome	18413736	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49135200-49141800	Weak transcription	Placenta	Placenta
3	chr13:49136800-49142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:49137000-49142000	Weak transcription	HMEC	breast
5	chr13:49137200-49153000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr13:49137400-49145200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr13:49138600-49142000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:49138800-49145600	Weak transcription	HUVEC	blood vessel
9	chr13:49139000-49144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:49139200-49141800	Weak transcription	Dnd41	blood
11	chr13:49139600-49144400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:49140000-49144200	Weak transcription	K562	blood
13	chr13:49140600-49142000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr13:49140800-49146400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:49141000-49145000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:49141200-49142000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr13:49141200-49142200	Enhancers	Rectal Smooth Muscle	rectum
18	chr13:49141200-49147000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr13:49141400-49141800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr13:49141400-49142000	Enhancers	Adipose Nuclei	Adipose
21	chr13:49141400-49142800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr13:49141400-49143400	Enhancers	Stomach Mucosa	stomach
23	chr13:49141400-49144800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr13:49141400-49145800	Enhancers	Fetal Stomach	stomach
25	chr13:49141400-49146200	Enhancers	HepG2	liver
26	chr13:49141400-49146400	Enhancers	Fetal Lung	lung
27	chr13:49141400-49146600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr13:49141600-49141800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:49141600-49141800	Enhancers	Aorta	Aorta
30	chr13:49141600-49141800	Enhancers	Fetal Kidney	kidney
31	chr13:49141600-49142000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:49141600-49142000	Enhancers	HSMM	muscle
33	chr13:49141600-49142000	Enhancers	Osteobl	bone
34	chr13:49141600-49142400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr13:49141600-49142600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:49141600-49142600	Enhancers	Primary hematopoietic stem cells	blood
37	chr13:49141600-49142600	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr13:49141600-49142600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr13:49141600-49142600	Flanking Active TSS	HSMMtube	muscle
40	chr13:49141800-49142000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:49141800-49142000	Enhancers	Brain Anterior Caudate	brain
42	chr13:49141800-49142000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr13:49141800-49142000	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr13:49141800-49142200	Enhancers	Ovary	ovary
45	chr13:49141800-49142400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:49141800-49142400	Active TSS	Psoas Muscle	Psoas
47	chr13:49141800-49142400	Active TSS	NHDF-Ad	bronchial
48	chr13:49141800-49142600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:49141800-49142600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:49141800-49142600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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