Variant report

Variant	esv3459576
Chromosome Location	chr2:54744109-54744687
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	chr2:54743659..54744325-chr2:54801308..54802130,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf73-2	chr2:54743773-54744815	expReg_chr2_4103_+

Extended variants
information (count: 21 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6545421	chr2:54744111-54744112	Enhancers Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs550724337	chr2:54744133-54744134	Enhancers Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs386646259	chr2:54744140-54744141	Enhancers Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs114645320	chr2:54744142-54744143	Enhancers Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs181884200	chr2:54744171-54744172	Enhancers Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs573143196	chr2:54744223-54744224	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
7	rs77177608	chr2:54744247-54744248	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
8	rs56917850	chr2:54744267-54744268	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
9	rs398060198	chr2:54744271-54744272	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
10	rs372699474	chr2:54744336-54744337	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
11	rs555480423	chr2:54744337-54744338	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
12	rs376943819	chr2:54744354-54744355	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
13	rs142657818	chr2:54744379-54744380	Enhancers Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
14	rs557167072	chr2:54744482-54744483	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs544213363	chr2:54744487-54744488	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs369466200	chr2:54744489-54744490	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs542675131	chr2:54744580-54744581	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs386508394	chr2:54744589-54744590	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs186816621	chr2:54744592-54744593	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs146752525	chr2:54744682-54744683	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs559440577	chr2:54744686-54744687	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54719000-54751800	Weak transcription	Aorta	Aorta
2	chr2:54730400-54747600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54732800-54754800	Weak transcription	Fetal Intestine Small	intestine
4	chr2:54733600-54747000	Weak transcription	Gastric	stomach
5	chr2:54737000-54751400	Weak transcription	HUVEC	blood vessel
6	chr2:54737600-54753800	Weak transcription	Fetal Brain Male	brain
7	chr2:54738200-54746200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:54738200-54746400	Weak transcription	NHLF	lung
9	chr2:54738200-54748200	Weak transcription	Fetal Stomach	stomach
10	chr2:54738200-54751600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:54738400-54746200	Weak transcription	A549	lung
12	chr2:54738400-54751400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:54739400-54746400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:54740400-54744200	Weak transcription	Lung	lung
15	chr2:54740400-54746200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:54740400-54746200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:54740400-54746200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:54740400-54746200	Weak transcription	Right Atrium	heart
19	chr2:54740400-54746400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:54740400-54746400	Weak transcription	Psoas Muscle	Psoas
21	chr2:54740400-54747000	Weak transcription	Pancreas	Pancrea
22	chr2:54740400-54747800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:54740400-54751600	Weak transcription	Placenta	Placenta
24	chr2:54740400-54770200	Weak transcription	Esophagus	oesophagus
25	chr2:54740600-54745200	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:54740600-54746200	Weak transcription	NHDF-Ad	bronchial
27	chr2:54740600-54746800	Weak transcription	Osteobl	bone
28	chr2:54740600-54747000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:54740600-54749800	Weak transcription	HepG2	liver
30	chr2:54740600-54753400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:54740600-54761800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:54740800-54745000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:54740800-54745000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:54740800-54745800	Weak transcription	Brain Angular Gyrus	brain
35	chr2:54740800-54746400	Weak transcription	Brain Anterior Caudate	brain
36	chr2:54740800-54746400	Weak transcription	HSMM	muscle
37	chr2:54740800-54746800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:54740800-54747000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:54741000-54746200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:54741000-54748000	Weak transcription	Adipose Nuclei	Adipose
41	chr2:54742000-54747000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:54742200-54744200	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:54742400-54744200	Weak transcription	Fetal Lung	lung
44	chr2:54742400-54745200	Weak transcription	Brain Substantia Nigra	brain
45	chr2:54742400-54745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:54742400-54747400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:54742400-54748000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:54742600-54746200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:54742600-54746600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:54742600-54746800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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