Variant report

Variant	esv3401507
Chromosome Location	chr2:48423464-48423918
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	chr2:48415132..48417658-chr2:48422363..48423907,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXN2-4	chr2:48423238-48423721	NONHSAT070616

Extended variants
information (count: 15 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550813985	chr2:48423494-48423495	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs558675363	chr2:48423497-48423498	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs183416286	chr2:48423523-48423524	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs144013651	chr2:48423524-48423525	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs377295036	chr2:48423537-48423538	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs148672722	chr2:48423541-48423542	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs186541867	chr2:48423629-48423630	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
8	rs534311981	chr2:48423654-48423655	Enhancers Weak transcription Bivalent Enhancer	lncRNA	n/a	Overlapped CNVs	n/a
9	rs552961248	chr2:48423734-48423735	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs192760339	chr2:48423769-48423770	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs535498769	chr2:48423798-48423799	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs556800359	chr2:48423801-48423802	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs13430424	chr2:48423854-48423855	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs11683689	chr2:48423881-48423882	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs7569620	chr2:48423898-48423899	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:84)

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
Bladder cancer	21909424	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
small cell lung cancer	20016488	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
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	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
Breast cancer	22522925	CNVD

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48419000-48423600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:48421400-48424600	Enhancers	Brain Hippocampus Middle	brain
3	chr2:48422000-48425200	Enhancers	Brain Substantia Nigra	brain
4	chr2:48422000-48426400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr2:48422400-48423600	Weak transcription	Brain Angular Gyrus	brain
6	chr2:48422400-48424000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:48422400-48424600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:48422600-48424400	Weak transcription	Lung	lung
9	chr2:48422600-48425000	Enhancers	Fetal Muscle Leg	muscle
10	chr2:48423200-48423600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:48423200-48424000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr2:48423200-48424000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr2:48423200-48424000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:48423200-48424000	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:48423200-48424000	Enhancers	Fetal Intestine Large	intestine
16	chr2:48423200-48424000	Enhancers	Stomach Mucosa	stomach
17	chr2:48423200-48424200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr2:48423200-48424200	Enhancers	Fetal Brain Male	brain
19	chr2:48423200-48424600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr2:48423200-48424600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:48423200-48424600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:48423200-48424600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:48423200-48424600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:48423200-48424600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:48423200-48424600	Enhancers	Brain Anterior Caudate	brain
26	chr2:48423200-48424600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:48423200-48424600	Enhancers	Fetal Muscle Trunk	muscle
28	chr2:48423200-48424600	Enhancers	Placenta	Placenta
29	chr2:48423200-48424600	Enhancers	HSMM	muscle
30	chr2:48423200-48424600	Enhancers	HSMMtube	muscle
31	chr2:48423200-48425600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr2:48423200-48426800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:48423400-48423600	Enhancers	Pancreas	Pancrea
34	chr2:48423400-48423600	Enhancers	Right Ventricle	heart
35	chr2:48423400-48423800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:48423400-48423800	Enhancers	Fetal Brain Female	brain
37	chr2:48423400-48423800	Enhancers	Left Ventricle	heart
38	chr2:48423400-48423800	Enhancers	Right Atrium	heart
39	chr2:48423400-48424000	Enhancers	H9 Cell Line	embryonic stem cell
40	chr2:48423400-48424000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:48423400-48424000	Enhancers	Spleen	Spleen
42	chr2:48423400-48424200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr2:48423400-48424600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:48423400-48424600	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:48423400-48424600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr2:48423400-48424600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:48423400-48424800	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:48423400-48425000	Enhancers	Liver	Liver
49	chr2:48423400-48425000	Enhancers	Gastric	stomach
50	chr2:48423400-48425200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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