Variant report

Variant	esv3425414
Chromosome Location	chr2:100652945-100655493
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	chr2:100647488..100649170-chr2:100654840..100656524,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LONRF2-3	chr2:100652786-100653065	NONHSAT072767

Extended variants
information (count: 99 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:99 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574388873	chr2:100652957-100652958	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs201223785	chr2:100653007-100653008	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs34548598	chr2:100653048-100653049	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs397985294	chr2:100653055-100653056	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs542217802	chr2:100653085-100653086	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs148316492	chr2:100653114-100653115	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs555814295	chr2:100653159-100653160	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs191494766	chr2:100653173-100653174	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs573312928	chr2:100653188-100653189	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs564848530	chr2:100653215-100653216	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs13424200	chr2:100653244-100653245	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs536618662	chr2:100653296-100653297	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs60910274	chr2:100653297-100653298	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs112337784	chr2:100653305-100653306	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs397700070	chr2:100653309-100653310	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs543633992	chr2:100653322-100653323	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs13020567	chr2:100653323-100653324	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs563013336	chr2:100653360-100653361	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs368943527	chr2:100653361-100653362	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs548527791	chr2:100653401-100653402	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs183649146	chr2:100653416-100653417	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs141481777	chr2:100653440-100653441	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs113627243	chr2:100653462-100653463	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs150819530	chr2:100653470-100653471	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs571551405	chr2:100653479-100653480	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs377671197	chr2:100653483-100653484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs114538082	chr2:100653497-100653498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs186632031	chr2:100653513-100653514	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs374299542	chr2:100653546-100653547	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs202147395	chr2:100653621-100653622	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs570131047	chr2:100653741-100653742	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs535964257	chr2:100653771-100653772	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs79674633	chr2:100653802-100653803	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs555688069	chr2:100653826-100653827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs13020141	chr2:100653842-100653843	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs369399368	chr2:100653952-100653953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs373169569	chr2:100653953-100653954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs376372037	chr2:100653955-100653956	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs192701330	chr2:100653966-100653967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs13020691	chr2:100654024-100654025	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs60363335	chr2:100654121-100654122	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs541458215	chr2:100654152-100654153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs190382871	chr2:100654157-100654158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs13021114	chr2:100654202-100654203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs13021115	chr2:100654204-100654205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs113013344	chr2:100654221-100654222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs139273517	chr2:100654305-100654306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs12712062	chr2:100654307-100654308	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs543573101	chr2:100654312-100654313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs546078740	chr2:100654343-100654344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	17483303	CNVD
Medulloblastoma	20607354	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	21509527	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Glioblastoma multiforme	21138945	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100624800-100657800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:100633600-100653000	Weak transcription	Fetal Lung	lung
3	chr2:100633600-100660600	Weak transcription	Lung	lung
4	chr2:100637200-100658400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:100639000-100660600	Weak transcription	Primary T cells from cord blood	blood
6	chr2:100639600-100657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:100644600-100668400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:100646400-100662600	Weak transcription	Gastric	stomach
9	chr2:100648200-100666800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:100650600-100656800	Weak transcription	Fetal Brain Female	brain
11	chr2:100651200-100653000	Strong transcription	Primary B cells from cord blood	blood
12	chr2:100651800-100659600	Weak transcription	Left Ventricle	heart
13	chr2:100652000-100656200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:100652600-100653800	Enhancers	Fetal Brain Male	brain
15	chr2:100652800-100661400	Weak transcription	Ovary	ovary
16	chr2:100653000-100653600	Enhancers	Fetal Lung	lung
17	chr2:100653000-100656000	Weak transcription	Primary B cells from cord blood	blood
18	chr2:100653200-100667200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:100653400-100653600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:100653400-100653600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:100653400-100653600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:100653400-100653600	Enhancers	Fetal Heart	heart
23	chr2:100653400-100653600	Enhancers	Pancreas	Pancrea
24	chr2:100653600-100654600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:100653600-100656800	Weak transcription	Fetal Heart	heart
26	chr2:100653600-100657600	Weak transcription	Fetal Lung	lung
27	chr2:100653800-100657800	Weak transcription	Fetal Brain Male	brain
28	chr2:100654200-100654600	Weak transcription	Thymus	Thymus
29	chr2:100654600-100654800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:100654600-100654800	Enhancers	Thymus	Thymus
31	chr2:100654600-100656400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:100654800-100655000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:100654800-100655800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:100654800-100668200	Weak transcription	Thymus	Thymus
35	chr2:100655000-100656400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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