Variant report

Variant	nsv456407
Chromosome Location	chr2:40158363-40208665
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	chr2:40164512..40166990-chr2:40173493..40175018,2	MCF-7	breast:
2	chr2:40164512..40166990-chr2:40173493..40175018,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-2	chr2:40185553-40185606	ucscGeneNc_uc002rrw_2

Extended variants
information (count: 2815 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:2815 , 50 per page) page: 1 2 3 4 5 6 7 ... 57

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2058626	chr2:40158363-40158364	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs541949542	chr2:40158366-40158367	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs561308063	chr2:40158376-40158377	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs74485883	chr2:40158384-40158385	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs186220880	chr2:40158434-40158435	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534538540	chr2:40158435-40158436	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs532866883	chr2:40158448-40158449	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs78331262	chr2:40158472-40158473	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs574424979	chr2:40158474-40158475	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs536724962	chr2:40158481-40158482	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs115325946	chr2:40158497-40158498	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs553167115	chr2:40158501-40158502	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs568369499	chr2:40158518-40158519	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs117053713	chr2:40158582-40158583	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs191885590	chr2:40158585-40158586	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs6752226	chr2:40158599-40158600	Weak transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs142472391	chr2:40158600-40158601	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs111518047	chr2:40158601-40158602	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs559755055	chr2:40158607-40158608	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs556782267	chr2:40158610-40158611	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs535699551	chr2:40158613-40158614	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs563190331	chr2:40158614-40158615	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs557287870	chr2:40158629-40158630	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs370733364	chr2:40158637-40158638	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs13397429	chr2:40158646-40158647	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs574129560	chr2:40158672-40158673	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs541538518	chr2:40158695-40158696	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs560165809	chr2:40158698-40158699	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs576548183	chr2:40158752-40158753	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs540782175	chr2:40158762-40158763	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs574924639	chr2:40158774-40158775	Weak transcription Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs543786592	chr2:40158801-40158802	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs532854080	chr2:40158813-40158814	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs72934810	chr2:40158822-40158823	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs372929090	chr2:40158838-40158839	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs145934021	chr2:40158839-40158840	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs542239892	chr2:40158921-40158922	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs548306796	chr2:40158937-40158938	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs566914705	chr2:40158957-40158958	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs534036374	chr2:40158989-40158990	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs138616028	chr2:40158998-40158999	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs182582826	chr2:40159018-40159019	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs558815169	chr2:40159034-40159035	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs561203574	chr2:40159073-40159074	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs374356156	chr2:40159076-40159077	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs570353233	chr2:40159080-40159081	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs368582167	chr2:40159081-40159082	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs375532081	chr2:40159106-40159107	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs556066743	chr2:40159119-40159120	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs369862960	chr2:40159167-40159168	Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
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
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
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Williams Syndrome	20824207	CNVD

Chromatin state (count:153 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40141600-40164800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:40147000-40167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:40152000-40158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:40156400-40160200	Weak transcription	Fetal Stomach	stomach
5	chr2:40156800-40158600	Weak transcription	HSMM	muscle
6	chr2:40156800-40158800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:40157000-40159200	Genic enhancers	Dnd41	blood
8	chr2:40157600-40158600	Enhancers	Fetal Thymus	thymus
9	chr2:40158600-40158800	Genic enhancers	Fetal Thymus	thymus
10	chr2:40158600-40159200	ZNF genes & repeats	HSMM	muscle
11	chr2:40158800-40159400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:40158800-40159400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:40158800-40159600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:40158800-40159600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:40158800-40164800	Weak transcription	Fetal Thymus	thymus
16	chr2:40159000-40159400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:40159000-40159600	Enhancers	NHEK	skin
18	chr2:40159200-40160200	Weak transcription	Dnd41	blood
19	chr2:40159200-40164800	Weak transcription	HSMM	muscle
20	chr2:40159400-40160000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:40159400-40165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:40159600-40160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:40159600-40162000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:40160000-40160600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:40160000-40161200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:40160200-40160400	Enhancers	Fetal Stomach	stomach
27	chr2:40160200-40164600	Enhancers	Dnd41	blood
28	chr2:40160400-40161000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:40160400-40161200	Weak transcription	Fetal Stomach	stomach
30	chr2:40160600-40164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:40161200-40161400	Enhancers	Fetal Stomach	stomach
32	chr2:40161200-40165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:40162000-40162600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:40164600-40166400	Flanking Active TSS	Dnd41	blood
35	chr2:40164800-40165000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:40164800-40166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:40164800-40166200	Enhancers	Fetal Thymus	thymus
38	chr2:40164800-40166400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:40164800-40166400	Enhancers	HSMM	muscle
40	chr2:40164800-40166400	Enhancers	Osteobl	bone
41	chr2:40165000-40165600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:40165000-40166400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:40165000-40166600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:40165000-40166600	Enhancers	NH-A	brain
45	chr2:40165000-40166800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:40165000-40175800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:40165200-40165600	Enhancers	HSMMtube	muscle
48	chr2:40165200-40166000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr2:40165200-40166400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr2:40165200-40166400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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