Variant report

Variant	nsv964496
Chromosome Location	chr21:40861855-40863688
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	chr21:40854953..40857406-chr21:40860627..40862371,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCA5L-1	chr21:40863470-40863824	NONHSAT082197

Extended variants
information (count: 74 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:74 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550577311	chr21:40861872-40861873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs117935442	chr21:40861929-40861930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs181101323	chr21:40861933-40861934	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs554523245	chr21:40861949-40861950	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs145471617	chr21:40861981-40861982	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs540403987	chr21:40862069-40862070	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs559918043	chr21:40862124-40862125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537114516	chr21:40862127-40862128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs149208549	chr21:40862129-40862130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs577323083	chr21:40862146-40862147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs185602280	chr21:40862185-40862186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs8128795	chr21:40862244-40862245	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs190986693	chr21:40862256-40862257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs2837049	chr21:40862312-40862313	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs561638319	chr21:40862317-40862318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs142447557	chr21:40862320-40862321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs8127748	chr21:40862333-40862334	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs147964410	chr21:40862337-40862338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs546762835	chr21:40862352-40862353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs549234303	chr21:40862360-40862361	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs182753898	chr21:40862393-40862394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs567545043	chr21:40862449-40862450	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs186092080	chr21:40862494-40862495	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs568073423	chr21:40862507-40862508	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs11911099	chr21:40862508-40862509	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368902555	chr21:40862529-40862530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs534916225	chr21:40862563-40862564	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs8128567	chr21:40862579-40862580	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs191823348	chr21:40862589-40862590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs571361798	chr21:40862642-40862643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs35076609	chr21:40862645-40862646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577260862	chr21:40862656-40862657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs79999292	chr21:40862666-40862667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs78565325	chr21:40862669-40862670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs55916184	chr21:40862679-40862680	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs544717649	chr21:40862680-40862681	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs570202303	chr21:40862681-40862682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs398061748	chr21:40862682-40862683	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs377598213	chr21:40862709-40862710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs6517553	chr21:40862722-40862723	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs7277107	chr21:40862760-40862761	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs542503767	chr21:40862796-40862797	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs183443730	chr21:40862928-40862929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs59759460	chr21:40862938-40862939	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs575095422	chr21:40862953-40862954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs2837050	chr21:40863001-40863002	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs533029270	chr21:40863026-40863027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs148121716	chr21:40863084-40863085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs566895170	chr21:40863085-40863086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs539120443	chr21:40863088-40863089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Cancer	16751803	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Down syndrome	17412756	CNVD
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Renal cell carcinoma	19461508	CNVD
Seminomas	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Wilms tumour	21544195	CNVD
Ewing''s sarcoma	17952124	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute myeloid leukemia	16864856	CNVD
Mental retardation	21031080	CNVD
Polymicrogyria	21031080	CNVD
periventricular nodular heterotopia	21031080	CNVD
Myelodysplastic syndrome	21606161	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Down syndrome	20877625	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Prostate cancer	21147910	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164919	CNVD

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
3	chr21:40846800-40862800	Weak transcription	Gastric	stomach
4	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr21:40848400-40863600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr21:40848400-40872400	Weak transcription	Left Ventricle	heart
7	chr21:40852600-40863400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr21:40853000-40862200	Weak transcription	Brain Anterior Caudate	brain
9	chr21:40853000-40865800	Weak transcription	Brain Hippocampus Middle	brain
10	chr21:40856800-40874000	Weak transcription	Aorta	Aorta
11	chr21:40857000-40874200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr21:40857200-40874000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr21:40857200-40874600	Weak transcription	Fetal Heart	heart
14	chr21:40860800-40863400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr21:40861600-40863400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr21:40861600-40872000	Weak transcription	Psoas Muscle	Psoas
17	chr21:40863400-40863800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr21:40863400-40864200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr21:40863600-40863800	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr21:40863600-40864000	Enhancers	HepG2	liver

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