Variant report

Variant	esv3384461
Chromosome Location	chr21:37910382-37913780
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLCS-2	chr21:37909493-37910751	l_2208_chr21:37904790-37910751_brain

Extended variants
information (count: 167 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:167 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9305590	chr21:37910446-37910447	Weak transcription Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs374857471	chr21:37910474-37910475	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
3	rs188078736	chr21:37910491-37910492	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
4	rs545495532	chr21:37910534-37910535	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
5	rs192533139	chr21:37910536-37910537	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
6	rs573793061	chr21:37910557-37910558	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
7	rs183251377	chr21:37910582-37910583	Weak transcription Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
8	rs9305591	chr21:37910600-37910601	Weak transcription Flanking Active TSS Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs113089668	chr21:37910611-37910612	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs9305592	chr21:37910625-37910626	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs545406796	chr21:37910655-37910656	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs70940557	chr21:37910660-37910661	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs2835388	chr21:37910661-37910662	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs560254553	chr21:37910666-37910667	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs11702700	chr21:37910671-37910672	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs545924113	chr21:37910688-37910689	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs146966387	chr21:37910711-37910712	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs187646445	chr21:37910718-37910719	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs9305594	chr21:37910772-37910773	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs9305595	chr21:37910869-37910870	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs192616281	chr21:37910894-37910895	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs369678437	chr21:37910902-37910903	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs199979395	chr21:37910922-37910923	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs201855048	chr21:37910929-37910930	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs559862929	chr21:37910930-37910931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs571200782	chr21:37910931-37910932	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs371519434	chr21:37910937-37910938	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs547135145	chr21:37910938-37910939	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs184888948	chr21:37910983-37910984	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs536420763	chr21:37910988-37910989	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs189773168	chr21:37910993-37910994	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs192251640	chr21:37911002-37911003	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs538982501	chr21:37911003-37911004	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs150865051	chr21:37911023-37911024	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs75344422	chr21:37911057-37911058	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs75140784	chr21:37911058-37911059	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs397866445	chr21:37911065-37911066	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs572311802	chr21:37911083-37911084	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs138331875	chr21:37911096-37911097	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs561198276	chr21:37911117-37911118	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs547389809	chr21:37911129-37911130	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs77984870	chr21:37911148-37911149	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs370683511	chr21:37911159-37911160	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs184313857	chr21:37911187-37911188	Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs188748534	chr21:37911208-37911209	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs369388094	chr21:37911238-37911239	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs532664243	chr21:37911248-37911249	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs373159933	chr21:37911255-37911256	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs79807929	chr21:37911264-37911265	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs560001515	chr21:37911275-37911276	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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
Ovarian cancer	22174824	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	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
Acute myeloid leukemia	17237825	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
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Down syndrome	20877625	CNVD
Acute myeloid leukemia	21251322	CNVD
Down syndrome	21154855	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37897000-37911600	Weak transcription	Pancreas	Pancrea
2	chr21:37908000-37911800	Weak transcription	Gastric	stomach
3	chr21:37908400-37911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:37908400-37911800	Weak transcription	Fetal Kidney	kidney
5	chr21:37908800-37910400	Enhancers	GM12878-XiMat	blood
6	chr21:37908800-37911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:37909400-37914400	Weak transcription	Placenta	Placenta
8	chr21:37910400-37910600	Flanking Active TSS	GM12878-XiMat	blood
9	chr21:37910600-37911000	Enhancers	GM12878-XiMat	blood
10	chr21:37911000-37911200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr21:37911000-37911400	Flanking Active TSS	GM12878-XiMat	blood
12	chr21:37911200-37911400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr21:37911400-37911800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr21:37911400-37911800	Enhancers	GM12878-XiMat	blood
15	chr21:37911600-37911800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
16	chr21:37911600-37912000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr21:37911600-37912000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:37911600-37912400	ZNF genes & repeats	Pancreas	Pancrea
19	chr21:37911800-37912000	ZNF genes & repeats	Fetal Kidney	kidney
20	chr21:37911800-37912200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr21:37911800-37912200	Enhancers	Gastric	stomach
22	chr21:37911800-37912800	Flanking Active TSS	GM12878-XiMat	blood
23	chr21:37912000-37912400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr21:37912000-37912400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
25	chr21:37912200-37912400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:37912200-37912400	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
27	chr21:37912400-37914200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr21:37912400-37914800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr21:37912400-37916400	Weak transcription	Pancreas	Pancrea
30	chr21:37912800-37914600	Active TSS	GM12878-XiMat	blood

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