Variant report

Variant	nsv825718
Chromosome Location	chr11:3838740-3839759
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	chr11:3838017..3840276-chr11:3860830..3863822,2	MCF-7	breast:
2	chr11:3839155..3841334-chr11:4117148..4119265,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STIM1-1	chr11:3837982-3839379	ENSG00000250404.1

Variant related genes	Relation type
ENSG00000177105	chromatin interactions

Extended variants
information (count: 50 )
Associated
traits (count: 60 )

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371314694	chr11:3838742-3838743	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs562379346	chr11:3838743-3838744	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs201474442	chr11:3838747-3838748	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs369695308	chr11:3838797-3838798	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs7114556	chr11:3838812-3838813	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs147311015	chr11:3838822-3838823	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs527486161	chr11:3838839-3838840	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs112175793	chr11:3838861-3838862	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs139231774	chr11:3838887-3838888	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs61899363	chr11:3838899-3838900	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs537780002	chr11:3838906-3838907	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs7946577	chr11:3838910-3838911	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs555759251	chr11:3838942-3838943	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs10835147	chr11:3838953-3838954	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs539912091	chr11:3838961-3838962	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs535779435	chr11:3838970-3838971	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs373303100	chr11:3839013-3839014	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs544558279	chr11:3839103-3839104	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs557982169	chr11:3839115-3839116	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs74707441	chr11:3839136-3839137	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs1139042	chr11:3839161-3839162	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs1142533	chr11:3839165-3839166	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs1142534	chr11:3839177-3839178	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs573430018	chr11:3839186-3839187	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs534419106	chr11:3839218-3839219	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs1975670	chr11:3839286-3839287	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs373853005	chr11:3839287-3839288	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs112928434	chr11:3839292-3839293	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs386372940	chr11:3839304-3839305	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs371358568	chr11:3839305-3839306	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs187349241	chr11:3839358-3839359	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs563253902	chr11:3839369-3839370	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs574372584	chr11:3839373-3839374	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs370848274	chr11:3839375-3839376	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs193107231	chr11:3839403-3839404	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs562501834	chr11:3839464-3839465	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs577608329	chr11:3839483-3839484	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs576683219	chr11:3839519-3839520	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs185549796	chr11:3839534-3839535	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs61899364	chr11:3839555-3839556	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs80209061	chr11:3839557-3839558	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs79509418	chr11:3839558-3839559	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs75818904	chr11:3839559-3839560	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs398015224	chr11:3839573-3839574	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs11029894	chr11:3839603-3839604	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs545641726	chr11:3839609-3839610	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs545040113	chr11:3839614-3839615	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs189254894	chr11:3839634-3839635	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs192642343	chr11:3839682-3839683	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs369831702	chr11:3839750-3839751	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	19432969	CNVD
Alzheimer''s disease	17576883	CNVD
Long-qt syndrome	17576883	CNVD
Emphysema	19352772	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Chordoma	18071362	CNVD
Breast cancer	16608533	CNVD
Cancer	21183584	CNVD
Gastric adenocarcinoma	19115996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	19759907	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Thyroid cancer	19087340	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Parathyroid adenoma	22454399	CNVD
Chordoma	21602918	CNVD
Breast cancer	21949216	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	19222835	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Beckwith-Wiedemann syndrome	21518781	CNVD
Wilms tumour	21518781	CNVD
Hepatoblastoma	21518781	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Gastric cancer	17908304	CNVD
Barrett''s syndrome	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Multiple myeloma	20724749	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Myelofibrosis	22110671	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Neuroblastoma	21124317	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Schizophrenia	21399695	CNVD
Gastric cancer	16891809	CNVD
Cancer	17160897	CNVD
Multiple myeloma	16616336	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830200-3845200	Weak transcription	Spleen	Spleen
2	chr11:3830200-3845400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:3830200-3852400	Weak transcription	Fetal Brain Male	brain
4	chr11:3830400-3844600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:3830400-3844600	Weak transcription	Brain Germinal Matrix	brain
6	chr11:3830400-3844600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:3830400-3844600	Weak transcription	Thymus	Thymus
8	chr11:3830400-3845000	Weak transcription	Fetal Brain Female	brain
9	chr11:3830400-3846800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:3830400-3847200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:3830600-3844600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:3830600-3844800	Weak transcription	NHLF	lung
13	chr11:3830600-3845000	Weak transcription	GM12878-XiMat	blood
14	chr11:3830600-3845200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:3830600-3845600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:3830600-3847000	Weak transcription	Colonic Mucosa	Colon
17	chr11:3830600-3848000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
19	chr11:3830800-3844000	Weak transcription	Brain Angular Gyrus	brain
20	chr11:3830800-3844400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:3830800-3844800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr11:3830800-3845200	Weak transcription	Pancreas	Pancrea
23	chr11:3830800-3845400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr11:3830800-3845400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:3830800-3845600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:3830800-3845800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:3830800-3845800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr11:3830800-3846000	Weak transcription	A549	lung
29	chr11:3830800-3846200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:3830800-3846200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:3830800-3846200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:3830800-3846600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:3831000-3842000	Weak transcription	Liver	Liver
34	chr11:3831000-3844800	Weak transcription	Dnd41	blood
35	chr11:3831000-3845400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:3831000-3845400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:3831000-3845800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:3831000-3845800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:3831000-3845800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr11:3831000-3846200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:3831000-3847600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:3831200-3846200	Weak transcription	Hela-S3	cervix
43	chr11:3831200-3847800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:3831400-3846200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:3831600-3846200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:3831600-3847200	Weak transcription	HepG2	liver
47	chr11:3832000-3844600	Weak transcription	Esophagus	oesophagus
48	chr11:3832200-3841000	Weak transcription	NHEK	skin
49	chr11:3832400-3845600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:3832600-3842200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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