Variant report

Variant	nsv947893
Chromosome Location	chr10:43368929-43376338
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43370478..43372425-chr10:43586111..43588010,2	MCF-7	breast:
2	chr10:43369343..43371320-chr10:43469616..43472165,2	MCF-7	breast:
3	chr10:43366376..43368491-chr10:43369258..43371520,2	MCF-7	breast:
4	chr10:43368762..43369411-chr10:43606065..43606957,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BMS1-1	chr10:43367957-43369508	XLOC_008465

Variant related genes	Relation type
ENSG00000234944	chromatin interactions

Extended variants
information (count: 375 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:375 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs75383817	chr10:43368951-43368952	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs80287407	chr10:43369011-43369012	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs147372854	chr10:43369019-43369020	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs200576854	chr10:43369025-43369026	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs539641020	chr10:43369070-43369071	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs558068854	chr10:43369075-43369076	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs2744074	chr10:43369124-43369125	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs576342060	chr10:43369139-43369140	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs544222173	chr10:43369208-43369209	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs139530599	chr10:43369240-43369241	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs573471710	chr10:43369244-43369245	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs574487703	chr10:43369266-43369267	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs541905013	chr10:43369267-43369268	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs182796433	chr10:43369278-43369279	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs572318949	chr10:43369286-43369287	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs546013575	chr10:43369288-43369289	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs188309401	chr10:43369334-43369335	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs2744073	chr10:43369352-43369353	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs550170893	chr10:43369359-43369360	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs114044907	chr10:43369390-43369391	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs529313506	chr10:43369394-43369395	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs529399108	chr10:43369399-43369400	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs547440515	chr10:43369415-43369416	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs145254399	chr10:43369450-43369451	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs190470745	chr10:43369525-43369526	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs551537239	chr10:43369543-43369544	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs147604972	chr10:43369555-43369556	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs544365266	chr10:43369598-43369599	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs371054327	chr10:43369600-43369601	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs369702693	chr10:43369601-43369602	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs564181450	chr10:43369645-43369646	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs140885410	chr10:43369646-43369647	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs533201862	chr10:43369647-43369648	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs149745094	chr10:43369668-43369669	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs574304102	chr10:43369687-43369688	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs535438132	chr10:43369695-43369696	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs145211751	chr10:43369707-43369708	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs572159297	chr10:43369711-43369712	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs546050558	chr10:43369745-43369746	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs367874069	chr10:43369748-43369749	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs527441057	chr10:43369876-43369877	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs2744072	chr10:43369916-43369917	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs149132070	chr10:43369919-43369920	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs543313052	chr10:43369998-43369999	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs374483559	chr10:43369999-43370000	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs183058281	chr10:43370001-43370002	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs547370641	chr10:43370043-43370044	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs559449216	chr10:43370055-43370056	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs533224098	chr10:43370070-43370071	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs551571870	chr10:43370080-43370081	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Lung cancer	18438408	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
Mental retardation	21062444	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	22241247	CNVD
Intellectual disability	21811512	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Obesity	21956041	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21948486	CNVD
Dysmorphic features	21948486	CNVD
Epilepsy	21948486	CNVD
Breast cancer	21509527	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43362200-43370600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:43363200-43371400	Weak transcription	Fetal Heart	heart
3	chr10:43365000-43370400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:43367200-43370800	Weak transcription	NHDF-Ad	bronchial
5	chr10:43367200-43373000	Weak transcription	Spleen	Spleen
6	chr10:43367800-43370200	Weak transcription	Fetal Lung	lung
7	chr10:43367800-43370600	Weak transcription	Colonic Mucosa	Colon
8	chr10:43367800-43370800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr10:43368000-43369200	Weak transcription	Lung	lung
10	chr10:43369200-43372400	Enhancers	Lung	lung
11	chr10:43369400-43369600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:43369800-43371200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr10:43370200-43372400	Enhancers	Fetal Lung	lung
14	chr10:43370200-43372400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr10:43370400-43370800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr10:43370400-43371200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:43370600-43370800	Bivalent Enhancer	Fetal Stomach	stomach
18	chr10:43370600-43371000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr10:43370600-43371200	Enhancers	Colonic Mucosa	Colon
20	chr10:43370600-43371200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr10:43370600-43371400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:43370600-43371800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr10:43370800-43371000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:43370800-43371000	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr10:43370800-43371200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:43370800-43371200	Enhancers	Gastric	stomach
27	chr10:43370800-43371400	Bivalent Enhancer	Placenta	Placenta
28	chr10:43370800-43371400	Enhancers	NHDF-Ad	bronchial
29	chr10:43370800-43371800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr10:43370800-43371800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:43370800-43371800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr10:43370800-43371800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:43370800-43371800	Enhancers	Brain Anterior Caudate	brain
34	chr10:43370800-43371800	Enhancers	Brain Cingulate Gyrus	brain
35	chr10:43370800-43372400	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr10:43370800-43372600	Enhancers	Fetal Stomach	stomach
37	chr10:43371000-43371200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr10:43371000-43371200	Enhancers	Liver	Liver
39	chr10:43371000-43371200	Active TSS	Brain Substantia Nigra	brain
40	chr10:43371000-43371400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr10:43371000-43371400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:43371000-43371400	Enhancers	Brain Angular Gyrus	brain
43	chr10:43371000-43371600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr10:43371000-43371600	Enhancers	HSMMtube	muscle
45	chr10:43371000-43371800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr10:43371000-43371800	Enhancers	Adipose Nuclei	Adipose
47	chr10:43371000-43371800	Enhancers	Brain Hippocampus Middle	brain
48	chr10:43371000-43371800	Enhancers	A549	lung
49	chr10:43371200-43371400	Enhancers	Left Ventricle	heart
50	chr10:43371200-43371600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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