Variant report

Variant	nsv1062302
Chromosome Location	chr19:23721174-23743106
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	chr19:23716991..23718899-chr19:23719198..23721188,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPSAP58-1	chr19:23740397-23740511	XLOC_013022
2	lnc-RPSAP58-1	chr19:23741124-23741230	XLOC_013022
3	lnc-RPSAP58-1	chr19:23741124-23741642	XLOC_013022
4	lnc-RPSAP58-1	chr19:23734519-23734611	XLOC_013022

Variant related genes	Relation type
SKIV2L2	miRNA target sites
MASTL	miRNA target sites
USP6NL	miRNA target sites
NEO1	miRNA target sites

Extended variants
information (count: 1233 )
Associated
traits (count: 44 )

Variant overlapped rSNPs/rCNVs (count:1233 , 50 per page) page: 1 2 3 4 5 6 7 ... 25

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1088407	chr19:23721174-23721175	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs375482276	chr19:23721182-23721183	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs541850349	chr19:23721183-23721184	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs560684225	chr19:23721192-23721193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs192643469	chr19:23721202-23721203	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs185430123	chr19:23721209-23721210	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs188442176	chr19:23721212-23721213	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs111291970	chr19:23721225-23721226	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs550487277	chr19:23721248-23721249	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs569040167	chr19:23721257-23721258	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs529731771	chr19:23721321-23721322	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs532671273	chr19:23721334-23721335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs112018949	chr19:23721335-23721336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs559769030	chr19:23721394-23721395	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs552274891	chr19:23721404-23721405	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs571084826	chr19:23721465-23721466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs538426571	chr19:23721491-23721492	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs528508426	chr19:23721492-23721493	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs145277860	chr19:23721497-23721498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs548561190	chr19:23721525-23721526	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs386808099	chr19:23721535-23721536	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs1088406	chr19:23721537-23721538	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs553891302	chr19:23721545-23721546	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs572076456	chr19:23721553-23721554	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs193053911	chr19:23721578-23721579	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs564217210	chr19:23721629-23721630	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs142794838	chr19:23721636-23721637	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs544065242	chr19:23721644-23721645	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs184724924	chr19:23721647-23721648	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs529947453	chr19:23721663-23721664	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs151047483	chr19:23721687-23721688	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs559907437	chr19:23721719-23721720	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs189168120	chr19:23721720-23721721	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs552335711	chr19:23721733-23721734	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs570554763	chr19:23721770-23721771	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs538489041	chr19:23721771-23721772	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs35058520	chr19:23721793-23721794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs146862625	chr19:23721795-23721796	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs371866052	chr19:23721821-23721822	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs534731630	chr19:23721836-23721837	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs114221559	chr19:23721845-23721846	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs535792026	chr19:23721908-23721909	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs12608824	chr19:23721964-23721965	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs572132600	chr19:23721989-23721990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs191442046	chr19:23722000-23722001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557869804	chr19:23722008-23722009	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs199795630	chr19:23722048-23722049	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs372603918	chr19:23722116-23722117	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs374058465	chr19:23722120-23722121	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs183608637	chr19:23722135-23722136	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:44)

Disease	PMID	Source
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Prostate cancer	16573809	CNVD
Chordoma	18071362	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myelofibrosis	22110671	CNVD
Cancer	21183584	CNVD
Colorectal cancer	20459617	CNVD
Ductal carcinoma	22052326	CNVD
Cancer	20164920	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23720000-23722200	Enhancers	Placenta Amnion	Placenta Amnion
2	chr19:23720800-23722000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:23721000-23728400	Enhancers	Placenta	Placenta
4	chr19:23722000-23723600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:23722200-23722400	Enhancers	Stomach Mucosa	stomach
6	chr19:23722200-23723200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:23722400-23723000	Weak transcription	Stomach Mucosa	stomach
8	chr19:23722400-23724000	Enhancers	Dnd41	blood
9	chr19:23723000-23723800	Enhancers	Stomach Mucosa	stomach
10	chr19:23723200-23725600	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:23723600-23727200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:23725600-23729600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:23727200-23727400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:23727400-23728200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:23728200-23728600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:23728400-23729400	Weak transcription	Placenta	Placenta
17	chr19:23728600-23730000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:23729400-23730400	Enhancers	Placenta	Placenta
19	chr19:23729600-23730400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:23730000-23730200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr19:23730000-23730400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:23730400-23730600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:23730400-23731400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:23730400-23731600	Weak transcription	Placenta	Placenta
25	chr19:23730400-23732000	Enhancers	NHEK	skin
26	chr19:23730600-23734200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:23730800-23731000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr19:23731000-23733800	Enhancers	HMEC	breast
29	chr19:23731200-23733000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr19:23731400-23733800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr19:23731600-23732600	Enhancers	Hela-S3	cervix
32	chr19:23731600-23733800	Enhancers	Placenta	Placenta
33	chr19:23731600-23734400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:23732000-23732200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:23732000-23732400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:23732000-23732800	Flanking Active TSS	NHEK	skin
37	chr19:23732600-23733000	Active TSS	Hela-S3	cervix
38	chr19:23732800-23734000	Enhancers	NHEK	skin
39	chr19:23733000-23734000	Enhancers	Hela-S3	cervix
40	chr19:23733800-23737200	Weak transcription	Placenta	Placenta
41	chr19:23733800-23737400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:23734000-23734400	Weak transcription	Hela-S3	cervix
43	chr19:23734200-23737000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:23734400-23734600	Enhancers	Hela-S3	cervix
45	chr19:23734600-23736400	Weak transcription	Hela-S3	cervix
46	chr19:23736200-23736800	ZNF genes & repeats	HMEC	breast
47	chr19:23736400-23737400	Enhancers	Hela-S3	cervix
48	chr19:23736800-23738400	Enhancers	HMEC	breast
49	chr19:23736800-23738400	Enhancers	NHEK	skin
50	chr19:23737000-23737800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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