Variant report

Variant	nsv961340
Chromosome Location	chr2:114024257-114025895
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	chr2:114023172..114025279-chr2:114025318..114027200,2	MCF-7	breast:
2	chr2:114023172..114025279-chr2:114025318..114027200,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:114023053-114024550	ENSG00000189223
2	lnc-PSD4-1	chr2:114023053-114034158	ENSG00000189223.9
3	lnc-PSD4-1	chr2:114023053-114024587	ENSG00000189223

Variant related genes	Relation type
SLC39A6	miRNA target sites
C12orf35	miRNA target sites

Extended variants
information (count: 51 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:51 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs568173192	chr2:114024257-114024258	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs532679002	chr2:114024308-114024309	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs114934707	chr2:114024337-114024338	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs78987244	chr2:114024420-114024421	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs560070999	chr2:114024447-114024448	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs576837359	chr2:114024487-114024488	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs708633	chr2:114024505-114024506	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs560704055	chr2:114024566-114024567	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs7596648	chr2:114024594-114024595	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs549632651	chr2:114024605-114024606	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs562665993	chr2:114024625-114024626	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs372079076	chr2:114024826-114024827	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs531862876	chr2:114024842-114024843	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs7580516	chr2:114024846-114024847	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs191416057	chr2:114024910-114024911	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs571591731	chr2:114024923-114024924	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs534257083	chr2:114024945-114024946	Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs183820553	chr2:114025025-114025026	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs141072096	chr2:114025028-114025029	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs536850086	chr2:114025032-114025033	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs545907518	chr2:114025037-114025038	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs145669415	chr2:114025108-114025109	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs576786557	chr2:114025125-114025126	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs78439361	chr2:114025205-114025206	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs539008386	chr2:114025222-114025223	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs188756806	chr2:114025250-114025251	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs571950686	chr2:114025255-114025256	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs147742095	chr2:114025268-114025269	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs142582959	chr2:114025297-114025298	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs150239437	chr2:114025298-114025299	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs193280432	chr2:114025315-114025316	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs563191071	chr2:114025360-114025361	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs35324868	chr2:114025367-114025368	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs17043176	chr2:114025372-114025373	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs1446246	chr2:114025402-114025403	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs184978430	chr2:114025451-114025452	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs186682148	chr2:114025520-114025521	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs547994926	chr2:114025525-114025526	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs567744512	chr2:114025551-114025552	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs536769095	chr2:114025556-114025557	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs372005951	chr2:114025572-114025573	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs570301781	chr2:114025586-114025587	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs566440255	chr2:114025594-114025595	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs539276508	chr2:114025595-114025596	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs559011782	chr2:114025607-114025608	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs138840777	chr2:114025661-114025662	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs148958776	chr2:114025667-114025668	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs143694632	chr2:114025726-114025727	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs574192576	chr2:114025770-114025771	Genic enhancers Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs138218512	chr2:114025886-114025887	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Colorectal cancer	16272173	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
myoclonus epilepsy	18472482	CNVD
Benign familial neonatal-infantile seizures	18472482	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Colorectal cancer	16912164	CNVD
Ischaemic stroke	16980335	CNVD
Acute myeloid leukemia	18000384	CNVD
Nephronophthisis	17901113	CNVD
small cell lung cancer	20016488	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Hypoplastic left heart syndrome	22349727	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113999600-114028400	Weak transcription	Ovary	ovary
2	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
3	chr2:114016200-114028000	Weak transcription	Fetal Brain Female	brain
4	chr2:114016400-114026000	Weak transcription	Fetal Heart	heart
5	chr2:114019200-114026800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:114019400-114028200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:114019600-114026000	Weak transcription	Spleen	Spleen
8	chr2:114020000-114027800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:114021200-114028200	Strong transcription	Duodenum Mucosa	Duodenum
10	chr2:114021400-114024800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:114021600-114026200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:114021600-114028200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr2:114022000-114024600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:114022200-114026400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:114022200-114027600	Genic enhancers	Fetal Kidney	kidney
16	chr2:114022400-114025000	Strong transcription	Fetal Thymus	thymus
17	chr2:114023000-114026800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:114023000-114027200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:114023200-114026800	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:114023200-114039800	Weak transcription	Gastric	stomach
21	chr2:114023400-114025000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:114023400-114025000	Weak transcription	Pancreas	Pancrea
23	chr2:114023400-114027000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:114023600-114024600	Enhancers	HSMMtube	muscle
25	chr2:114023600-114026200	Genic enhancers	HSMM	muscle
26	chr2:114023800-114026200	Weak transcription	Adipose Nuclei	Adipose
27	chr2:114024000-114025000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:114024000-114025800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:114024000-114025800	Enhancers	Fetal Muscle Trunk	muscle
30	chr2:114024000-114030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:114024200-114026000	Weak transcription	Lung	lung
32	chr2:114024200-114026800	Enhancers	Fetal Muscle Leg	muscle
33	chr2:114024200-114029000	Weak transcription	Placenta	Placenta
34	chr2:114024600-114024800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:114024600-114025400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr2:114024600-114025600	Weak transcription	HSMMtube	muscle
37	chr2:114025000-114025200	Enhancers	Pancreas	Pancrea
38	chr2:114025000-114028200	Weak transcription	Fetal Thymus	thymus
39	chr2:114025400-114027800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:114025600-114026600	Enhancers	HSMMtube	muscle
41	chr2:114025800-114027000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr2:114025800-114028600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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