Variant report

Variant	nsv525326
Chromosome Location	chr12:25187170-25190791
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:25188438-25188786	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr12:25188472-25188813	H1-neurons	neurons:	n/a	n/a
3	ZKSCAN1	chr12:25187654-25187752	Hela-S3	cervix:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYRM5-3	chr12:25189519-25189620	NONHSAT027338
2	lnc-LYRM5-3	chr12:25188414-25188721	NONHSAT027338

Variant related genes	Relation type
LRMP	TF binding region

Extended variants
information (count: 139 )
Associated
traits (count: 95 )

Variant overlapped rSNPs/rCNVs (count:139 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs699053	chr12:25187170-25187171	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs558728070	chr12:25187177-25187178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs565364209	chr12:25187216-25187217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs570685166	chr12:25187312-25187313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs181022909	chr12:25187321-25187322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563984568	chr12:25187337-25187338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs374622325	chr12:25187343-25187344	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs368727941	chr12:25187346-25187347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs553424731	chr12:25187348-25187349	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs575055928	chr12:25187368-25187369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs542308673	chr12:25187437-25187438	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs529529914	chr12:25187464-25187465	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs183546155	chr12:25187473-25187474	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs543572356	chr12:25187491-25187492	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs368251368	chr12:25187492-25187493	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs113570364	chr12:25187518-25187519	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs76399914	chr12:25187584-25187585	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs543513661	chr12:25187592-25187593	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs144825023	chr12:25187593-25187594	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs374220023	chr12:25187605-25187606	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188619846	chr12:25187642-25187643	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs148407081	chr12:25187648-25187649	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs602789	chr12:25187677-25187678	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs145012644	chr12:25187692-25187693	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs529990771	chr12:25187700-25187701	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs181064797	chr12:25187709-25187710	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs565917348	chr12:25187739-25187740	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs61914763	chr12:25187766-25187767	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs530933807	chr12:25187779-25187780	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs185901918	chr12:25187788-25187789	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs570909748	chr12:25187833-25187834	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs191639448	chr12:25187838-25187839	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs547170675	chr12:25187845-25187846	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs568702857	chr12:25187861-25187862	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs2035546	chr12:25187871-25187872	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs552058224	chr12:25187959-25187960	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs147596429	chr12:25188004-25188005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs576070654	chr12:25188042-25188043	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs371603211	chr12:25188048-25188049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs537024923	chr12:25188061-25188062	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs558712047	chr12:25188102-25188103	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs140400033	chr12:25188211-25188212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs540907453	chr12:25188333-25188334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs559457058	chr12:25188389-25188390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs181708425	chr12:25188402-25188403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs532086189	chr12:25188410-25188411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs563950075	chr12:25188429-25188430	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs4963844	chr12:25188464-25188465	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs537620318	chr12:25188466-25188467	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs555668579	chr12:25188471-25188472	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:95)

Disease	PMID	Source
Malignant germ cell tumour	17285132	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	17133270	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	16397240	CNVD
Neurodevelopmental disorder	22521361	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	21509527	CNVD
Autism	22102821	CNVD
Follicular lymphoma	18703704	CNVD
Lung cancer	18438408	CNVD
Lung cancer	21911935	CNVD
Breast cancer	22048815	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Heart disease	21282601	CNVD
Ovarian cancer	20844748	CNVD
Lung cancer	17925434	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Gastric cancer	24379144	CNVD
Gastric cancer	19545448	CNVD
Lung cancer	20031968	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung adenocarcinoma	19826477	CNVD
Lung cancer	19525976	CNVD
Lung cancer	19826477	CNVD
Non-small cell lung cancer	19451690	CNVD
Non-small cell lung cancer	17504988	CNVD
Bipolar disorder	19114987	CNVD
Lung cancer	19671679	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	21364760	CNVD
Lung cancer	21569311	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Lung adenocarcinoma	17982442	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Ovarian cancer	21720365	CNVD
Cancer	17699850	CNVD
Ovarian cancer	17699850	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164920	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25179200-25193600	Weak transcription	GM12878-XiMat	blood
2	chr12:25187400-25187800	Enhancers	Fetal Brain Female	brain
3	chr12:25187400-25188000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:25187600-25187800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:25187600-25187800	Bivalent Enhancer	Osteobl	bone
6	chr12:25187600-25188000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
7	chr12:25188800-25189000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:25189000-25190800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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