Variant report

Variant	esv3410033
Chromosome Location	chr12:42478138-42478733
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42477798..42480028-chr12:42482266..42483853,2	K562	blood:
2	chr12:42471227..42474055-chr12:42478487..42480397,2	K562	blood:
3	chr12:42477955..42479692-chr12:42628844..42631560,2	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	GXYLT1	hsa-miR-124-3p	chr12:42478397-42478414
2	GXYLT1	hsa-miR-124-3p	chr12:42478403-42478396

Variant related genes	Relation type
ENSG00000222884	chromatin interactions
ENSG00000015153	chromatin interactions

Extended variants
information (count: 81 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:81 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs74237799	chr12:42478139-42478140	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs541987508	chr12:42478154-42478155	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs80010544	chr12:42478157-42478158	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs560608145	chr12:42478162-42478163	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs78809998	chr12:42478170-42478171	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs79038967	chr12:42478172-42478173	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs80066129	chr12:42478177-42478178	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs76266834	chr12:42478182-42478183	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs150289475	chr12:42478186-42478187	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs527701322	chr12:42478211-42478212	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs552112460	chr12:42478213-42478214	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs78256920	chr12:42478223-42478224	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs370749394	chr12:42478241-42478242	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs76213508	chr12:42478245-42478246	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs532319661	chr12:42478246-42478247	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs79916609	chr12:42478248-42478249	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs371779065	chr12:42478263-42478264	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs11399537	chr12:42478264-42478265	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs71779450	chr12:42478265-42478266	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs74825547	chr12:42478267-42478268	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs77510937	chr12:42478276-42478277	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs74365263	chr12:42478281-42478282	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs550176506	chr12:42478287-42478288	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs75265726	chr12:42478296-42478297	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs568989443	chr12:42478297-42478298	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs77817250	chr12:42478307-42478308	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs77977555	chr12:42478308-42478309	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs78267080	chr12:42478315-42478316	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs547998608	chr12:42478316-42478317	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs75382603	chr12:42478319-42478320	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs73280049	chr12:42478351-42478352	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs149476151	chr12:42478354-42478355	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs74079513	chr12:42478371-42478372	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs74077811	chr12:42478376-42478377	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs533558974	chr12:42478405-42478406	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a
36	rs558634413	chr12:42478409-42478410	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a
37	rs576899720	chr12:42478410-42478411	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a
38	rs200969639	chr12:42478412-42478413	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	Overlapped CNVs	n/a
39	rs844046	chr12:42478413-42478414	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs76529577	chr12:42478417-42478418	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs76759461	chr12:42478421-42478422	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs74537202	chr12:42478426-42478427	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs76928826	chr12:42478428-42478429	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs79248724	chr12:42478430-42478431	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs80039249	chr12:42478432-42478433	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs76954354	chr12:42478435-42478436	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs201960212	chr12:42478438-42478439	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs78734766	chr12:42478452-42478453	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs80231759	chr12:42478461-42478462	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs78498412	chr12:42478462-42478463	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	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
Ewing''s sarcoma	21437220	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
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42464600-42484000	Weak transcription	HSMM	muscle
2	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
3	chr12:42469400-42491800	Weak transcription	Ovary	ovary
4	chr12:42470400-42479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:42470400-42484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:42470600-42484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:42470800-42480000	Weak transcription	A549	lung
9	chr12:42470800-42485600	Weak transcription	Aorta	Aorta
10	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:42471200-42479000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:42471200-42483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:42471400-42485600	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:42471800-42483400	Weak transcription	Fetal Stomach	stomach
15	chr12:42471800-42486600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
17	chr12:42472200-42487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:42472800-42489000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:42473400-42480200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:42473600-42479200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:42473600-42481000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:42473600-42483600	Weak transcription	Adipose Nuclei	Adipose
23	chr12:42473600-42484000	Weak transcription	HUVEC	blood vessel
24	chr12:42473600-42484200	Weak transcription	Primary T cells from cord blood	blood
25	chr12:42473800-42484000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:42474000-42479000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:42474000-42479400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:42474000-42484000	Weak transcription	NH-A	brain
29	chr12:42474000-42484200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:42474000-42496000	Weak transcription	Fetal Intestine Large	intestine
31	chr12:42474200-42479600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:42474200-42484000	Weak transcription	Osteobl	bone
33	chr12:42474200-42486000	Weak transcription	GM12878-XiMat	blood
34	chr12:42474200-42487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:42474200-42490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:42474400-42480400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:42474600-42479400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:42474600-42479400	Weak transcription	Dnd41	blood
39	chr12:42474600-42479800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:42474600-42480600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:42474600-42482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
44	chr12:42474800-42487600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:42474800-42487600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:42474800-42491800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:42475000-42484200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:42475000-42491800	Weak transcription	Brain Substantia Nigra	brain
49	chr12:42475400-42485600	Weak transcription	Left Ventricle	heart
50	chr12:42475600-42479400	Weak transcription	Monocytes-CD14+_RO01746	blood

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