Variant report

Variant	esv2569136
Chromosome Location	chr4:100022259-100023911
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	chr4:100008642..100013321-chr4:100020625..100023682,5	MCF-7	breast:
2	chr4:100008526..100011791-chr4:100020409..100023760,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METAP1-3	chr4:100023514-100023816	NONHSAT097519
2	lnc-METAP1-3	chr4:100023514-100023816	ENSG00000246090

Variant related genes	Relation type
ENSG00000246090	chromatin interactions
ENSG00000197894	chromatin interactions

Extended variants
information (count: 54 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:54 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4396997	chr4:100022263-100022264	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs545470179	chr4:100022273-100022274	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs564142432	chr4:100022288-100022289	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs199574925	chr4:100022332-100022333	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs200214733	chr4:100022341-100022342	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs531888898	chr4:100022382-100022383	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs568389213	chr4:100022434-100022435	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs1453872	chr4:100022482-100022483	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs1453873	chr4:100022571-100022572	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs529520694	chr4:100022594-100022595	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs547866442	chr4:100022596-100022597	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs566175417	chr4:100022622-100022623	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs1453874	chr4:100022724-100022725	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs577876467	chr4:100022765-100022766	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs551470315	chr4:100022772-100022773	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs6815947	chr4:100022814-100022815	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs367971462	chr4:100022840-100022841	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs537724639	chr4:100022844-100022845	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs556428492	chr4:100022845-100022846	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs538898059	chr4:100022875-100022876	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs2851277	chr4:100022910-100022911	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs192432943	chr4:100022958-100022959	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs535752462	chr4:100022962-100022963	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs115729062	chr4:100022987-100022988	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs79300254	chr4:100023036-100023037	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs77161052	chr4:100023037-100023038	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs571792356	chr4:100023051-100023052	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs545910442	chr4:100023052-100023053	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs563897841	chr4:100023053-100023054	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs576002850	chr4:100023054-100023055	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs543717333	chr4:100023055-100023056	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs542454014	chr4:100023189-100023190	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs560677455	chr4:100023286-100023287	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs184346079	chr4:100023326-100023327	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs6148594	chr4:100023377-100023378	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs562371737	chr4:100023392-100023393	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs538584685	chr4:100023423-100023424	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs529662143	chr4:100023434-100023435	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs4699705	chr4:100023469-100023470	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs553898014	chr4:100023473-100023474	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs548002093	chr4:100023536-100023537	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
42	rs188053634	chr4:100023573-100023574	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs375054676	chr4:100023640-100023641	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs192838993	chr4:100023665-100023666	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs4699706	chr4:100023680-100023681	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs533248475	chr4:100023684-100023685	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs551875413	chr4:100023720-100023721	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs184554828	chr4:100023779-100023780	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs560694839	chr4:100023792-100023793	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs369589695	chr4:100023793-100023794	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Melanoma	20688739	CNVD
Gastric cancer	16891809	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100011400-100025800	Weak transcription	Esophagus	oesophagus
2	chr4:100011600-100025600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
4	chr4:100014400-100024000	Weak transcription	HMEC	breast
5	chr4:100020400-100024400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:100020600-100034800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:100020800-100022800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:100020800-100032800	Weak transcription	Fetal Intestine Small	intestine
9	chr4:100020800-100038600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:100021000-100023600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:100021000-100032200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:100021000-100041200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:100021400-100022400	Enhancers	K562	blood
14	chr4:100021400-100022600	Enhancers	Adipose Nuclei	Adipose
15	chr4:100021400-100022800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:100021400-100023000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:100021400-100025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:100021600-100022800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:100021600-100024400	Weak transcription	Small Intestine	intestine
20	chr4:100021800-100022400	Weak transcription	Placenta	Placenta
21	chr4:100022000-100022600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:100022000-100023000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:100022200-100024000	Weak transcription	Osteobl	bone
24	chr4:100022200-100024200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:100022200-100024600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:100022200-100025400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr4:100022400-100022600	Enhancers	Placenta	Placenta
28	chr4:100022600-100023600	Weak transcription	Placenta	Placenta
29	chr4:100022600-100024800	Weak transcription	Adipose Nuclei	Adipose
30	chr4:100022600-100025000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:100022800-100023800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:100022800-100024000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:100022800-100024000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:100023800-100025800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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