Variant report

Variant	esv3403194
Chromosome Location	chr7:127945462-127945866
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	CEBPB	chr7:127945691-127945856	A549	lung:	n/a	n/a
2	E2F4	chr7:127945326-127945481	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr7:127945512-127946419	K562	blood:	n/a	n/a
4	POLR2A	chr7:127945168-127946823	K562	blood:	n/a	n/a
5	POLR2A	chr7:127945716-127945844	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr7:127945623-127945929	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr7:127945508-127946971	K562	blood:	n/a	n/a
8	POLR2A	chr7:127945547-127945956	K562	blood:	n/a	n/a
9	POLR2A	chr7:127945793-127945834	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBM28-3	chr7:127937738-127947816	NONHSAT123178
2	lnc-RBM28-3	chr7:127944240-127946359	NONHSAT123179

Variant related genes	Relation type
ENSG00000242261	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs140090037	chr7:127945468-127945469	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs75083738	chr7:127945525-127945526	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs113713924	chr7:127945547-127945548	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs12706848	chr7:127945566-127945567	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs545937712	chr7:127945568-127945569	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs558235448	chr7:127945593-127945594	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs6948206	chr7:127945596-127945597	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs6947825	chr7:127945648-127945649	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs3208853	chr7:127945667-127945668	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs529919521	chr7:127945674-127945675	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs117583999	chr7:127945724-127945725	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs191126316	chr7:127945730-127945731	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs531047295	chr7:127945796-127945797	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs368012614	chr7:127945799-127945800	Weak transcription Strong transcription Genic enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs372281345	chr7:127945821-127945822	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs544394904	chr7:127945826-127945827	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs75252380	chr7:127945854-127945855	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs570541729	chr7:127945855-127945856	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Melanoma	18172304	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	17952124	CNVD
Wilms tumour	21544195	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Squamous cell cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	17387387	CNVD
Low-grade fibromyxoid sarcoma	0	CNVD
Oligodendroglial tumors	17285580	CNVD
Endometrial cancer	22040021	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	21264507	CNVD
Shwachman-Diamond syndrome	22934832	CNVD
Colorectal cancer	19359472	CNVD
Cutaneous malignant melanoma	17690212	CNVD
Leukemia	17361228	CNVD
Breast cancer	16461572	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Malignant melanoma	17690212	CNVD
Renal cell carcinoma	18592004	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Multiple myeloma	17550852	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Neurodevelopmental disorder	22521361	CNVD
abortions and stillbirths	19751515	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Burkitt''s lymphoma	19759907	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21858162	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	21251322	CNVD
Prostate cancer	16573809	CNVD
Medulloblastoma	16783165	CNVD
Biliary cancer	19435499	CNVD
Adenocarcinoma	21044232	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Melanoma	19188590	CNVD
Hepatocellular carcinoma	16785998	CNVD
Glioblastoma multiforme	18628472	CNVD
Basal cell lymphoma	21115979	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
abnormal development	18461090	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Malignant melanoma	17260012	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Prostate cancer	17217626	CNVD
Coffin-Siris syndrome	21572526	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Retinitis pigmentosa	17160897	CNVD
Colorblindness	17160897	CNVD
Multiple myeloma	16616336	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127917000-127945600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:127924600-127950000	Weak transcription	Psoas Muscle	Psoas
3	chr7:127930800-127949200	Weak transcription	Fetal Kidney	kidney
4	chr7:127938600-127945800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:127938800-127946000	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:127939400-127946200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:127939400-127962800	Weak transcription	Right Atrium	heart
8	chr7:127939600-127982200	Weak transcription	Stomach Mucosa	stomach
9	chr7:127940000-127946600	Weak transcription	Fetal Heart	heart
10	chr7:127940000-127980800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr7:127940200-127953000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr7:127940200-127953800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:127940200-127955600	Strong transcription	Fetal Stomach	stomach
14	chr7:127940400-127946200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:127940400-127955400	Strong transcription	Aorta	Aorta
16	chr7:127940400-127980000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr7:127940600-127946200	Weak transcription	HepG2	liver
18	chr7:127940600-127980000	Strong transcription	Liver	Liver
19	chr7:127940800-127946000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr7:127940800-127946400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:127940800-127955200	Strong transcription	Fetal Intestine Small	intestine
22	chr7:127940800-127955400	Strong transcription	Lung	lung
23	chr7:127940800-127963800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr7:127940800-127971400	Strong transcription	Fetal Brain Female	brain
25	chr7:127941000-127946000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:127941000-127954400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:127941000-127960400	Strong transcription	Primary T cells from cord blood	blood
28	chr7:127941200-127945600	Weak transcription	Brain Germinal Matrix	brain
29	chr7:127941400-127945600	Weak transcription	NHEK	skin
30	chr7:127941400-127946200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:127941400-127947400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr7:127941400-127955400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:127941400-127963400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:127941600-127945600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr7:127941600-127979600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr7:127941600-127980000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:127941800-127946600	Weak transcription	NH-A	brain
38	chr7:127941800-127949800	Weak transcription	Small Intestine	intestine
39	chr7:127941800-127954400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:127941800-127955600	Strong transcription	Thymus	Thymus
41	chr7:127942000-127946000	Weak transcription	HUVEC	blood vessel
42	chr7:127942000-127948800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr7:127942000-127980400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:127942000-127980600	Strong transcription	Fetal Muscle Leg	muscle
45	chr7:127942400-127945800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr7:127942600-127946000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr7:127942600-127979600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr7:127942800-127948400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr7:127943000-127961400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:127943000-127964800	Strong transcription	Cortex derived primary cultured neurospheres	brain

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