Variant report

Variant	esv3416930
Chromosome Location	chr4:7980394-7980991
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7978137..7980891-chr4:8001316..8003240,2	MCF-7	breast:
2	chr4:7972595..7975049-chr4:7979721..7982181,5	MCF-7	breast:
3	chr4:7973238..7976056-chr4:7980066..7981632,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371568681	chr4:7980413-7980414	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs559210036	chr4:7980446-7980447	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs34457410	chr4:7980451-7980452	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs538332903	chr4:7980469-7980470	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs553419595	chr4:7980472-7980473	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs571733395	chr4:7980500-7980501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs542167230	chr4:7980563-7980564	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs558291960	chr4:7980612-7980613	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs80235495	chr4:7980637-7980638	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs7699704	chr4:7980639-7980640	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs7699715	chr4:7980652-7980653	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs190954828	chr4:7980653-7980654	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs548419789	chr4:7980655-7980656	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs570530560	chr4:7980709-7980710	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs1878323	chr4:7980725-7980726	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs530126782	chr4:7980732-7980733	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs11734838	chr4:7980737-7980738	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs112327867	chr4:7980746-7980747	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs537729360	chr4:7980750-7980751	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs552533418	chr4:7980752-7980753	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs537951663	chr4:7980783-7980784	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs111668469	chr4:7980822-7980823	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs571042551	chr4:7980831-7980832	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs150648856	chr4:7980880-7980881	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs553450447	chr4:7980886-7980887	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs571765784	chr4:7980903-7980904	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs368362078	chr4:7980940-7980941	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs535887192	chr4:7980969-7980970	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs538705964	chr4:7980971-7980972	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Schizophrenia	22241247	CNVD
Autosomal-dominant microtia	18179897	CNVD
Glioma	17123091	CNVD
Colorectal cancer	20459617	CNVD
Breast cancer	17133270	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
2	chr4:7972200-7980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:7973600-7980400	Weak transcription	Ovary	ovary
4	chr4:7974400-7989400	Weak transcription	Gastric	stomach
5	chr4:7974600-7980400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:7975000-7980400	Weak transcription	Pancreas	Pancrea
7	chr4:7975600-7983600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:7975600-7984800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:7975800-7981600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:7975800-7988400	Weak transcription	Aorta	Aorta
11	chr4:7975800-8004800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:7976000-7981200	Weak transcription	Osteobl	bone
13	chr4:7976000-7988000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:7977600-7980400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:7978200-7980600	Weak transcription	Spleen	Spleen
16	chr4:7978400-7980600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:7978800-7987800	Weak transcription	Fetal Kidney	kidney
18	chr4:7978800-8006000	Weak transcription	Brain Anterior Caudate	brain
19	chr4:7979000-7982000	Enhancers	HMEC	breast
20	chr4:7979200-7981800	Enhancers	Fetal Intestine Small	intestine
21	chr4:7979600-7981000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr4:7979600-7981600	Enhancers	Duodenum Mucosa	Duodenum
23	chr4:7979600-7981800	Enhancers	Fetal Intestine Large	intestine
24	chr4:7979600-7982000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr4:7979600-7982000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:7979600-7982000	Enhancers	HSMMtube	muscle
27	chr4:7979600-7982200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:7979600-8011400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr4:7979800-7980400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:7979800-7980400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:7979800-7980400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr4:7979800-7980400	Enhancers	NHLF	lung
33	chr4:7979800-7980600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:7979800-7980600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:7979800-7980800	Enhancers	Fetal Muscle Leg	muscle
36	chr4:7979800-7980800	Enhancers	Fetal Stomach	stomach
37	chr4:7979800-7980800	Enhancers	Stomach Smooth Muscle	stomach
38	chr4:7979800-7980800	Flanking Active TSS	Hela-S3	cervix
39	chr4:7979800-7981000	Enhancers	Fetal Lung	lung
40	chr4:7979800-7981000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr4:7979800-7981200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr4:7979800-7981200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:7979800-7981400	Enhancers	Fetal Heart	heart
44	chr4:7979800-7981600	Enhancers	Esophagus	oesophagus
45	chr4:7979800-7981600	Enhancers	Placenta	Placenta
46	chr4:7979800-7981800	Enhancers	Fetal Thymus	thymus
47	chr4:7979800-7982000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:7979800-7982000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:7979800-7982000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr4:7979800-7982000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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