Variant report

Variant	esv3419447
Chromosome Location	chr4:3663554-3666552
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3654292..3658387-chr4:3660533..3665112,5	MCF-7	breast:
2	chr4:3666324..3668294-chr4:3766330..3768153,2	MCF-7	breast:
3	chr4:3658292..3659804-chr4:3662299..3664956,2	K562	blood:
4	chr4:3662225..3664999-chr4:3667626..3669601,2	MCF-7	breast:
5	chr4:3665678..3668678-chr4:3669594..3672149,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184160	chromatin interactions

Extended variants
information (count: 223 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:223 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs146238271	chr4:3663556-3663557	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs537725027	chr4:3663557-3663558	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs557096017	chr4:3663558-3663559	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs71608297	chr4:3663569-3663570	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs372172371	chr4:3663570-3663571	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs59070560	chr4:3663582-3663583	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs559418869	chr4:3663626-3663627	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs575536685	chr4:3663627-3663628	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs571951489	chr4:3663635-3663636	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs16844729	chr4:3663641-3663642	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs112337648	chr4:3663647-3663648	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs11730367	chr4:3663657-3663658	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs177771	chr4:3663721-3663722	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs13106594	chr4:3663758-3663759	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs551318942	chr4:3663772-3663773	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs563139368	chr4:3663801-3663802	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs76409495	chr4:3663819-3663820	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs177770	chr4:3663825-3663826	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs56766959	chr4:3663857-3663858	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs535258065	chr4:3663858-3663859	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs61680191	chr4:3663859-3663860	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs187976922	chr4:3663872-3663873	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs537355787	chr4:3663885-3663886	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs373806151	chr4:3663889-3663890	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs557586980	chr4:3663894-3663895	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs148465437	chr4:3663895-3663896	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs536237304	chr4:3663909-3663910	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs375773339	chr4:3663926-3663927	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs533947784	chr4:3663939-3663940	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs190890433	chr4:3663944-3663945	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs572979329	chr4:3663945-3663946	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs16844732	chr4:3663948-3663949	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs183137920	chr4:3663966-3663967	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs577719473	chr4:3663972-3663973	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs543397089	chr4:3663974-3663975	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs550889894	chr4:3664006-3664007	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs58650467	chr4:3664019-3664020	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs78033956	chr4:3664063-3664064	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs542620557	chr4:3664114-3664115	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs115430747	chr4:3664118-3664119	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs74504804	chr4:3664125-3664126	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs188368164	chr4:3664128-3664129	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs139231354	chr4:3664143-3664144	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs531132903	chr4:3664164-3664165	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs145364135	chr4:3664165-3664166	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs79972233	chr4:3664182-3664183	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs566851920	chr4:3664193-3664194	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs177769	chr4:3664206-3664207	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs552971903	chr4:3664211-3664212	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs116551326	chr4:3664224-3664225	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
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
Urothelial carcinoma	21177765	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
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Lung cancer	18438408	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3657400-3663800	Bivalent Enhancer	Fetal Muscle Leg	muscle
2	chr4:3658400-3664400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr4:3658600-3678000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:3661400-3663800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:3662200-3664000	Enhancers	Fetal Brain Male	brain
6	chr4:3662400-3663800	Enhancers	Brain Germinal Matrix	brain
7	chr4:3662600-3664600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr4:3662600-3664600	Weak transcription	Fetal Kidney	kidney
9	chr4:3662800-3664200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:3662800-3666400	Weak transcription	Brain Anterior Caudate	brain
11	chr4:3663200-3664400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr4:3663400-3663600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:3663600-3663800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:3663600-3663800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
15	chr4:3663800-3664200	Weak transcription	Brain Germinal Matrix	brain
16	chr4:3664000-3664400	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr4:3664200-3664400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:3664200-3664400	Enhancers	Brain Germinal Matrix	brain
19	chr4:3664400-3664800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:3664400-3668400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:3664400-3668400	Weak transcription	Brain Germinal Matrix	brain
22	chr4:3664600-3665200	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
23	chr4:3664600-3665400	ZNF genes & repeats	Fetal Kidney	kidney
24	chr4:3665400-3665600	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:3665400-3667000	Weak transcription	Fetal Kidney	kidney
26	chr4:3665800-3667400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:3666000-3666200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr4:3666400-3667200	Enhancers	Brain Anterior Caudate	brain

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