Variant report

Variant	esv1840619
Chromosome Location	chr1:223017325-223023604
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	chr1:222982122..222983710-chr1:223020117..223022019,2	MCF-7	breast:
2	chr1:222988083..222989956-chr1:223020235..223022517,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM177B-4	chr1:223021225-223021478	NONHSAT009719
2	lnc-FAM177B-4	chr1:223020681-223021478	l_198_chr1:223020680-223033680_testes

Variant related genes	Relation type
ENSG00000154309	chromatin interactions
ENSG00000228106	chromatin interactions

Extended variants
information (count: 220 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:220 , 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	rs534149560	chr1:223017325-223017326	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs555794573	chr1:223017328-223017329	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs546758799	chr1:223017356-223017357	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs534202887	chr1:223017361-223017362	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs574241421	chr1:223017377-223017378	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs150589362	chr1:223017385-223017386	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs149291940	chr1:223017399-223017400	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs71301073	chr1:223017404-223017405	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs201838855	chr1:223017405-223017406	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs567977458	chr1:223017416-223017417	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs181912642	chr1:223017495-223017496	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs139599794	chr1:223017578-223017579	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs575445873	chr1:223017620-223017621	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs34791822	chr1:223017621-223017622	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs564119623	chr1:223017681-223017682	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs34344184	chr1:223017770-223017771	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs540187244	chr1:223017776-223017777	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs549845361	chr1:223017787-223017788	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs561854114	chr1:223017810-223017811	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs529162668	chr1:223017812-223017813	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs141970608	chr1:223017819-223017820	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs562331070	chr1:223017887-223017888	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs533296954	chr1:223017970-223017971	Enhancers Flanking Active TSS Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs551464411	chr1:223018029-223018030	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs566914793	chr1:223018034-223018035	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs72742224	chr1:223018046-223018047	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	mRNA abundance
27	rs544816157	chr1:223018055-223018056	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs146293140	chr1:223018140-223018141	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs185101320	chr1:223018188-223018189	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs34264264	chr1:223018199-223018200	Enhancers Flanking Active TSS Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs538514911	chr1:223018263-223018264	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs2378613	chr1:223018270-223018271	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs189372091	chr1:223018277-223018278	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs539190735	chr1:223018312-223018313	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs35970216	chr1:223018323-223018324	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs572865560	chr1:223018331-223018332	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs539873561	chr1:223018336-223018337	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs181782581	chr1:223018386-223018387	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs573890247	chr1:223018389-223018390	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs573761401	chr1:223018405-223018406	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs560513377	chr1:223018426-223018427	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs544097789	chr1:223018463-223018464	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs139644947	chr1:223018468-223018469	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs553507033	chr1:223018491-223018492	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs144286518	chr1:223018509-223018510	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs551125346	chr1:223018511-223018512	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs560405392	chr1:223018576-223018577	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs145379615	chr1:223018610-223018611	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs527765302	chr1:223018611-223018612	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs35270996	chr1:223018621-223018622	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Acute myeloid leukemia	17268525	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	20808228	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Leukoplakia	24403051	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222989400-223026800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:222990400-223027400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:223002600-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:223007800-223017400	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:223010800-223027600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:223013600-223030800	Weak transcription	Ovary	ovary
7	chr1:223015800-223017400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:223016000-223017400	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:223016000-223018400	Enhancers	Stomach Mucosa	stomach
10	chr1:223016200-223017600	Enhancers	Rectal Smooth Muscle	rectum
11	chr1:223016400-223018200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:223016800-223017400	Enhancers	Liver	Liver
13	chr1:223016800-223017400	Enhancers	Fetal Intestine Large	intestine
14	chr1:223016800-223017400	Enhancers	Fetal Intestine Small	intestine
15	chr1:223016800-223017400	Enhancers	HepG2	liver
16	chr1:223016800-223018400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:223016800-223018400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:223016800-223018400	Enhancers	A549	lung
19	chr1:223016800-223019400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:223017000-223017400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:223017000-223018200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:223017000-223018200	Enhancers	Fetal Kidney	kidney
23	chr1:223017000-223018400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr1:223017000-223018600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr1:223017000-223018800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:223017000-223019200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr1:223017200-223017400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr1:223017200-223017400	Enhancers	Aorta	Aorta
29	chr1:223017200-223017600	Enhancers	Small Intestine	intestine
30	chr1:223017200-223017800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr1:223017200-223018200	Enhancers	Fetal Lung	lung
32	chr1:223017200-223018400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr1:223017400-223017600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr1:223017400-223017600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:223017400-223017600	Enhancers	Colon Smooth Muscle	Colon
36	chr1:223017400-223017800	Enhancers	Brain Anterior Caudate	brain
37	chr1:223017400-223017800	Active TSS	NHDF-Ad	bronchial
38	chr1:223017400-223018400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:223017400-223019800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:223017600-223017800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:223017600-223018000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:223017600-223019400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:223017600-223042400	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:223017800-223018000	Flanking Active TSS	NHDF-Ad	bronchial
45	chr1:223017800-223018200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:223017800-223018200	Weak transcription	Brain Anterior Caudate	brain
47	chr1:223017800-223018600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:223018000-223018400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:223018000-223018400	Enhancers	NHDF-Ad	bronchial
50	chr1:223018200-223018400	Enhancers	Brain Anterior Caudate	brain

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