Variant report

Variant	nsv523253
Chromosome Location	chr1:179516072-179518459
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	chr1:179517896-179517946	HepG2	liver:	n/a	chr1:179517919-179517930
2	FOXA1	chr1:179518446-179518623	T-47D	breast:	n/a	n/a
3	GATA3	chr1:179518237-179518593	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179510162..179513711-chr1:179513904..179516885,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-1	chr1:179517817-179518057	ENSG00000261250.1

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000261250	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:73 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1410587	chr1:179516072-179516073	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs963062	chr1:179516281-179516282	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs536850163	chr1:179516336-179516337	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs192431420	chr1:179516362-179516363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs570366157	chr1:179516375-179516376	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs16854276	chr1:179516547-179516548	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs558717353	chr1:179516583-179516584	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs572385855	chr1:179516594-179516595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs184091713	chr1:179516603-179516604	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs7541890	chr1:179516614-179516615	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs7541899	chr1:179516646-179516647	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs75105432	chr1:179516648-179516649	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs10494516	chr1:179516716-179516717	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs10913815	chr1:179516738-179516739	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs115257398	chr1:179516749-179516750	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs371961631	chr1:179516753-179516754	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs559113541	chr1:179516875-179516876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs7519700	chr1:179517003-179517004	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs114993777	chr1:179517032-179517033	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs151222822	chr1:179517067-179517068	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs117335445	chr1:179517080-179517081	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs550442483	chr1:179517133-179517134	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs10494515	chr1:179517140-179517141	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs6662262	chr1:179517163-179517164	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs188531575	chr1:179517170-179517171	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs566210948	chr1:179517174-179517175	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs371062675	chr1:179517183-179517184	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs140371861	chr1:179517189-179517190	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs181341060	chr1:179517201-179517202	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs548490268	chr1:179517234-179517235	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs537139361	chr1:179517274-179517275	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs374229967	chr1:179517311-179517312	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs928016	chr1:179517366-179517367	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs149986766	chr1:179517416-179517417	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs11586725	chr1:179517466-179517467	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs146541272	chr1:179517472-179517473	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs541810683	chr1:179517479-179517480	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs561663102	chr1:179517493-179517494	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs530660006	chr1:179517514-179517515	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs928017	chr1:179517521-179517522	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs185902374	chr1:179517544-179517545	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs115613178	chr1:179517557-179517558	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs560467371	chr1:179517630-179517631	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs552455629	chr1:179517646-179517647	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs11577538	chr1:179517714-179517715	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs114151450	chr1:179517827-179517828	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs113974865	chr1:179517831-179517832	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs16854292	chr1:179517833-179517834	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs568097857	chr1:179517848-179517849	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs1410588	chr1:179517860-179517861	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:88)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	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
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
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	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
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	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
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Glioblastoma multiforme	17369134	CNVD
Cancer	17440070	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	16397240	CNVD
Mental retardation	17847001	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	23248035	CNVD
Metanephric adenoma	20802469	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:179514000-179518200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:179515400-179516200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:179515400-179516800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:179515400-179517800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:179515600-179521800	Enhancers	Placenta	Placenta
7	chr1:179516000-179517800	Weak transcription	Pancreas	Pancrea
8	chr1:179516200-179516600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:179516600-179516800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:179516800-179519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:179516800-179520200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:179517800-179518000	Enhancers	Fetal Muscle Leg	muscle
13	chr1:179517800-179518200	Enhancers	Pancreas	Pancrea
14	chr1:179517800-179518600	Enhancers	Gastric	stomach
15	chr1:179518200-179519000	Weak transcription	Pancreas	Pancrea
16	chr1:179518400-179519000	Enhancers	Sigmoid Colon	Sigmoid Colon

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