Variant report

Variant	nsv522746
Chromosome Location	chr1:179501365-179518459
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:179513921-179514233	HepG2	liver:	n/a	chr1:179514062-179514073
2	CEBPB	chr1:179517896-179517946	HepG2	liver:	n/a	chr1:179517919-179517930
3	CTCF	chr1:179509394-179509474	LNCaP	prostate:	n/a	n/a
4	FOS	chr1:179502988-179503090	MCF10A-Er-Src	breast:	n/a	chr1:179503015-179503026
5	FOXA1	chr1:179518446-179518623	T-47D	breast:	n/a	n/a
6	GATA3	chr1:179518237-179518593	T-47D	breast:	n/a	n/a
7	IRF3	chr1:179514281-179514290	GM12878	blood:	n/a	n/a
8	MAFK	chr1:179504041-179504173	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:179510343-179510345	A549	lung:	n/a	n/a
10	POLR2A	chr1:179510296-179510324	A549	lung:	n/a	n/a
11	POLR2A	chr1:179510414-179510483	A549	lung:	n/a	n/a
12	POLR2A	chr1:179510387-179510389	A549	lung:	n/a	n/a
13	POLR2A	chr1:179510370-179510372	A549	lung:	n/a	n/a
14	POLR2A	chr1:179510268-179510295	A549	lung:	n/a	n/a
15	STAT3	chr1:179502865-179503012	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr1:179501311-179501508	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr1:179502864-179503069	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr1:179502995-179503024	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr1:179511194-179511394	MCF10A-Er-Src	breast:	n/a	chr1:179511270-179511278

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179510162..179513711-chr1:179513904..179516885,3	K562	blood:
2	chr1:179510342..179513205-chr1:179522865..179525249,2	MCF-7	breast:
3	chr1:179510162..179512565-chr1:179513904..179515636,2	K562	blood:
4	chr1:179510162..179512565-chr1:179513904..179515636,2	K562	blood:
5	chr1:179510162..179513711-chr1:179513904..179516885,3	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDRD5-2	chr1:179503628-179504097	NONHSAT007864
2	lnc-NPHS2-1	chr1:179517817-179518057	ENSG00000261250.1
3	lnc-NPHS2-1	chr1:179512336-179515388	ENSG00000261250.1

No data

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

Extended variants
information (count: 707 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:707 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6696896	chr1:179501365-179501366	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs553995659	chr1:179501398-179501399	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs530950599	chr1:179501405-179501406	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs574026671	chr1:179501411-179501412	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs542943514	chr1:179501423-179501424	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs35613488	chr1:179501426-179501427	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs75304957	chr1:179501461-179501462	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs562350727	chr1:179501505-179501506	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs527750294	chr1:179501553-179501554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs4651042	chr1:179501583-179501584	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs369842002	chr1:179501587-179501588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs371231041	chr1:179501597-179501598	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs544795432	chr1:179501605-179501606	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs117545209	chr1:179501618-179501619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs190005575	chr1:179501636-179501637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546829449	chr1:179501643-179501644	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560309785	chr1:179501653-179501654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs4652406	chr1:179501654-179501655	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs114735923	chr1:179501694-179501695	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs552397659	chr1:179501725-179501726	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs4652407	chr1:179501737-179501738	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs551465081	chr1:179501781-179501782	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs571748177	chr1:179501787-179501788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs534279836	chr1:179501847-179501848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs201247960	chr1:179501866-179501867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs549577107	chr1:179501870-179501871	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs4652408	chr1:179501871-179501872	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs147465654	chr1:179501914-179501915	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs182547194	chr1:179501999-179502000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs571932098	chr1:179502034-179502035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs200251852	chr1:179502036-179502037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs201536817	chr1:179502037-179502038	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs560741548	chr1:179502038-179502039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs543204441	chr1:179502045-179502046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs397725859	chr1:179502066-179502067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs138275801	chr1:179502079-179502080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs545021644	chr1:179502110-179502111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs188223631	chr1:179502230-179502231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs114607471	chr1:179502231-179502232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs41267596	chr1:179502258-179502259	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs12408477	chr1:179502357-179502358	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs143941085	chr1:179502394-179502395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs549433031	chr1:179502395-179502396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563224730	chr1:179502493-179502494	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs376616595	chr1:179502543-179502544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs16854244	chr1:179502599-179502600	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs372436480	chr1:179502627-179502628	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs193195685	chr1:179502672-179502673	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs551794913	chr1:179502675-179502676	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs183858875	chr1:179502691-179502692	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:179498600-179509600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:179501200-179509600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:179509600-179510400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:179509600-179510600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
6	chr1:179510000-179510600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:179510600-179511000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:179514000-179514200	Enhancers	Pancreas	Pancrea
10	chr1:179514000-179518200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:179514400-179515400	Enhancers	Fetal Muscle Leg	muscle
12	chr1:179514400-179515600	Weak transcription	Pancreas	Pancrea
13	chr1:179515400-179516200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:179515400-179516800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:179515400-179517800	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:179515600-179516000	Enhancers	Pancreas	Pancrea
17	chr1:179515600-179521800	Enhancers	Placenta	Placenta
18	chr1:179516000-179517800	Weak transcription	Pancreas	Pancrea
19	chr1:179516200-179516600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:179516600-179516800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:179516800-179519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:179516800-179520200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:179517800-179518000	Enhancers	Fetal Muscle Leg	muscle
24	chr1:179517800-179518200	Enhancers	Pancreas	Pancrea
25	chr1:179517800-179518600	Enhancers	Gastric	stomach
26	chr1:179518200-179519000	Weak transcription	Pancreas	Pancrea
27	chr1:179518400-179519000	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links