Variant report

Variant	nsv1008890
Chromosome Location	chr1:169917450-169956450
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	BACH1	chr1:169955146-169955152	K562	blood:	n/a	n/a
2	CEBPB	chr1:169953584-169953585	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr1:169953474-169953649	K562	blood:	n/a	n/a
4	CEBPB	chr1:169920135-169920408	HepG2	liver:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
5	CEBPB	chr1:169953500-169953638	HepG2	liver:	n/a	n/a
6	CEBPB	chr1:169920089-169920421	IMR90	lung:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
7	CEBPB	chr1:169920115-169920364	K562	blood:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
8	CEBPB	chr1:169920105-169920380	A549	lung:	n/a	chr1:169920249-169920258 chr1:169920248-169920259 chr1:169920247-169920258
9	CTCF	chr1:169932721-169932758	GM19240	blood:	n/a	n/a
10	CTCF	chr1:169926841-169926902	Kidney_OC	kidney:	n/a	n/a
11	CTCF	chr1:169944840-169944990	AG09319	gingival:	n/a	n/a
12	CTCF	chr1:169951340-169951490	HepG2	liver:	n/a	chr1:169951427-169951440
13	CUX1	chr1:169943514-169943612	K562	blood:	n/a	n/a
14	CUX1	chr1:169943282-169943471	GM12878	blood:	n/a	n/a
15	EP300	chr1:169937046-169937893	SK-N-SH	brain:	n/a	n/a
16	EP300	chr1:169955476-169955581	K562	blood:	n/a	n/a
17	EP300	chr1:169937349-169937727	SK-N-SH_RA	brain:	n/a	n/a
18	EP300	chr1:169937342-169937642	SK-N-SH_RA	brain:	n/a	n/a
19	EP300	chr1:169922354-169922368	K562	blood:	n/a	n/a
20	GATA2	chr1:169928101-169928458	SH-SY5Y	brain:	n/a	chr1:169928371-169928381 chr1:169928243-169928255
21	GATA2	chr1:169937314-169937695	SH-SY5Y	brain:	n/a	n/a
22	GATA3	chr1:169936518-169936617	SH-SY5Y	brain:	n/a	n/a
23	GATA3	chr1:169937216-169937729	SK-N-SH	brain:	n/a	chr1:169937265-169937275
24	GATA3	chr1:169955632-169955693	SH-SY5Y	brain:	n/a	n/a
25	GATA3	chr1:169955318-169955736	MCF-7	breast:	n/a	n/a
26	GATA3	chr1:169928128-169928498	SH-SY5Y	brain:	n/a	chr1:169928371-169928381 chr1:169928243-169928255
27	GATA3	chr1:169937235-169937683	SH-SY5Y	brain:	n/a	chr1:169937265-169937275
28	GATA3	chr1:169918241-169918770	SK-N-SH	brain:	n/a	n/a
29	GATA3	chr1:169918154-169918674	SK-N-SH	brain:	n/a	n/a
30	GATA3	chr1:169929536-169929591	SH-SY5Y	brain:	n/a	n/a
31	JUN	chr1:169936755-169936860	K562	blood:	n/a	n/a
32	JUN	chr1:169922440-169922488	K562	blood:	n/a	n/a
33	MAFF	chr1:169954915-169955283	K562	blood:	n/a	chr1:169955094-169955112
34	MAFF	chr1:169920706-169920885	HepG2	liver:	n/a	chr1:169920803-169920821
35	MAFF	chr1:169956204-169956404	HepG2	liver:	n/a	n/a
36	MAFF	chr1:169954911-169955280	HepG2	liver:	n/a	chr1:169955094-169955112
37	MAFK	chr1:169956197-169956473	HepG2	liver:	n/a	chr1:169956321-169956332 chr1:169956321-169956337 chr1:169956320-169956334 chr1:169956322-169956333 chr1:169956321-169956332 chr1:169956321-169956336
38	MAFK	chr1:169920704-169920891	HepG2	liver:	n/a	chr1:169920774-169920788
39	MAFK	chr1:169954918-169955282	K562	blood:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
40	MAFK	chr1:169954916-169955270	HepG2	liver:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
41	MAFK	chr1:169956182-169956451	HepG2	liver:	n/a	chr1:169956321-169956332 chr1:169956321-169956337 chr1:169956320-169956334 chr1:169956322-169956333 chr1:169956321-169956332 chr1:169956321-169956336
42	MAFK	chr1:169954910-169955281	IMR90	lung:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
43	MAFK	chr1:169954934-169955279	Hela-S3	cervix:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
44	MAFK	chr1:169954914-169955283	HepG2	liver:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
45	MAFK	chr1:169954844-169955364	GM12878	blood:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
46	MAFK	chr1:169954923-169955222	H1-hESC	embryonic stem cell:	n/a	chr1:169955095-169955110 chr1:169955100-169955111 chr1:169955100-169955111 chr1:169955098-169955112 chr1:169955095-169955111
47	MAZ	chr1:169943064-169943211	GM12878	blood:	n/a	n/a
48	MYC	chr1:169923208-169923303	MCF10A-Er-Src	breast:	n/a	n/a
49	MYC	chr1:169951180-169951270	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr1:169949490-169949609	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169953487..169956228-chr1:169957640..169960024,2	MCF-7	breast:
2	chr1:169927495..169930307-chr1:170507858..170509808,2	K562	blood:
3	chr1:169915601..169917304-chr1:169919424..169921809,3	MCF-7	breast:
4	chr1:169913226..169915577-chr1:169917390..169920061,2	MCF-7	breast:
5	chr1:169942236..169943172-chrX:26753938..26754794,2	MCF-7	breast:
6	chr1:169861655..169864221-chr1:169940931..169943553,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCYL3-1	chr1:169927085-169927387	NONHSAT007483

Variant related genes	Relation type
MRPS10P1	TF binding region
RN7SL269P	TF binding region
ENSG00000000457	chromatin interactions
ENSG00000120370	chromatin interactions
ENSG00000235378	chromatin interactions

Extended variants
information (count: 1362 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:1362 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181316031	chr1:169917454-169917455	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs186319964	chr1:169917476-169917477	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs59795603	chr1:169917509-169917510	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs574718270	chr1:169917558-169917559	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs533517214	chr1:169917568-169917569	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs145098186	chr1:169917574-169917575	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs535821130	chr1:169917582-169917583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs139964410	chr1:169917643-169917644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs554918319	chr1:169917659-169917660	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs576365058	chr1:169917660-169917661	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs543645686	chr1:169917680-169917681	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs565072396	chr1:169917690-169917691	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs368829339	chr1:169917754-169917755	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs77225638	chr1:169917814-169917815	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs559329495	chr1:169917968-169917969	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs191138744	chr1:169918015-169918016	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs547752366	chr1:169918035-169918036	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs182116206	chr1:169918038-169918039	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs145638961	chr1:169918050-169918051	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs546043827	chr1:169918067-169918068	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs186656033	chr1:169918071-169918072	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs545817218	chr1:169918129-169918130	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs548008140	chr1:169918132-169918133	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs140945355	chr1:169918134-169918135	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs367917908	chr1:169918270-169918271	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs191117751	chr1:169918331-169918332	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs570939590	chr1:169918369-169918370	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs78059007	chr1:169918379-169918380	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs148052313	chr1:169918451-169918452	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs1415552	chr1:169918472-169918473	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs546799971	chr1:169918478-169918479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs372128090	chr1:169918514-169918515	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs568506918	chr1:169918552-169918553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs1156321	chr1:169918566-169918567	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs12122764	chr1:169918631-169918632	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs185340080	chr1:169918697-169918698	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs576451110	chr1:169918699-169918700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs575864013	chr1:169918715-169918716	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs372392260	chr1:169918721-169918722	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs537334489	chr1:169918740-169918741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs141794263	chr1:169918771-169918772	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs35832958	chr1:169918782-169918783	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs189655208	chr1:169918854-169918855	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs10919272	chr1:169918865-169918866	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs182554798	chr1:169918870-169918871	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs574145716	chr1:169918889-169918890	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs75231152	chr1:169918910-169918911	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs139559617	chr1:169918942-169918943	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs188434908	chr1:169918971-169918972	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs149310445	chr1:169918993-169918994	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
Glioblastoma multiforme	21080181	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	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
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
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21509527	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
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Lung cancer	18438408	CNVD
Cancer	20164920	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:313 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169904000-169929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:169904000-169934800	Weak transcription	Fetal Heart	heart
4	chr1:169904000-169949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
6	chr1:169909200-169946000	Weak transcription	Primary T cells from cord blood	blood
7	chr1:169910400-169946200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:169911200-169948800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:169911400-169923000	Weak transcription	Liver	Liver
10	chr1:169911400-169946200	Weak transcription	Dnd41	blood
11	chr1:169911400-169948600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:169911600-169918400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:169911600-169927000	Weak transcription	Fetal Intestine Large	intestine
14	chr1:169911600-169945800	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:169911800-169946400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:169911800-169949600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:169911800-169951200	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:169911800-169968400	Weak transcription	Psoas Muscle	Psoas
19	chr1:169912000-169918600	Weak transcription	NHLF	lung
20	chr1:169912000-169922400	Weak transcription	HSMM	muscle
21	chr1:169912000-169946200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:169912000-169953600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:169912000-169966000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:169912000-169968600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:169912400-169918000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr1:169912400-169918200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:169912400-169950400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:169912600-169918800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:169912800-169967200	Weak transcription	NHDF-Ad	bronchial
30	chr1:169913400-169953600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:169913800-169938800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:169913800-169968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:169914000-169920800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:169914000-169945800	Weak transcription	Adipose Nuclei	Adipose
35	chr1:169914000-169946200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:169914000-169968400	Weak transcription	Ovary	ovary
37	chr1:169914200-169921200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:169914200-169923000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:169914200-169945800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:169914600-169923800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:169914600-169923800	Weak transcription	Esophagus	oesophagus
42	chr1:169914600-169933400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:169914600-169961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:169914600-169968000	Weak transcription	Fetal Stomach	stomach
45	chr1:169914800-169946000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:169914800-169984000	Weak transcription	Left Ventricle	heart
47	chr1:169914800-169984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:169914800-169988800	Weak transcription	Fetal Intestine Small	intestine
49	chr1:169915200-169950800	Weak transcription	Fetal Lung	lung
50	chr1:169917000-169918000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links