Variant report

Variant	nsv522490
Chromosome Location	chr1:227446008-227450144
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	ARID3A	chr1:227448086-227448709	K562	blood:	n/a	n/a
2	BHLHE40	chr1:227448130-227448424	K562	blood:	n/a	n/a
3	CBX3	chr1:227448012-227448616	K562	blood:	n/a	n/a
4	CCNT2	chr1:227448099-227448516	K562	blood:	n/a	chr1:227448339-227448359
5	CEBPB	chr1:227448026-227448660	K562	blood:	n/a	n/a
6	CEBPB	chr1:227448104-227448470	K562	blood:	n/a	n/a
7	CEBPD	chr1:227447950-227448584	K562	blood:	n/a	n/a
8	CEBPD	chr1:227447955-227448536	K562	blood:	n/a	n/a
9	CHD1	chr1:227447090-227447093	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr1:227445628-227446012	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr1:227445900-227446050	A549	lung:	n/a	n/a
12	CTCF	chr1:227448115-227448422	K562	blood:	n/a	n/a
13	CTCF	chr1:227445626-227446008	K562	blood:	n/a	n/a
14	CTCF	chr1:227445860-227446010	GM12871	blood:	n/a	n/a
15	CTCF	chr1:227448060-227448210	K562	blood:	n/a	n/a
16	CTCF	chr1:227448140-227448290	K562	blood:	n/a	n/a
17	CUX1	chr1:227446616-227446671	K562	blood:	n/a	n/a
18	EP300	chr1:227448104-227448468	K562	blood:	n/a	n/a
19	EP300	chr1:227450141-227450173	K562	blood:	n/a	n/a
20	EP300	chr1:227448014-227448566	K562	blood:	n/a	chr1:227448019-227448029
21	GATA1	chr1:227448128-227448328	PBDEFetal	blood:	n/a	n/a
22	GATA1	chr1:227447596-227448841	PBDE	blood:	n/a	chr1:227448479-227448489 chr1:227448480-227448489 chr1:227448350-227448360 chr1:227448347-227448359 chr1:227448612-227448628 chr1:227448478-227448490 chr1:227448480-227448487 chr1:227448339-227448356 chr1:227448526-227448536 chr1:227448478-227448491 chr1:227448612-227448628 chr1:227448350-227448357
23	GATA2	chr1:227448060-227448551	K562	blood:	n/a	chr1:227448479-227448489 chr1:227448480-227448489 chr1:227448350-227448360 chr1:227448347-227448359 chr1:227448478-227448490 chr1:227448480-227448487 chr1:227448339-227448356 chr1:227448526-227448536 chr1:227448478-227448491 chr1:227448350-227448357
24	HCFC1	chr1:227448204-227448262	K562	blood:	n/a	n/a
25	HMGN3	chr1:227448162-227448516	K562	blood:	n/a	chr1:227448481-227448488
26	IRF1	chr1:227445630-227446201	K562	blood:	n/a	chr1:227446009-227446022 chr1:227446012-227446022 chr1:227446008-227446021 chr1:227446008-227446021 chr1:227446009-227446023 chr1:227446008-227446021 chr1:227446007-227446021 chr1:227446009-227446023
27	IRF1	chr1:227447557-227448532	K562	blood:	n/a	chr1:227447958-227447972 chr1:227448452-227448466 chr1:227447956-227447969 chr1:227447919-227447929 chr1:227448452-227448465 chr1:227447915-227447929 chr1:227447958-227447968
28	IRF1	chr1:227447767-227448472	K562	blood:	n/a	chr1:227447958-227447972 chr1:227448452-227448466 chr1:227447956-227447969 chr1:227447919-227447929 chr1:227448452-227448465 chr1:227447915-227447929 chr1:227447958-227447968
29	JUND	chr1:227448148-227448531	K562	blood:	n/a	n/a
30	MAFK	chr1:227448242-227448309	K562	blood:	n/a	n/a
31	MAX	chr1:227448075-227448400	K562	blood:	n/a	n/a
32	MAX	chr1:227448071-227448349	K562	blood:	n/a	n/a
33	MAX	chr1:227448171-227448416	K562	blood:	n/a	n/a
34	MAZ	chr1:227448066-227448433	K562	blood:	n/a	n/a
35	MXI1	chr1:227448108-227448488	K562	blood:	n/a	chr1:227448202-227448211
36	MYC	chr1:227448114-227448544	K562	blood:	n/a	n/a
37	MYC	chr1:227446757-227446790	MCF10A-Er-Src	breast:	n/a	n/a
38	MYC	chr1:227448094-227448424	K562	blood:	n/a	n/a
39	NFYA	chr1:227448086-227448448	K562	blood:	n/a	n/a
40	NFYB	chr1:227448089-227448494	K562	blood:	n/a	n/a
41	RCOR1	chr1:227448084-227448357	K562	blood:	n/a	n/a
42	RCOR1	chr1:227448039-227448641	K562	blood:	n/a	n/a
43	RFX5	chr1:227447920-227448417	K562	blood:	n/a	n/a
44	SMC3	chr1:227448109-227448265	K562	blood:	n/a	n/a
45	STAT5A	chr1:227447995-227448566	K562	blood:	n/a	chr1:227448184-227448192
46	TAL1	chr1:227448027-227448778	K562	blood:	n/a	chr1:227448339-227448357
47	TBL1XR1	chr1:227448214-227448387	K562	blood:	n/a	n/a
48	TBL1XR1	chr1:227447985-227448518	K562	blood:	n/a	n/a
49	TBP	chr1:227448114-227448422	K562	blood:	n/a	n/a
50	TEAD4	chr1:227447960-227448525	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:227442920..227447581-chr1:227503938..227508329,6	K562	blood:
2	chr1:227446023..227447555-chr1:227505720..227507442,2	K562	blood:
3	chr1:227446907..227449535-chr1:227450206..227452004,2	K562	blood:
4	chr1:227445055..227447131-chr1:227475888..227477429,2	K562	blood:
5	chr1:227447057..227450743-chr1:227504946..227508409,3	MCF-7	breast:
6	chr1:227447102..227448619-chr1:227452855..227454756,2	K562	blood:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000236636	chromatin interactions
ENSG00000143776	chromatin interactions

Extended variants
information (count: 150 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:150 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs16847527	chr1:227446008-227446009	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs2813966	chr1:227446055-227446056	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs560877045	chr1:227446088-227446089	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs571420243	chr1:227446096-227446097	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs561651955	chr1:227446111-227446112	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs187364675	chr1:227446127-227446128	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs551289972	chr1:227446173-227446174	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs548467221	chr1:227446180-227446181	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs569610009	chr1:227446182-227446183	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs540018171	chr1:227446242-227446243	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs372736235	chr1:227446267-227446268	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs190473033	chr1:227446272-227446273	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs566924877	chr1:227446315-227446316	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs534046074	chr1:227446341-227446342	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs555687685	chr1:227446349-227446350	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs573695839	chr1:227446410-227446411	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs537891486	chr1:227446418-227446419	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs138490020	chr1:227446464-227446465	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs75890175	chr1:227446475-227446476	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs183055947	chr1:227446561-227446562	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs376639027	chr1:227446564-227446565	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs397944055	chr1:227446566-227446567	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs542624802	chr1:227446583-227446584	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs10916110	chr1:227446607-227446608	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs116053370	chr1:227446619-227446620	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs542361843	chr1:227446631-227446632	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs576002558	chr1:227446632-227446633	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs16847534	chr1:227446640-227446641	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs549835086	chr1:227446671-227446672	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs77980628	chr1:227446692-227446693	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs368541680	chr1:227446709-227446710	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs115343521	chr1:227446732-227446733	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs566955431	chr1:227446820-227446821	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs185880865	chr1:227446903-227446904	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs7526283	chr1:227446928-227446929	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs7542505	chr1:227446937-227446938	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs116619974	chr1:227446953-227446954	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs556158604	chr1:227446978-227446979	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs533345538	chr1:227447013-227447014	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs566869754	chr1:227447025-227447026	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs1513618	chr1:227447061-227447062	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs538562922	chr1:227447067-227447068	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs553882567	chr1:227447159-227447160	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs148857340	chr1:227447187-227447188	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs1513617	chr1:227447213-227447214	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs375544433	chr1:227447220-227447221	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs554688417	chr1:227447228-227447229	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs571042302	chr1:227447238-227447239	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs576231237	chr1:227447255-227447256	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs74599093	chr1:227447282-227447283	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:90)

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
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	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
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227414200-227453800	Weak transcription	HSMM	muscle
3	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
5	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
6	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:227432600-227448000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
10	chr1:227433200-227452800	Weak transcription	Ovary	ovary
11	chr1:227434000-227446800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:227434000-227447000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:227434000-227453400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
15	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
16	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
17	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:227435600-227453600	Weak transcription	Fetal Intestine Small	intestine
21	chr1:227438800-227448000	Weak transcription	Psoas Muscle	Psoas
22	chr1:227438800-227449400	Weak transcription	Right Atrium	heart
23	chr1:227440000-227456600	Weak transcription	HepG2	liver
24	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
25	chr1:227441200-227450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:227441800-227449600	Weak transcription	A549	lung
27	chr1:227441800-227452000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:227442400-227449600	Weak transcription	Brain Angular Gyrus	brain
29	chr1:227443200-227446800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:227445600-227446200	Flanking Active TSS	K562	blood
32	chr1:227445800-227448000	Weak transcription	Pancreas	Pancrea
33	chr1:227445800-227458400	Weak transcription	NHEK	skin
34	chr1:227446000-227446200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:227446000-227446400	Enhancers	Brain Substantia Nigra	brain
36	chr1:227446000-227447400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:227446000-227448600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:227446200-227446600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:227446200-227448000	Enhancers	K562	blood
40	chr1:227446400-227446600	Weak transcription	Brain Substantia Nigra	brain
41	chr1:227446600-227447000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:227446600-227447200	Enhancers	Brain Substantia Nigra	brain
43	chr1:227446600-227448200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr1:227446600-227448600	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:227446800-227447400	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:227446800-227447400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:227446800-227447400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:227446800-227447400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:227446800-227447400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:227447000-227447200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links