Variant report

Variant	esv3420090
Chromosome Location	chr1:220250879-220252927
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:220251438-220251554	HepG2	liver:	n/a	chr1:220251494-220251505
2	EP300	chr1:220250157-220250966	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr1:220250097-220250956	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr1:220250035-220251013	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:220250210-220250895	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr1:220250173-220250879	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:220251384-220251461	A549	lung:	n/a	n/a
8	POLR2A	chr1:220251373-220251380	A549	lung:	n/a	n/a
9	POLR2A	chr1:220251365-220251371	A549	lung:	n/a	n/a
10	TCF12	chr1:220250051-220250885	SK-N-SH	brain:	n/a	n/a
11	TCF7L2	chr1:220252152-220252271	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:220250989-220251039	Hepatocyte	liver:	n/a
2	chr1:220250989-220251039	ovcar-3	ovarian:	n/a
3	chr1:220250989-220251039	HepG2	liver:	n/a
4	chr1:220250989-220251039	BJ	skin:	n/a
5	chr1:220250989-220251039	IMR90	lung:	fetal
6	chr1:220250989-220251039	RPTEC	kidney:	n/a
7	chr1:220250989-220251039	HCT-116	colon:	n/a
8	chr1:220250989-220251039	HNPCEpiC	eye:	n/a
9	chr1:220250989-220251039	HEEpiC	esophagus:	n/a
10	chr1:220250989-220251039	SK-N-SH	brain:	n/a
11	chr1:220250989-220251039	MCF-7	breast:	n/a
12	chr1:220250989-220251039	PrEC	prostate:	n/a
13	chr1:220250989-220251039	NH-A	brain:	n/a
14	chr1:220250989-220251039	GM19239	blood:	n/a
15	chr1:220250989-220251039	NHDF-neo	bronchial:	n/a
16	chr1:220250989-220251039	NT2-D1	testis:	n/a
17	chr1:220250989-220251039	LNCaP	prostate:	n/a
18	chr1:220250989-220251039	SKMC	muscle:	n/a
19	chr1:220250989-220251039	HRCEpiC	kidney:	n/a
20	chr1:220250989-220251039	ProgFib	skin:	n/a
21	chr1:220250989-220251039	AoSMC	blood vessel:	n/a
22	chr1:220250989-220251039	AG09319	gingival:	n/a
23	chr1:220250989-220251039	HAEpiC	amniotic membrane:	n/a
24	chr1:220250989-220251039	BE2_C	brain:	n/a
25	chr1:220250989-220251039	MCF10A-Er-Src	breast:	n/a
26	chr1:220250989-220251039	CMK	blood:	n/a
27	chr1:220250989-220251039	HCM	heart:	n/a
28	chr1:220250989-220251039	HEK293	kidney:	embryo
29	chr1:220250989-220251039	HUVEC	blood vessel:	n/a
30	chr1:220250989-220251039	SAEC	small airway:	n/a
31	chr1:220250989-220251039	AG04450	lung:	fetal
32	chr1:220250989-220251039	HIPEpiC	eye:	n/a
33	chr1:220250989-220251039	HCPEpiC	choroid plexus:	n/a
34	chr1:220250989-220251039	HMEC	breast:	n/a
35	chr1:220250989-220251039	AG10803	skin:	n/a
36	chr1:220250989-220251039	NHBE	bronchial:	n/a
37	chr1:220250989-220251039	HL-60	blood:	n/a
38	chr1:220250989-220251039	Hela-S3	cervix:	n/a
39	chr1:220250989-220251039	K562	blood:	n/a
40	chr1:220250989-220251039	HRE	kidney:	n/a
41	chr1:220250989-220251039	GM12892	blood:	n/a
42	chr1:220250989-220251039	U87	brain:	n/a
43	chr1:220250989-220251039	A549	lung:	n/a
44	chr1:220250989-220251039	H1-hESC	embryonic stem cell:	embryo
45	chr1:220250989-220251039	T-47D	breast:	n/a
46	chr1:220250989-220251039	HPAEpiC	pulmonary alveolar:	n/a
47	chr1:220250989-220251039	SK-N-MC	brain:	n/a
48	chr1:220250989-220251039	PANC-1	pancreas:	n/a
49	chr1:220250989-220251039	HCF	heart:	n/a
50	chr1:220250989-220251039	AG09309	skin:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220250499..220254001-chr1:220255278..220257878,3	K562	blood:
2	chr1:220236160..220238551-chr1:220252332..220254009,2	K562	blood:

No data

Variant related genes	Relation type
BPNT1	TF binding region
BPNT1	CpG island

Extended variants
information (count: 83 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:83 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534016618	chr1:220250909-220250910	Weak transcription Strong transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs145912839	chr1:220250918-220250919	Weak transcription Strong transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs567197158	chr1:220250938-220250939	Weak transcription Strong transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs138515982	chr1:220251086-220251087	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs141577233	chr1:220251127-220251128	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs114889823	chr1:220251128-220251129	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs547111820	chr1:220251184-220251185	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs538711292	chr1:220251187-220251188	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs558402802	chr1:220251196-220251197	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs578180892	chr1:220251227-220251228	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs184339612	chr1:220251228-220251229	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs189624197	chr1:220251302-220251303	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs181132179	chr1:220251310-220251311	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs542985400	chr1:220251323-220251324	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs143493321	chr1:220251330-220251331	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184906354	chr1:220251345-220251346	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs545059077	chr1:220251368-220251369	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs564741372	chr1:220251380-220251381	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs530616703	chr1:220251386-220251387	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs566997509	chr1:220251420-220251421	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs550643368	chr1:220251424-220251425	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs147996736	chr1:220251452-220251453	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs535465231	chr1:220251456-220251457	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs529687227	chr1:220251461-220251462	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs546600054	chr1:220251546-220251547	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs201312727	chr1:220251548-220251549	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs566444446	chr1:220251598-220251599	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs372484353	chr1:220251645-220251646	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs202023986	chr1:220251656-220251657	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs116121256	chr1:220251660-220251661	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs35600968	chr1:220251666-220251667	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs558679502	chr1:220251729-220251730	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs571907868	chr1:220251730-220251731	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs181658496	chr1:220251737-220251738	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs9430910	chr1:220251763-220251764	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs9430911	chr1:220251764-220251765	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs186239691	chr1:220251787-220251788	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs58834658	chr1:220251821-220251822	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs66897228	chr1:220251822-220251823	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs35619743	chr1:220251829-220251830	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs397687983	chr1:220251830-220251831	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs373842943	chr1:220251843-220251844	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs574296427	chr1:220251852-220251853	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs199679040	chr1:220251856-220251857	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs191012875	chr1:220251890-220251891	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs377329229	chr1:220251899-220251900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs182548890	chr1:220251901-220251902	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs370403113	chr1:220251904-220251905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs185783284	chr1:220251949-220251950	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs553341364	chr1:220251952-220251953	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
Breast cancer	17603634	CNVD
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
Acute lymphoblastic leukemia	17443227	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
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
Acute lymphoblastic leukemia	22237106	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Holoprosencephaly	19184110	CNVD
Breast cancer	21069454	CNVD
Malignant fibrous histiocytomas	21085701	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
Pleomorphic liposarcoma	18784837	CNVD
Autism	14699429	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pancreatic cancer	17952125	CNVD
Tetralogy of Fallot	22912587	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:147 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220220400-220257600	Weak transcription	Stomach Mucosa	stomach
2	chr1:220220600-220262400	Weak transcription	Pancreas	Pancrea
3	chr1:220220600-220262400	Weak transcription	NHLF	lung
4	chr1:220220800-220261600	Weak transcription	Fetal Brain Male	brain
5	chr1:220234400-220253600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:220236400-220262800	Weak transcription	Esophagus	oesophagus
7	chr1:220238000-220262800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:220238000-220267400	Weak transcription	Spleen	Spleen
9	chr1:220238200-220262800	Weak transcription	Gastric	stomach
10	chr1:220239400-220262000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:220239600-220255200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:220239600-220261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:220239600-220262400	Weak transcription	Right Ventricle	heart
14	chr1:220241200-220256800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:220241200-220258200	Weak transcription	Hela-S3	cervix
16	chr1:220241200-220261800	Weak transcription	A549	lung
17	chr1:220241200-220262000	Weak transcription	HMEC	breast
18	chr1:220241200-220262400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:220241200-220262400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:220241400-220262400	Weak transcription	NHEK	skin
21	chr1:220241600-220253000	Strong transcription	Fetal Intestine Small	intestine
22	chr1:220242600-220262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:220243800-220262400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:220245800-220251800	Strong transcription	Fetal Lung	lung
25	chr1:220246200-220262000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:220246400-220251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:220246400-220255000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:220246400-220255000	Weak transcription	HSMMtube	muscle
29	chr1:220246400-220256000	Weak transcription	Fetal Kidney	kidney
30	chr1:220246400-220261600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:220246400-220261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:220246400-220262000	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:220246400-220262400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:220246400-220262400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:220246400-220262400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:220246400-220262400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:220246400-220262400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:220246400-220262400	Weak transcription	Brain Substantia Nigra	brain
39	chr1:220246400-220262400	Weak transcription	Fetal Brain Female	brain
40	chr1:220246600-220251000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:220246600-220251000	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:220246600-220253600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:220246600-220262400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:220246600-220262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:220246600-220262400	Weak transcription	Colonic Mucosa	Colon
46	chr1:220246800-220262400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:220246800-220262400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:220246800-220262400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:220246800-220262400	Weak transcription	Fetal Heart	heart
50	chr1:220246800-220262400	Weak transcription	Thymus	Thymus

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