Variant report

Variant	esv3428377
Chromosome Location	chr21:46350818-46351144
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	ATF2	chr21:46351008-46351474	GM12878	blood:	n/a	n/a
2	BCL11A	chr21:46351119-46351342	GM12878	blood:	n/a	n/a
3	BCL3	chr21:46351036-46351467	GM12878	blood:	n/a	n/a
4	BHLHE40	chr21:46350678-46351617	GM12878	blood:	n/a	n/a
5	CEBPB	chr21:46350960-46351158	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr21:46350949-46351595	GM12878	blood:	n/a	n/a
7	CHD1	chr21:46350754-46351942	GM12878	blood:	n/a	chr21:46351189-46351199
8	CHD2	chr21:46351063-46351513	GM12878	blood:	n/a	chr21:46351189-46351199
9	CUX1	chr21:46350729-46351885	GM12878	blood:	n/a	n/a
10	EBF1	chr21:46349672-46351552	GM12878	blood:	n/a	chr21:46351222-46351233 chr21:46351223-46351232 chr21:46351223-46351232 chr21:46351221-46351234
11	EBF1	chr21:46349081-46351931	GM12878	blood:	n/a	chr21:46351222-46351233 chr21:46351223-46351232 chr21:46351223-46351232 chr21:46351221-46351234
12	EBF1	chr21:46350249-46351549	GM12878	blood:	n/a	chr21:46351222-46351233 chr21:46351223-46351232 chr21:46351223-46351232 chr21:46351221-46351234
13	EGR1	chr21:46350967-46351383	GM12878	blood:	n/a	chr21:46351187-46351201 chr21:46351207-46351216 chr21:46351196-46351209
14	EGR1	chr21:46351016-46351329	GM12878	blood:	n/a	chr21:46351187-46351201 chr21:46351207-46351216 chr21:46351196-46351209
15	EGR1	chr21:46351068-46351282	K562	blood:	n/a	chr21:46351187-46351201 chr21:46351207-46351216 chr21:46351196-46351209
16	EGR1	chr21:46350987-46351295	K562	blood:	n/a	chr21:46351187-46351201 chr21:46351207-46351216 chr21:46351196-46351209
17	ELF1	chr21:46350568-46351535	GM12878	blood:	n/a	chr21:46351065-46351077
18	ELF1	chr21:46349709-46352433	GM12878	blood:	n/a	chr21:46351065-46351077 chr21:46351566-46351578
19	EP300	chr21:46350996-46351442	GM12878	blood:	n/a	n/a
20	EP300	chr21:46351046-46351492	GM12878	blood:	n/a	n/a
21	ETS1	chr21:46351012-46351407	GM12878	blood:	n/a	chr21:46351208-46351215 chr21:46351189-46351200 chr21:46351202-46351216 chr21:46351110-46351124 chr21:46351111-46351122 chr21:46351204-46351215
22	FOXM1	chr21:46350943-46351533	GM12878	blood:	n/a	n/a
23	FOXP2	chr21:46350924-46351485	SK-N-MC	brain:	n/a	n/a
24	IKZF1	chr21:46350899-46351446	GM12878	blood:	n/a	n/a
25	MAX	chr21:46350644-46351487	NB4	blood:	n/a	chr21:46350706-46350715 chr21:46351194-46351204 chr21:46351169-46351179
26	MAX	chr21:46350524-46352252	GM12878	blood:	n/a	chr21:46350706-46350715 chr21:46351194-46351204 chr21:46351169-46351179
27	MAZ	chr21:46349461-46351638	GM12878	blood:	n/a	chr21:46350706-46350715 chr21:46351194-46351204 chr21:46349715-46349722 chr21:46351169-46351179 chr21:46349713-46349724 chr21:46349990-46350000 chr21:46350112-46350122 chr21:46350108-46350118 chr21:46349714-46349723
28	MEF2A	chr21:46350997-46351409	GM12878	blood:	n/a	n/a
29	MEF2C	chr21:46350927-46351463	GM12878	blood:	n/a	n/a
30	MTA3	chr21:46351033-46351564	GM12878	blood:	n/a	n/a
31	MTA3	chr21:46350159-46350875	GM12878	blood:	n/a	n/a
32	MTA3	chr21:46349056-46351679	GM12878	blood:	n/a	n/a
33	MXI1	chr21:46350613-46351526	GM12878	blood:	n/a	n/a
34	MYC	chr21:46351024-46351460	NB4	blood:	n/a	chr21:46351194-46351204 chr21:46351169-46351179
35	NFATC1	chr21:46351011-46351505	GM12878	blood:	n/a	chr21:46351263-46351277
36	NFATC1	chr21:46350982-46351481	GM12878	blood:	n/a	chr21:46351263-46351277
37	NFIC	chr21:46350574-46351538	GM12878	blood:	n/a	n/a
38	NFIC	chr21:46350894-46351241	GM12878	blood:	n/a	n/a
39	PAX5	chr21:46351075-46351548	GM12878	blood:	n/a	chr21:46351207-46351216
40	PML	chr21:46350758-46351594	GM12878	blood:	n/a	n/a
41	POLR2A	chr21:46350243-46352923	GM12892	blood:	n/a	n/a
42	POLR2A	chr21:46349053-46353060	GM18951	blood:	n/a	n/a
43	POLR2A	chr21:46350220-46353474	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr21:46350950-46351554	HL-60	blood:	n/a	n/a
45	POLR2A	chr21:46351051-46351939	GM12892	blood:	n/a	n/a
46	POLR2A	chr21:46349243-46352888	GM18526	blood:	n/a	n/a
47	POLR2A	chr21:46350875-46351900	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr21:46348892-46353194	GM12878	blood:	n/a	n/a
49	POLR2A	chr21:46350964-46351642	HL-60	blood:	n/a	n/a
50	POLR2A	chr21:46350843-46352202	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:46351118-46351168	AG04449	skin:	fetal
2	chr21:46350872-46350922	HRCEpiC	kidney:	n/a
3	chr21:46350872-46350922	Hepatocyte	liver:	n/a
4	chr21:46350872-46350922	T-47D	breast:	n/a
5	chr21:46350872-46350922	HCT-116	colon:	n/a
6	chr21:46350872-46350922	HCPEpiC	choroid plexus:	n/a
7	chr21:46351118-46351168	MCF-7	breast:	n/a
8	chr21:46350872-46350922	AG09319	gingival:	n/a
9	chr21:46350872-46350922	AoSMC	blood vessel:	n/a
10	chr21:46351118-46351168	CMK	blood:	n/a
11	chr21:46350872-46350922	SKMC	muscle:	n/a
12	chr21:46351118-46351168	GM12892	blood:	n/a
13	chr21:46351118-46351168	PrEC	prostate:	n/a
14	chr21:46351118-46351168	HRCEpiC	kidney:	n/a
15	chr21:46351118-46351168	AG09319	gingival:	n/a
16	chr21:46350872-46350922	SK-N-SH	brain:	n/a
17	chr21:46351118-46351168	AG09309	skin:	n/a
18	chr21:46351118-46351168	HRE	kidney:	n/a
19	chr21:46351118-46351168	SK-N-SH	brain:	n/a
20	chr21:46350872-46350922	AG04450	lung:	fetal
21	chr21:46351118-46351168	ECC-1	luminal epithelium:	n/a
22	chr21:46350872-46350922	PrEC	prostate:	n/a
23	chr21:46351118-46351168	SK-N-SH_RA	brain:	n/a
24	chr21:46351118-46351168	HRPEpiC	eye:	n/a
25	chr21:46351118-46351168	Hepatocyte	liver:	n/a
26	chr21:46350872-46350922	A549	lung:	n/a
27	chr21:46350872-46350922	AG10803	skin:	n/a
28	chr21:46350872-46350922	NT2-D1	testis:	n/a
29	chr21:46351118-46351168	SKMC	muscle:	n/a
30	chr21:46351118-46351168	HEEpiC	esophagus:	n/a
31	chr21:46351118-46351168	NT2-D1	testis:	n/a
32	chr21:46351118-46351168	HIPEpiC	eye:	n/a
33	chr21:46351118-46351168	Jurkat	blood:	n/a
34	chr21:46350872-46350922	PFSK-1	brain:	n/a
35	chr21:46351118-46351168	HAEpiC	amniotic membrane:	n/a
36	chr21:46350872-46350922	GM12878	blood:	n/a
37	chr21:46351118-46351168	U87	brain:	n/a
38	chr21:46350872-46350922	HUVEC	blood vessel:	n/a
39	chr21:46350872-46350922	NHDF-neo	bronchial:	n/a
40	chr21:46351118-46351168	HUVEC	blood vessel:	n/a
41	chr21:46351118-46351168	HCM	heart:	n/a
42	chr21:46350872-46350922	Jurkat	blood:	n/a
43	chr21:46351118-46351168	HCF	heart:	n/a
44	chr21:46350872-46350922	HCF	heart:	n/a
45	chr21:46350872-46350922	HEEpiC	esophagus:	n/a
46	chr21:46350872-46350922	BJ	skin:	n/a
47	chr21:46350872-46350922	NHBE	bronchial:	n/a
48	chr21:46350872-46350922	HAEpiC	amniotic membrane:	n/a
49	chr21:46351118-46351168	PFSK-1	brain:	n/a
50	chr21:46351118-46351168	SK-N-MC	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
2	chr21:46348891..46351856-chr21:46356275..46360285,3	K562	blood:
3	chr21:46349055..46351032-chr21:46493561..46495184,2	MCF-7	breast:
4	chr21:46348334..46352514-chr21:46492914..46497675,5	K562	blood:
5	chr21:46345821..46352717-chr21:46492682..46495835,7	MCF-7	breast:
6	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:
7	chr21:46220263..46223201-chr21:46349640..46352735,4	K562	blood:
8	chr21:46234565..46238085-chr21:46349825..46353215,3	MCF-7	breast:
9	chr21:46288744..46296879-chr21:46346201..46354260,26	MCF-7	breast:

Variant related genes	Relation type
ITGB2	TF binding region
ENSG00000273027	TF binding region
ITGB2	CpG island
ENSG00000273027	CpG island
ENSG00000197381	chromatin interactions
ENSG00000184787	chromatin interactions
ENSG00000183250	chromatin interactions
ENSG00000160256	chromatin interactions
ENSG00000268856	chromatin interactions
ENSG00000183255	chromatin interactions
ENSG00000236519	chromatin interactions
ENSG00000184900	chromatin interactions
ENSG00000235374	chromatin interactions

Extended variants
information (count: 9 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs377479485	chr21:46350872-46350873	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
2	rs140593860	chr21:46350972-46350973	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
3	rs575607056	chr21:46350999-46351000	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
4	rs9978207	chr21:46351012-46351013	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
5	rs150492639	chr21:46351025-46351026	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
6	rs573987131	chr21:46351085-46351086	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
7	rs375621899	chr21:46351105-46351106	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
8	rs138378008	chr21:46351111-46351112	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
9	rs12626759	chr21:46351134-46351135	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Cancer	16751803	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Down syndrome	17412756	CNVD
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Renal cell carcinoma	19461508	CNVD
Seminomas	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Wilms tumour	21544195	CNVD
Ewing''s sarcoma	17952124	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute myeloid leukemia	16864856	CNVD
Mental retardation	21031080	CNVD
Polymicrogyria	21031080	CNVD
periventricular nodular heterotopia	21031080	CNVD
Myelodysplastic syndrome	21606161	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Glioblastoma multiforme	18628472	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-syndromic sensorineural hearing loss	17457615	CNVD
Ewing''s sarcoma	21437220	CNVD
Lung adenocarcinoma	17086460	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian neoplasms	16753589	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute myeloid leukemia	21358987	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Prostate cancer	23341502	CNVD
Ovarian cancer	21720365	CNVD
Urothelial carcinoma	21177765	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	21251322	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Cholangiocarcinoma	16830362	CNVD
Down syndrome	17334655	CNVD
Neuroticism	17667963	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Autoimmune polyendocrine syndrome	18200029	CNVD
Prostate cancer	19363497	CNVD
Lung cancer	17086460	CNVD
Olfactory neuroblastoma	18408657	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Multiple myeloma	16616336	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21509527	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	17142309	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	17426248	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	23813976	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46340600-46351400	Weak transcription	Right Atrium	heart
2	chr21:46345600-46351200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
3	chr21:46346000-46352000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr21:46346200-46352200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr21:46347000-46351800	Enhancers	Spleen	Spleen
6	chr21:46348200-46351000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr21:46348200-46351200	Enhancers	Primary hematopoietic stem cells	blood
8	chr21:46348200-46351400	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr21:46348400-46351000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr21:46349000-46351800	Flanking Active TSS	GM12878-XiMat	blood
11	chr21:46349200-46351200	Weak transcription	A549	lung
12	chr21:46349400-46351000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr21:46349400-46351000	Enhancers	HSMM	muscle
14	chr21:46349400-46351600	Bivalent Enhancer	NHEK	skin
15	chr21:46349600-46351200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr21:46349600-46351200	Weak transcription	HSMMtube	muscle
17	chr21:46349800-46351000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr21:46349800-46351200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
19	chr21:46349800-46351200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
20	chr21:46349800-46351200	Bivalent Enhancer	Placenta	Placenta
21	chr21:46349800-46351400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr21:46349800-46352400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr21:46350000-46351000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr21:46350000-46351400	Enhancers	Liver	Liver
25	chr21:46350000-46351600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr21:46350000-46351800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:46350000-46352400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr21:46350200-46351000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:46350200-46351000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr21:46350200-46351000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr21:46350200-46351000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr21:46350200-46351400	Flanking Active TSS	Fetal Thymus	thymus
33	chr21:46350200-46351800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr21:46350200-46351800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr21:46350200-46351800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr21:46350200-46351800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr21:46350200-46351800	Flanking Active TSS	Dnd41	blood
38	chr21:46350200-46352000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr21:46350200-46352600	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr21:46350400-46351000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
41	chr21:46350400-46351200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr21:46350400-46351200	Weak transcription	Pancreas	Pancrea
43	chr21:46350400-46351400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr21:46350400-46351400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr21:46350400-46351400	Enhancers	HepG2	liver
46	chr21:46350400-46352800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
47	chr21:46350600-46351000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr21:46350600-46351200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr21:46350600-46351200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr21:46350600-46351200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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