Variant report

Variant	esv3337818
Chromosome Location	chr21:40588653-40589057
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:49406853..49407429-chr21:40589018..40589538,2	MCF-7	breast:
2	21:40583765-40590917..21:40718004-40719183	GM12878	blood:
3	chr21:40554637..40556936-chr21:40588612..40590641,2	K562	blood:
4	21:40583765-40590917..21:40796857-40798340	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSMG1-1	chr21:40589019-40589103	ENSG00000237373.1
2	lnc-WRB-6	chr21:40588550-40588709	NONHSAT082155

Variant related genes	Relation type
ENSG00000272991	chromatin interactions
ENSG00000183527	chromatin interactions
ENSG00000205581	chromatin interactions
ENSG00000182093	chromatin interactions

Extended variants
information (count: 22 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570021523	chr21:40588678-40588679	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
2	rs114468680	chr21:40588682-40588683	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
3	rs377131549	chr21:40588694-40588695	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
4	rs2836940	chr21:40588696-40588697	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs183811594	chr21:40588713-40588714	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs371043041	chr21:40588811-40588812	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs4818005	chr21:40588819-40588820	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs553534049	chr21:40588830-40588831	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs189610811	chr21:40588840-40588841	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs542705413	chr21:40588899-40588900	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs201294206	chr21:40588923-40588924	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs192585784	chr21:40588942-40588943	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs67133519	chr21:40588948-40588949	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs2410106	chr21:40588950-40588951	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs202098838	chr21:40588961-40588962	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs8130275	chr21:40588962-40588963	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs555928887	chr21:40588979-40588980	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs78620824	chr21:40589000-40589001	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs76570110	chr21:40589002-40589003	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs563038898	chr21:40589021-40589022	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
21	rs67939044	chr21:40589023-40589024	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
22	rs7279236	chr21:40589033-40589034	Weak transcription Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	mRNA abundance

Variant related diseases (count:71)

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 myeloid leukemia	20729466	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
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Down syndrome	20877625	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Prostate cancer	21147910	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164919	CNVD

Chromatin state (count:134 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40592600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr21:40565400-40653600	Strong transcription	Dnd41	blood
14	chr21:40565600-40590200	Strong transcription	Liver	Liver
15	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr21:40565800-40590600	Strong transcription	Fetal Thymus	thymus
17	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:40566200-40590600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr21:40566200-40590600	Strong transcription	Adipose Nuclei	Adipose
20	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:40567400-40592400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:40570600-40589800	Weak transcription	Stomach Mucosa	stomach
24	chr21:40571400-40602400	Weak transcription	Fetal Brain Male	brain
25	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
26	chr21:40573800-40593600	Weak transcription	A549	lung
27	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
28	chr21:40575200-40589400	Weak transcription	NHEK	skin
29	chr21:40576200-40590400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr21:40576200-40597400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:40576400-40592400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr21:40576600-40589000	Strong transcription	Primary B cells from cord blood	blood
33	chr21:40576800-40589600	Weak transcription	HUVEC	blood vessel
34	chr21:40576800-40593600	Weak transcription	Right Atrium	heart
35	chr21:40577200-40593800	Weak transcription	Colon Smooth Muscle	Colon
36	chr21:40577200-40595400	Weak transcription	Colonic Mucosa	Colon
37	chr21:40577600-40589400	Weak transcription	Brain Hippocampus Middle	brain
38	chr21:40577600-40596000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr21:40577800-40598800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr21:40578000-40589000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr21:40578000-40589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr21:40578000-40595600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr21:40578000-40598800	Weak transcription	Gastric	stomach
44	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
45	chr21:40578400-40589400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr21:40578600-40595400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr21:40578600-40595400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
50	chr21:40579000-40598800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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