Variant report

Variant	rs1562996
Chromosome Location	chr9:21577870-21577871
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10757226	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13283078	0.86[ASN][1000 genomes]
rs1377192	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377193	1.00[ASN][1000 genomes]
rs1452653	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452654	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452660	0.96[AFR][1000 genomes]
rs1542302	0.90[AFR][1000 genomes]
rs1551919	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1869207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4141713	0.96[ASN][1000 genomes]
rs4978124	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475539	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7042262	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7046179	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7046475	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71504796	0.86[ASN][1000 genomes]
rs9298816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs973422	0.98[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031432	chr9:21472601-21608774	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
2	nsv540085	chr9:21472601-21608774	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	122 gene(s)	inside rSNPs	diseases
3	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21575800-21592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:21576000-21578800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:21576000-21578800	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr9:21576200-21578800	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr9:21576200-21578800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr9:21576400-21578000	Enhancers	GM12878-XiMat	blood
7	chr9:21576400-21578800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr9:21576600-21579000	Weak transcription	Stomach Mucosa	stomach
9	chr9:21576600-21579200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:21576800-21578000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:21576800-21578800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:21577000-21578000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:21577000-21578200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:21577000-21578400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:21577000-21578600	Enhancers	Primary T cells from cord blood	blood
16	chr9:21577000-21578600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:21577000-21578800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:21577000-21578800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr9:21577000-21578800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:21577000-21578800	Weak transcription	Thymus	Thymus
21	chr9:21577200-21578000	Enhancers	HMEC	breast
22	chr9:21577200-21578200	Flanking Active TSS	A549	lung
23	chr9:21577200-21578200	Enhancers	HUVEC	blood vessel
24	chr9:21577200-21578200	Enhancers	NH-A	brain
25	chr9:21577200-21578200	Enhancers	NHDF-Ad	bronchial
26	chr9:21577200-21578600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:21577200-21578800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:21577200-21585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:21577400-21578200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:21577400-21578200	Enhancers	NHEK	skin
31	chr9:21577400-21578800	Enhancers	NHLF	lung
32	chr9:21577400-21579600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:21577600-21578000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:21577800-21578000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:21577800-21578200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:21577800-21578400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:21577800-21578400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:21577800-21578600	Enhancers	Osteobl	bone
39	chr9:21577800-21578800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:21577800-21578800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:21577800-21578800	Enhancers	Hela-S3	cervix
42	chr9:21577800-21579000	Weak transcription	HSMM	muscle
43	chr9:21577800-21579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:21577800-21579200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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