Variant report

Variant	rs3088088
Chromosome Location	chr20:13691058-13691059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696371	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs1541059	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs1970933	0.97[AFR][1000 genomes]
rs2026058	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031934	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs34414644	0.97[ASN][1000 genomes]
rs4813139	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs56024260	0.97[ASN][1000 genomes]
rs6033809	0.82[AFR][1000 genomes]
rs6042314	0.88[CEU][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6042318	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs6042319	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs6074637	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs6079143	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079146	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs6079148	0.97[ASN][1000 genomes]
rs6079160	1.00[CHB][hapmap]
rs6079161	1.00[CHB][hapmap]
rs6079174	1.00[CHB][hapmap]
rs6079180	1.00[CHB][hapmap]
rs6110035	0.93[YRI][hapmap]
rs73094118	0.97[ASN][1000 genomes]
rs73094125	0.97[ASN][1000 genomes]

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	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3088088	ESF1	cis	brain	BrainEAC

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13682600-13691200	Weak transcription	Dnd41	blood
2	chr20:13689000-13694400	Weak transcription	Primary B cells from cord blood	blood
3	chr20:13690000-13694000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr20:13690200-13696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr20:13690400-13691800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:13690400-13692800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr20:13690400-13697000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:13690600-13691600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr20:13690600-13694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:13690600-13694000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr20:13690600-13695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
13	chr20:13690800-13691800	Weak transcription	Primary T cells from cord blood	blood
14	chr20:13691000-13691600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:13691000-13692600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:13691000-13692800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr20:13691000-13692800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr20:13691000-13693800	Weak transcription	Left Ventricle	heart

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