Variant report

Variant	rs2609392
Chromosome Location	chr1:223091868-223091869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1890615	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1970382	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2039780	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2039782	0.84[ASN][1000 genomes]
rs2254329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609343	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609394	0.81[ASN][1000 genomes]
rs2609395	0.83[ASN][1000 genomes]
rs2609396	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609397	0.83[ASN][1000 genomes]
rs2609398	0.81[ASN][1000 genomes]
rs2609401	0.80[ASN][1000 genomes]
rs2609402	0.80[ASN][1000 genomes]
rs2609404	0.80[ASN][1000 genomes]
rs2609408	0.80[ASN][1000 genomes]
rs2789960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789962	0.81[ASN][1000 genomes]
rs2789963	0.81[ASN][1000 genomes]
rs2789964	0.81[ASN][1000 genomes]
rs2789965	0.81[ASN][1000 genomes]
rs2789968	0.80[ASN][1000 genomes]
rs2789969	0.80[ASN][1000 genomes]
rs2789970	0.80[ASN][1000 genomes]
rs2789971	0.80[ASN][1000 genomes]
rs2789973	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35293291	0.85[ASN][1000 genomes]
rs35947998	0.96[YRI][hapmap]
rs4846782	0.86[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9651261	0.85[ASN][1000 genomes]
rs9651262	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223071600-223092400	Weak transcription	Ovary	ovary
2	chr1:223083200-223101400	Weak transcription	Fetal Heart	heart
3	chr1:223083600-223101600	Weak transcription	Fetal Stomach	stomach
4	chr1:223088800-223092600	Weak transcription	HSMMtube	muscle
5	chr1:223089000-223096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:223089400-223092200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:223089600-223092400	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr1:223089800-223092000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:223089800-223092000	Weak transcription	NHLF	lung
10	chr1:223090600-223092200	Weak transcription	Osteobl	bone
11	chr1:223090800-223092200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:223090800-223092800	Weak transcription	Fetal Lung	lung
13	chr1:223090800-223101600	Weak transcription	Pancreas	Pancrea
14	chr1:223091000-223092000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:223091000-223094800	Weak transcription	Stomach Mucosa	stomach
16	chr1:223091200-223092600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:223091200-223092800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:223091200-223097000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:223091400-223092000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:223091400-223092000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:223091600-223092600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:223091800-223092200	Enhancers	NHEK	skin

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