Variant report

Variant	rs2609407
Chromosome Location	chr1:223090963-223090964
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10495205	0.81[AFR][1000 genomes]
rs17163548	0.83[ASN][1000 genomes]
rs17163550	0.83[ASN][1000 genomes]
rs17163557	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163559	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163564	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609385	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609386	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609388	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609390	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609399	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609400	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609403	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609405	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609406	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789961	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789966	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789967	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789975	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2841041	0.82[EUR][1000 genomes]
rs35185132	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73128670	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:20 , 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	chr1:223088200-223091000	Enhancers	Stomach Mucosa	stomach
5	chr1:223088600-223091600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:223088800-223092600	Weak transcription	HSMMtube	muscle
7	chr1:223089000-223096400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:223089400-223092200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:223089600-223091200	ZNF genes & repeats	Fetal Muscle Leg	muscle
10	chr1:223089600-223092400	ZNF genes & repeats	Primary B cells from cord blood	blood
11	chr1:223089800-223092000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:223089800-223092000	Weak transcription	NHLF	lung
13	chr1:223090400-223091000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
14	chr1:223090400-223091200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:223090600-223091000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:223090600-223091200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:223090600-223092200	Weak transcription	Osteobl	bone
18	chr1:223090800-223092200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:223090800-223092800	Weak transcription	Fetal Lung	lung
20	chr1:223090800-223101600	Weak transcription	Pancreas	Pancrea

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