Variant report

Variant	rs1590952
Chromosome Location	chr13:38960711-38960712
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1011484	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10507469	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10507470	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17057355	1.00[CHB][hapmap]
rs17057710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17057848	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17057900	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019516	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2173948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231320	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455408	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455413	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481887	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481888	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481892	1.00[ASN][1000 genomes]
rs2485779	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496468	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56306542	1.00[ASN][1000 genomes]
rs7322186	1.00[ASN][1000 genomes]
rs73460283	1.00[ASN][1000 genomes]
rs74047550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74047551	1.00[EUR][1000 genomes]
rs74047552	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74047553	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74047554	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532217	1.00[ASN][1000 genomes]
rs9548328	1.00[ASN][1000 genomes]
rs9888482	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900006	chr13:38924871-38970825	Genic enhancers ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38957200-38962400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:38959200-38961200	Enhancers	HMEC	breast
3	chr13:38959400-38960800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:38959400-38962600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:38959600-38962600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:38960000-38961200	Enhancers	NHEK	skin
7	chr13:38960200-38961000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:38960200-38961200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:38960200-38961200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:38960400-38961000	Active TSS	Fetal Kidney	kidney
11	chr13:38960600-38961000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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