Variant report

Variant	rs272488
Chromosome Location	chr1:86806372-86806373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10493790	0.92[CHB][hapmap]
rs11161810	0.90[ASN][1000 genomes]
rs11161812	0.92[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11161814	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs11161816	0.92[CHB][hapmap]
rs1158833	0.92[CHB][hapmap]
rs1182098	0.92[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1182099	0.92[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1182101	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12119411	0.92[ASN][1000 genomes]
rs12123660	0.90[ASN][1000 genomes]
rs12125965	0.88[ASN][1000 genomes]
rs12130284	0.88[ASN][1000 genomes]
rs12145243	0.92[CHB][hapmap]
rs12403033	0.92[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12406320	0.84[CHB][hapmap]
rs1413431	0.92[CHB][hapmap]
rs1413432	0.90[ASN][1000 genomes]
rs17409304	0.92[CHB][hapmap]
rs17449526	0.92[CHB][hapmap]
rs272489	0.97[ASN][1000 genomes]
rs272490	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs272493	0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs272495	0.94[ASN][1000 genomes]
rs272496	0.94[ASN][1000 genomes]
rs272497	0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs272499	0.94[ASN][1000 genomes]
rs272501	0.94[ASN][1000 genomes]
rs272505	0.92[ASN][1000 genomes]
rs272509	0.92[ASN][1000 genomes]
rs272512	0.92[ASN][1000 genomes]
rs272515	0.92[ASN][1000 genomes]
rs272518	0.92[ASN][1000 genomes]
rs3737673	0.92[CHB][hapmap]
rs421105	0.85[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs423991	0.94[ASN][1000 genomes]
rs5026277	0.92[CHB][hapmap];0.80[CHD][hapmap];0.81[ASN][1000 genomes]
rs977919	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871866	chr1:86726619-86851420	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs272488	SEP15	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86805000-86806600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:86805400-86806400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:86805400-86817400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:86805600-86810800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:86805600-86810800	Weak transcription	Fetal Lung	lung
6	chr1:86806200-86806800	Enhancers	Primary neutrophils fromperipheralblood	blood

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