Variant report

Variant	rs2306717
Chromosome Location	chr4:22709609-22709610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10030690	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs11942704	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12498838	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12506107	0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs12509499	0.80[AFR][1000 genomes]
rs12509633	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1485826	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1485827	0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1485828	0.94[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs16872987	0.82[YRI][hapmap]
rs16873068	0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs17539365	0.85[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs17611607	0.86[ASN][1000 genomes]
rs2013715	0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2014512	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2127178	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28609379	0.85[ASN][1000 genomes]
rs2875116	0.83[ASN][1000 genomes]
rs6818185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6819056	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657828	0.80[ASW][hapmap];1.00[YRI][hapmap]
rs7682224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7695833	0.87[YRI][hapmap]
rs9884970	0.88[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv829883	chr4:22666326-22842517	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2306717	GPR125	cis	parietal	SCAN
rs2306717	PI4K2B	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22699200-22737600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr4:22699600-22717000	Weak transcription	Fetal Intestine Large	intestine
3	chr4:22701600-22711400	Weak transcription	Liver	Liver
4	chr4:22702600-22752600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:22709400-22709800	Active TSS	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links