Variant report

Variant	rs6438299
Chromosome Location	chr3:115860229-115860230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511355	0.88[CHB][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs12330535	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13078076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1461109	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1461116	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1461132	0.81[ASN][1000 genomes]
rs1461134	0.83[ASN][1000 genomes]
rs1468003	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1898	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1947689	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2864074	0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2864075	0.81[ASN][1000 genomes]
rs6438300	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs6438303	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs6438304	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs6807792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7618443	0.81[ASN][1000 genomes]
rs7629590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7638493	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs7640143	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs7641198	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs7644082	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9812548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834589	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9834897	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9835757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9870541	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872975	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875609	0.88[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs998807	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][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	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2756413	chr3:115721898-115908480	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2751975	chr3:115766285-115902901	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2755046	chr3:115818840-115942952	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv591345	chr3:115819376-115902901	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752728	chr3:115833212-115902901	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6438299	GMPR	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115854200-115861200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:115854800-115860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:115855200-115860800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:115855200-115864200	Weak transcription	Fetal Lung	lung
5	chr3:115858800-115860800	Enhancers	Colon Smooth Muscle	Colon
6	chr3:115859000-115860400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:115859000-115860400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:115859000-115860400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:115859400-115860600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:115859400-115866000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:115859600-115860400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:115859600-115860400	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:115860000-115861000	Enhancers	Brain Anterior Caudate	brain

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