Variant report

Variant	rs1004307
Chromosome Location	chr3:17875194-17875195
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10510478	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11128836	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11128838	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11128849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11128850	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11128857	0.85[ASN][1000 genomes]
rs11128871	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11914537	0.85[CHB][hapmap]
rs11915560	0.85[CHB][hapmap]
rs11923589	0.85[CHB][hapmap]
rs11923635	0.85[CHB][hapmap]
rs11925066	0.85[CHB][hapmap]
rs11927436	0.85[CHB][hapmap]
rs11927654	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12492504	0.80[EUR][1000 genomes]
rs12495352	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13062642	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13071301	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1430896	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1430904	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1469558	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17044053	0.85[CHB][hapmap]
rs17044072	0.85[CHB][hapmap]
rs17200916	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17200979	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17273111	0.89[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033373	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033374	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033377	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2033378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2033379	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2337387	0.92[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28796017	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4243834	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4260468	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs4312680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4330281	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4377510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4422341	0.85[ASN][1000 genomes]
rs4450852	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4611850	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4632574	0.80[EUR][1000 genomes]
rs4637311	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908942	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908965	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908967	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4908976	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4908978	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908979	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908981	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4908982	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908984	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4908985	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4908986	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4908988	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6577597	0.92[CEU][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6577598	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6771673	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780932	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784025	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6787380	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6794859	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802932	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804677	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6807020	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7619879	0.85[CHB][hapmap]
rs7627732	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7632834	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7633898	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7642860	0.85[CEU][hapmap]
rs7651998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8179891	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs919562	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9862290	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1004307	OXNAD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17873000-17882600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:17874000-17878200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:17874200-17875400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:17874200-17878200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:17874600-17875800	Enhancers	HMEC	breast
6	chr3:17874800-17875600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:17874800-17875800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:17874800-17876000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:17875000-17876000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:17875000-17876000	Enhancers	NHEK	skin
11	chr3:17875000-17876200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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