Variant report

Variant	rs712082
Chromosome Location	chr1:224726060-224726061
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10799582	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10916635	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916636	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916637	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916638	0.88[EUR][1000 genomes]
rs10916639	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916640	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12033478	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12043625	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12057775	0.91[CEU][hapmap];0.93[CHB][hapmap];0.89[EUR][1000 genomes]
rs12062991	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12068420	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12072482	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1317810	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499283	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16849369	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2050625	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2794804	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2794808	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654047	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61825839	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825840	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61825841	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6656824	0.98[EUR][1000 genomes]
rs698277	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs698280	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712068	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712070	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs712071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712072	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712073	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712074	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712075	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712076	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712084	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712085	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712087	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712092	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541415	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs791391	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs791393	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs791508	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs791509	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs791510	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs791511	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs791512	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs880368	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs983948	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs985301	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs989755	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs712082	LEFTY1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224694200-224727600	Weak transcription	Brain Anterior Caudate	brain
2	chr1:224712000-224730800	Weak transcription	Spleen	Spleen
3	chr1:224717600-224727800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224717800-224727200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224718000-224727000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224720400-224727400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224725200-224730400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:224725400-224727200	Weak transcription	Pancreas	Pancrea
9	chr1:224726000-224727200	Enhancers	Dnd41	blood

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