Variant report

Variant	rs6656824
Chromosome Location	chr1:224743343-224743344
allele	A/G
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	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.83[TSI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916635	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916637	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916638	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916639	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916640	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12033478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043625	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12057775	0.91[CEU][hapmap];0.93[CHB][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12062991	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12068420	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12072482	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1317810	0.98[EUR][1000 genomes]
rs1499283	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16849369	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2050625	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2794804	0.96[EUR][1000 genomes]
rs2794808	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4654047	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61825839	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61825840	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61825841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs698277	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698280	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs712068	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs712070	0.93[EUR][1000 genomes]
rs712071	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[EUR][1000 genomes]
rs712072	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes]
rs712073	0.95[EUR][1000 genomes]
rs712074	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712075	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712076	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712082	0.98[EUR][1000 genomes]
rs712084	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712085	0.98[EUR][1000 genomes]
rs712087	0.98[EUR][1000 genomes]
rs712092	0.92[CEU][hapmap];0.94[CHB][hapmap];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7541415	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs791391	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791393	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791508	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791509	0.95[EUR][1000 genomes]
rs791510	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs791511	0.95[EUR][1000 genomes]
rs791512	0.95[EUR][1000 genomes]
rs880368	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs983948	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs985301	0.94[EUR][1000 genomes]
rs989755	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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
rs6656824	LEFTY1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224731600-224746400	Weak transcription	Psoas Muscle	Psoas
2	chr1:224736800-224746400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:224740000-224762200	Weak transcription	Ovary	ovary
4	chr1:224741400-224751400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:224742000-224746000	Weak transcription	HMEC	breast
6	chr1:224742000-224746200	Weak transcription	NHDF-Ad	bronchial
7	chr1:224742000-224746400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:224742000-224753000	Weak transcription	Pancreas	Pancrea
9	chr1:224742600-224744400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:224742600-224746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:224742800-224745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:224743000-224746200	Weak transcription	NHEK	skin

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