Variant report

Variant	rs12421544
Chromosome Location	chr11:105038968-105038969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10502046	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10502047	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281540	0.85[EUR][1000 genomes]
rs12416756	0.85[EUR][1000 genomes]
rs12417050	1.00[CEU][hapmap];0.90[MEX][hapmap]
rs12417470	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs12419220	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12420524	0.85[EUR][1000 genomes]
rs12420557	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12420601	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12421898	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12787184	0.81[AMR][1000 genomes]
rs12796365	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12797290	0.81[AMR][1000 genomes]
rs12797298	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12797775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12800151	1.00[CEU][hapmap];0.90[MEX][hapmap]
rs12801987	1.00[CEU][hapmap];0.90[MEX][hapmap]
rs12806837	0.82[EUR][1000 genomes]
rs1354322	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1503386	0.85[EUR][1000 genomes]
rs1503395	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103670	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs17103773	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17103781	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103836	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103858	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103866	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17103873	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17103951	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376738	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17377910	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17378343	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1847301	0.81[AMR][1000 genomes]
rs2047840	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2047841	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2062807	0.85[EUR][1000 genomes]
rs2062808	0.85[EUR][1000 genomes]
rs2155817	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2409065	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3181328	1.00[CHB][hapmap]
rs34105770	0.81[AMR][1000 genomes]
rs34146979	0.81[AMR][1000 genomes]
rs34212668	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34255114	0.82[EUR][1000 genomes]
rs34806541	0.81[AMR][1000 genomes]
rs34819285	0.81[AMR][1000 genomes]
rs35120805	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35136587	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35394521	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35560124	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35565964	0.85[EUR][1000 genomes]
rs35743576	0.85[EUR][1000 genomes]
rs475266	0.89[CEU][hapmap]
rs4754122	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4754123	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4754124	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4754125	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4755076	0.85[EUR][1000 genomes]
rs4755077	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4755078	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4755079	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4755080	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4755081	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs481926	1.00[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs486123	1.00[CEU][hapmap]
rs530009	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs538943	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs567303	0.89[CEU][hapmap]
rs58131087	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60235102	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67835723	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7117758	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71484389	0.81[AMR][1000 genomes]
rs71484390	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71484394	0.85[EUR][1000 genomes]
rs71484399	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71484400	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71484401	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71484402	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7929852	0.85[EUR][1000 genomes]
rs7930712	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531430	chr11:104380924-105194452	Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv468862	chr11:104774014-105243371	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv556218	chr11:104774014-105243371	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv3385159	chr11:104786549-105051555	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1044970	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv541160	chr11:104809246-105225032	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv949337	chr11:104950007-105510193	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv528789	chr11:105014564-105133046	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1045900	chr11:105015999-105138877	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12421544	COP1	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105034600-105039200	Weak transcription	HUVEC	blood vessel
2	chr11:105037200-105039000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:105038600-105039400	Enhancers	NHDF-Ad	bronchial
4	chr11:105038800-105039600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links