Variant report

Variant	rs13025700
Chromosome Location	chr2:211168202-211168203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10179268	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155845	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675027	1.00[ASN][1000 genomes]
rs11678206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682370	1.00[ASN][1000 genomes]
rs11686587	1.00[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688922	1.00[ASN][1000 genomes]
rs11900095	1.00[EUR][1000 genomes]
rs12992714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002602	1.00[ASN][1000 genomes]
rs13009071	1.00[ASN][1000 genomes]
rs13009890	1.00[ASN][1000 genomes]
rs13011543	1.00[ASN][1000 genomes]
rs13015487	1.00[EUR][1000 genomes]
rs13017647	1.00[ASN][1000 genomes]
rs13019613	1.00[ASN][1000 genomes]
rs13020232	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021055	1.00[ASN][1000 genomes]
rs13022638	1.00[EUR][1000 genomes]
rs13023313	1.00[EUR][1000 genomes]
rs13025911	0.97[EUR][1000 genomes]
rs13415601	1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509568	1.00[CHB][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs1509570	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509571	1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509572	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844213	1.00[CHB][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2048277	1.00[EUR][1000 genomes]
rs2160020	1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs2539005	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263668	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263675	1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs263680	1.00[CHB][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263681	1.00[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263686	1.00[ASN][1000 genomes]
rs34334556	1.00[ASN][1000 genomes]
rs34693593	1.00[EUR][1000 genomes]
rs35125543	1.00[ASN][1000 genomes]
rs36080651	1.00[ASN][1000 genomes]
rs3732057	1.00[CHB][hapmap]
rs62202972	1.00[ASN][1000 genomes]
rs6435561	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714161	1.00[ASN][1000 genomes]
rs6716836	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732072	1.00[ASN][1000 genomes]
rs6732486	1.00[ASN][1000 genomes]
rs6732506	1.00[ASN][1000 genomes]
rs6735292	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6760874	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71350736	1.00[ASN][1000 genomes]
rs71350737	1.00[EUR][1000 genomes]
rs7557043	1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802749	chr2:210905194-211255611	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv1803710	chr2:211073376-211173763	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1012567	chr2:211087588-211315554	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv834520	chr2:211101265-211257068	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875767	chr2:211119233-211334647	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1014508	chr2:211142855-211215068	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1010916	chr2:211147730-211205281	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13025700	PLEKHM3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:211163400-211168600	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr2:211163400-211168800	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr2:211164600-211168800	Active TSS	Fetal Muscle Trunk	muscle
4	chr2:211166400-211174000	Weak transcription	Psoas Muscle	Psoas
5	chr2:211166600-211168600	Enhancers	HSMM	muscle
6	chr2:211167600-211168400	Active TSS	HSMMtube	muscle
7	chr2:211167600-211168800	Active TSS	Fetal Muscle Leg	muscle

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