Variant report

Variant	rs12623549
Chromosome Location	chr2:209075793-209075794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10192397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10497896	0.82[JPT][hapmap]
rs11676550	0.82[JPT][hapmap]
rs11883992	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12373582	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12474494	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12986551	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs12995124	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12995271	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13025862	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13387151	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704765	0.82[JPT][hapmap]
rs6705133	0.82[JPT][hapmap]
rs6710217	0.82[JPT][hapmap]
rs6710543	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs6722000	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6725512	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs6731295	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6749281	1.00[JPT][hapmap]
rs6751157	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs6751646	1.00[JPT][hapmap]
rs7572263	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs7579275	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs7583625	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9967885	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv875751	chr2:209042963-209110784	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12623549	PLEKHM3	cis	cerebellum	SCAN
rs12623549	C2orf80	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209062600-209080000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:209073000-209077800	Weak transcription	Adipose Nuclei	Adipose
3	chr2:209073200-209078400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:209075000-209076400	Enhancers	Fetal Thymus	thymus
5	chr2:209075400-209075800	Enhancers	Brain Anterior Caudate	brain

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