Variant report

Variant	rs2102727
Chromosome Location	chr8:52900613-52900614
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12550430	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996259	0.91[ASN][1000 genomes]
rs1996260	0.81[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2090259	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2090260	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147306	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4302862	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4873622	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873624	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873625	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873626	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873627	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873628	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873629	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873630	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873631	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4873632	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55996614	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57711556	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6473670	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6473671	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6473672	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6982231	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6983991	0.91[ASN][1000 genomes]
rs6987076	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6987717	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6992125	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6993367	1.00[YRI][hapmap]
rs6998696	0.90[ASN][1000 genomes]
rs7003916	0.90[ASN][1000 genomes]
rs7004360	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7008730	0.87[ASN][1000 genomes]
rs7012596	0.87[ASN][1000 genomes]
rs7820670	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964433	0.91[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	nsv817615	chr8:52252405-53023384	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1031672	chr8:52872448-52917469	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1020673	chr8:52878946-52917469	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1017700	chr8:52886765-52917469	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv520947	chr8:52887541-52915994	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv611353	chr8:52887541-52915994	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1027822	chr8:52897278-52916486	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2102727	PCMTD1	cis	cerebellum	SCAN
rs2102727	SMAD4	trans	parietal	SCAN
rs2102727	PCMTD1	cis	multi-tissue	Pritchard
rs2102727	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52887000-52906800	Weak transcription	Pancreas	Pancrea
2	chr8:52898600-52901200	Enhancers	HepG2	liver
3	chr8:52899400-52901600	Enhancers	GM12878-XiMat	blood
4	chr8:52899600-52902000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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