Variant report

Variant	rs16916654
Chromosome Location	chr8:52560702-52560703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10097328	1.00[CEU][hapmap]
rs10105608	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10106672	0.87[ASN][1000 genomes]
rs13274229	0.92[ASN][1000 genomes]
rs16916660	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916675	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28478150	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4541903	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4873569	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56037615	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61037356	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6473632	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473636	0.91[ASN][1000 genomes]
rs6986665	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7008275	0.87[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7010217	1.00[CEU][hapmap]
rs7017902	0.92[ASN][1000 genomes]
rs73678944	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7821482	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7827024	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7835028	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7837379	0.84[ASN][1000 genomes]
rs7839588	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9298459	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[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	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv890895	chr8:52190571-52615191	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv1018429	chr8:52411443-52878946	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
5	nsv1034856	chr8:52411443-52886765	Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv831313	chr8:52458835-52638968	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs16916654	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52557400-52561200	Enhancers	Fetal Heart	heart
2	chr8:52559600-52565600	Weak transcription	Aorta	Aorta
3	chr8:52559600-52565600	Weak transcription	Psoas Muscle	Psoas
4	chr8:52559600-52570400	Weak transcription	Left Ventricle	heart
5	chr8:52559800-52564200	Weak transcription	Fetal Lung	lung
6	chr8:52560000-52563000	Weak transcription	Adipose Nuclei	Adipose
7	chr8:52560200-52561200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr8:52560400-52563000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:52560400-52567800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr8:52560600-52561000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr8:52560600-52561200	Flanking Active TSS	GM12878-XiMat	blood

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