Variant report

Variant	rs10453128
Chromosome Location	chr8:52884308-52884309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10087958	0.82[ASN][1000 genomes]
rs12541514	0.80[ASN][1000 genomes]
rs12541693	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12544671	0.80[ASN][1000 genomes]
rs12544872	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12545423	0.82[ASN][1000 genomes]
rs12545755	0.81[ASN][1000 genomes]
rs12546159	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs12547887	0.81[ASN][1000 genomes]
rs12678795	0.80[ASN][1000 genomes]
rs16916966	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16916968	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs16917017	0.81[ASN][1000 genomes]
rs16917024	0.80[ASN][1000 genomes]
rs16917026	0.80[ASN][1000 genomes]
rs16917029	0.80[ASN][1000 genomes]
rs16917030	0.80[ASN][1000 genomes]
rs16917031	0.80[ASN][1000 genomes]
rs2138297	0.82[ASN][1000 genomes]
rs2176119	0.82[ASN][1000 genomes]
rs55870400	0.80[ASN][1000 genomes]
rs6473675	0.94[CHB][hapmap]
rs6473676	0.94[CHB][hapmap]
rs6473677	0.94[CHB][hapmap]
rs6473678	0.94[CHB][hapmap]
rs6982212	0.94[CHB][hapmap]
rs7005809	0.95[CHB][hapmap]
rs73681421	0.82[ASN][1000 genomes]
rs73681429	0.80[ASN][1000 genomes]
rs73681430	0.80[ASN][1000 genomes]
rs73681431	0.80[ASN][1000 genomes]
rs7813414	0.84[ASN][1000 genomes]
rs7816834	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7817558	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817892	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7819892	0.82[ASN][1000 genomes]
rs7833668	0.82[JPT][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs7834181	0.82[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs7838307	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs7844884	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs877248	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9298469	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10453128	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52875400-52884800	Weak transcription	Pancreas	Pancrea
2	chr8:52875800-52886200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:52881600-52886200	Weak transcription	Psoas Muscle	Psoas
4	chr8:52884000-52885600	Weak transcription	HepG2	liver

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