Variant report

Variant	rs7820670
Chromosome Location	chr8:52895021-52895022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:52811794..52813477-chr8:52893629..52895891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228801	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12550430	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1996259	0.90[ASN][1000 genomes]
rs1996260	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2090259	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2090260	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2102727	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147306	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4302862	0.90[ASN][1000 genomes]
rs4873622	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873624	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873625	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873626	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873627	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873628	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873629	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873630	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873631	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4873632	0.94[ASN][1000 genomes]
rs55996614	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57711556	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473670	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473671	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6473672	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6982231	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6983991	0.90[ASN][1000 genomes]
rs6987076	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6987717	0.89[ASN][1000 genomes]
rs6992125	0.90[ASN][1000 genomes]
rs6998696	0.90[ASN][1000 genomes]
rs7003916	0.90[ASN][1000 genomes]
rs7004360	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7008730	0.86[ASN][1000 genomes]
rs7012596	0.86[ASN][1000 genomes]
rs7844884	0.81[EUR][1000 genomes]
rs964433	0.90[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7820670	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52887000-52906800	Weak transcription	Pancreas	Pancrea
2	chr8:52893600-52898800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:52894000-52899400	Weak transcription	Placenta	Placenta
4	chr8:52895000-52895600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr8:52895000-52895600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr8:52895000-52895800	Enhancers	Skeletal Muscle Male	skeletal muscle

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