Variant report

Variant	rs7844884
Chromosome Location	chr8:52892727-52892728
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10087958	0.88[JPT][hapmap]
rs10453128	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10958307	0.90[ASN][1000 genomes]
rs12541514	0.91[ASN][1000 genomes]
rs12541693	1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs12544671	0.91[ASN][1000 genomes]
rs12544872	0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs12545423	0.93[ASN][1000 genomes]
rs12545755	0.92[ASN][1000 genomes]
rs12546159	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12547887	0.92[ASN][1000 genomes]
rs12678795	0.91[ASN][1000 genomes]
rs16917017	0.92[ASN][1000 genomes]
rs16917024	0.91[ASN][1000 genomes]
rs16917026	0.91[ASN][1000 genomes]
rs16917029	0.91[ASN][1000 genomes]
rs16917030	0.91[ASN][1000 genomes]
rs16917031	0.91[ASN][1000 genomes]
rs2280179	0.81[JPT][hapmap]
rs55870400	0.91[ASN][1000 genomes]
rs6473675	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6473676	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6473677	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6473678	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6982212	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7005809	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs73681421	0.93[ASN][1000 genomes]
rs73681429	0.91[ASN][1000 genomes]
rs73681430	0.91[ASN][1000 genomes]
rs73681431	0.91[ASN][1000 genomes]
rs73681434	0.90[ASN][1000 genomes]
rs7816834	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7817558	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7817892	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7820670	0.81[EUR][1000 genomes]
rs7838307	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs9298469	0.95[CHB][hapmap];0.88[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7844884	PCMTD1	Cis_1M	lymphoblastoid	RTeQTL
rs7844884	PCMTD1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52887000-52906800	Weak transcription	Pancreas	Pancrea
2	chr8:52891800-52892800	Enhancers	Placenta	Placenta
3	chr8:52892000-52893000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr8:52892600-52892800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:52892600-52892800	Enhancers	Fetal Intestine Small	intestine
6	chr8:52892600-52893000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr8:52892600-52895000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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