Variant report

Variant	rs4873573
Chromosome Location	chr8:52601751-52601752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10086425	0.81[CEU][hapmap]
rs10090123	0.85[EUR][1000 genomes]
rs10090972	0.83[EUR][1000 genomes]
rs10105030	0.81[CEU][hapmap]
rs1013621	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs1013622	0.81[CEU][hapmap]
rs10958294	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10958295	0.86[EUR][1000 genomes]
rs10958297	0.85[EUR][1000 genomes]
rs11774370	0.81[CEU][hapmap]
rs11775179	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11781376	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12335014	0.81[CEU][hapmap]
rs12548147	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12677123	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12677168	0.83[CEU][hapmap]
rs1317774	0.83[EUR][1000 genomes]
rs13251959	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13251960	0.83[EUR][1000 genomes]
rs13265125	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13268396	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13268711	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13274101	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13279413	0.83[EUR][1000 genomes]
rs13279418	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs16916673	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16916756	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16916858	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[MEX][hapmap]
rs28549751	0.83[EUR][1000 genomes]
rs34228216	0.87[AFR][1000 genomes]
rs34276635	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35153909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35365537	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36052716	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4242470	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4275221	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4291264	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4397396	0.86[EUR][1000 genomes]
rs4469447	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4873199	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4873611	0.81[CEU][hapmap]
rs6473660	0.81[CEU][hapmap]
rs6986544	0.81[CEU][hapmap]
rs6987346	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6995555	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7007297	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7007804	0.85[EUR][1000 genomes]
rs7462096	0.81[CEU][hapmap]
rs7823666	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7836565	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7839661	0.83[EUR][1000 genomes]
rs7845169	0.97[ASN][1000 genomes]
rs925762	0.81[CEU][hapmap]
rs9298462	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs9643785	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9650303	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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
7	nsv890898	chr8:52579964-52680933	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4873573	PCMTD1	cis	brain	seeQTL
rs4873573	LOC115294	cis	multi-tissue	Pritchard
rs4873573	PCMTD1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52599400-52604800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr8:52600600-52601800	Enhancers	Left Ventricle	heart
3	chr8:52601400-52601800	Enhancers	Right Atrium	heart
4	chr8:52601600-52601800	Enhancers	Right Ventricle	heart
5	chr8:52601600-52604200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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