Variant report

Variant	rs525559
Chromosome Location	chr6:49273112-49273113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs476180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs479383	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492172	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493184	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493700	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502946	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs528451	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs539581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs542538	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555933	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562077	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs579846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2755862	chr6:49081541-49298041	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs525559	CENPQ	cis	Adipose Subcutaneous	GTEx
rs525559	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs525559	CENPQ	cis	Artery Tibial	GTEx
rs525559	CENPQ	cis	Nerve Tibial	GTEx
rs525559	CENPQ	cis	Esophagus Mucosa	GTEx
rs525559	MUT	cis	Nerve Tibial	GTEx
rs525559	CENPQ	cis	lung	GTEx
rs525559	CENPQ	cis	multi-tissue	Pritchard
rs525559	CENPQ	cis	Thyroid	GTEx
rs525559	CENPQ	cis	Whole Blood	GTEx
rs525559	CENPQ	cis	Esophagus Muscularis	GTEx
rs525559	CENPQ	cis	Artery Aorta	GTEx
rs525559	CENPQ	cis	Muscle Skeletal	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49267200-49281000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:49273000-49273400	Flanking Active TSS	HUVEC	blood vessel

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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