Variant report

Variant	rs539581
Chromosome Location	chr6:49330830-49330831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1738334	0.84[AFR][1000 genomes]
rs476180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs479383	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs492172	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs493184	0.82[AMR][1000 genomes]
rs493700	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs502946	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525559	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs528451	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs542538	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555933	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs562077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs570475	0.85[AFR][1000 genomes]
rs579846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv462943	chr6:49319025-49376924	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv603080	chr6:49319025-49376924	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv970038	chr6:49329777-49331108	Inactive region	TF binding region	1 gene(s)	n/a	n/a

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs539581	CENPQ	cis	lung	GTEx
rs539581	TDRD6	cis	cerebellum	SCAN
rs539581	CENPQ	cis	multi-tissue	Pritchard
rs539581	CENPQ	cis	Muscle Skeletal	GTEx
rs539581	CENPQ	cis	Adipose Subcutaneous	GTEx
rs539581	CENPQ	cis	Artery Tibial	GTEx
rs539581	CENPQ	cis	Whole Blood	GTEx
rs539581	CENPQ	cis	Thyroid	GTEx
rs539581	MUT	cis	Nerve Tibial	GTEx
rs539581	CENPQ	cis	Artery Aorta	GTEx
rs539581	DEFB114	cis	cerebellum	SCAN
rs539581	CENPQ	cis	Nerve Tibial	GTEx
rs539581	CENPQ	cis	Esophagus Muscularis	GTEx
rs539581	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs539581	CENPQ	cis	lymphoblastoid	seeQTL
rs539581	CENPQ	cis	Esophagus Mucosa	GTEx

Chromatin state (count:0 , 50 per page) page:

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

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