Variant report

Variant	rs540785
Chromosome Location	chr6:49288384-49288385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1738334	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1924989	0.83[JPT][hapmap]
rs3930746	0.83[JPT][hapmap]
rs476180	0.85[YRI][hapmap]
rs479383	0.81[AFR][1000 genomes]
rs492172	0.85[AFR][1000 genomes]
rs502946	0.91[CHD][hapmap]
rs504213	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs539581	0.89[CHD][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap]
rs542538	0.81[AFR][1000 genomes]
rs555933	0.91[AFR][1000 genomes]
rs556046	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs562077	0.91[CHD][hapmap]
rs562112	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570475	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs571140	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9473535	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
3	esv3434790	chr6:49281547-49295228	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a
4	esv3472555	chr6:49281568-49295231	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a
5	esv3472556	chr6:49281633-49295152	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
6	esv3472557	chr6:49281695-49295113	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
7	esv13429	chr6:49281885-49295108	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
8	esv2762590	chr6:49286305-49295370	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs540785	CENPQ	cis	Adipose Subcutaneous	GTEx
rs540785	CENPQ	cis	Nerve Tibial	GTEx
rs540785	CENPQ	cis	lung	GTEx
rs540785	MUT	cis	Nerve Tibial	GTEx
rs540785	CENPQ	cis	Thyroid	GTEx
rs540785	CENPQ	cis	Artery Tibial	GTEx
rs540785	MUT	cis	multi-tissue	Pritchard
rs540785	C6orf139	cis	multi-tissue	Pritchard
rs540785	MUT	cis	Artery Tibial	GTEx
rs540785	CENPQ	cis	lymphoblastoid	seeQTL
rs540785	CENPQ	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49285000-49293600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:49286800-49288400	Enhancers	Primary hematopoietic stem cells	blood

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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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