Variant report

Variant	rs556046
Chromosome Location	chr6:49286340-49286341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1738334	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924989	0.83[JPT][hapmap]
rs3930746	0.83[JPT][hapmap]
rs502946	0.91[CHD][hapmap]
rs504213	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs539581	0.89[CHD][hapmap]
rs540785	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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs570475	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs571140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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
rs556046	CENPQ	cis	Adipose Subcutaneous	GTEx
rs556046	MUT	cis	Artery Tibial	GTEx
rs556046	CENPQ	cis	lung	GTEx
rs556046	MUT	cis	multi-tissue	Pritchard
rs556046	CENPQ	cis	Artery Tibial	GTEx
rs556046	MUT	cis	Nerve Tibial	GTEx
rs556046	CENPQ	cis	lymphoblastoid	seeQTL
rs556046	CENPQ	cis	Esophagus Muscularis	GTEx
rs556046	C6orf139	cis	multi-tissue	Pritchard
rs556046	CENPQ	cis	Nerve Tibial	GTEx
rs556046	CENPQ	cis	Thyroid	GTEx

Chromatin state (count:1 , 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

Quick Search:

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

what's new

Quick links