Variant report

Variant	rs6938215
Chromosome Location	chr6:49054765-49054766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10948484	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2496356	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2496368	0.88[ASN][1000 genomes]
rs2516121	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2516123	0.83[ASN][1000 genomes]
rs4289650	0.80[ASN][1000 genomes]
rs4295467	0.80[ASN][1000 genomes]
rs4510676	0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6458671	0.80[ASN][1000 genomes]
rs6458674	0.80[ASN][1000 genomes]
rs6458676	0.81[ASN][1000 genomes]
rs6901713	0.80[ASN][1000 genomes]
rs6927013	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs6927493	0.80[ASN][1000 genomes]
rs7746139	0.81[ASN][1000 genomes]
rs7776038	0.81[ASN][1000 genomes]
rs9367347	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9369860	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv603049	chr6:48931959-49169337	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885880	chr6:48975662-49102186	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6938215	CENPQ	cis	Artery Tibial	GTEx
rs6938215	CENPQ	cis	Adipose Subcutaneous	GTEx
rs6938215	MUT	cis	Nerve Tibial	GTEx
rs6938215	C6orf139	cis	multi-tissue	Pritchard
rs6938215	CENPQ	cis	Esophagus Muscularis	GTEx
rs6938215	MUT	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49040400-49089600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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