Variant report

Variant	rs9470983
Chromosome Location	chr6:39127045-39127046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10947783	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11960976	0.84[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12661995	0.81[AMR][1000 genomes]
rs1366326	0.85[GIH][hapmap]
rs56384501	0.88[ASN][1000 genomes]
rs6899384	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6916231	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72861353	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7747245	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7747840	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs7751196	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9369105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380832	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394575	0.90[CEU][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9470986	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9470983	CNPY3	cis	cerebellum	SCAN
rs9470983	C6orf108	cis	parietal	SCAN
rs9470983	ZFAND3	cis	cerebellum	SCAN
rs9470983	LITAF	trans	parietal	SCAN

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

No data

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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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