Variant report

Variant	rs6807267
Chromosome Location	chr3:54436824-54436825
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11713798	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs11715872	0.89[EUR][1000 genomes]
rs11717967	0.92[CEU][hapmap]
rs1375517	0.92[CEU][hapmap];0.84[CHB][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs1574200	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs17054035	0.84[CEU][hapmap]
rs1868505	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28499181	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56027715	0.89[EUR][1000 genomes]
rs59598269	0.87[EUR][1000 genomes]
rs6445649	0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445650	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445652	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6445654	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs6445662	0.92[CEU][hapmap]
rs7427395	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7431093	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7638153	0.80[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9818236	0.92[CHB][hapmap];0.87[CHD][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9835975	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1010348	chr3:54435563-54508115	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6807267	APPL1	cis	cerebellum	SCAN
rs6807267	TEX264	cis	parietal	SCAN
rs6807267	SEMA3G	cis	parietal	SCAN
rs6807267	MAPKAPK3	cis	parietal	SCAN

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

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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