Variant report

Variant	rs16891333
Chromosome Location	chr6:38920998-38920999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10755703	0.81[JPT][hapmap];0.86[LWK][hapmap];0.83[ASN][1000 genomes]
rs12208827	0.94[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13214237	1.00[CEU][hapmap]
rs13214471	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs1332011	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1412264	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1412270	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1537232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16891370	1.00[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2076514	0.86[CEU][hapmap]
rs2273094	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34826703	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35548896	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35928736	0.82[EUR][1000 genomes]
rs4573077	0.94[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56353223	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6924462	0.87[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7754034	1.00[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357293	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366989	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs9369095	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9369096	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9369097	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9369098	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394556	0.89[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs9394568	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv602962	chr6:38907202-38940282	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv948357	chr6:38920998-39035836	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16891333	MDGA1	cis	parietal	SCAN
rs16891333	FANCE	cis	parietal	SCAN

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

No data

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