Variant report

Variant	rs620729
Chromosome Location	chr6:11508671-11508672
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1522446	0.95[YRI][hapmap]
rs2327440	0.95[JPT][hapmap]
rs4711303	0.89[JPT][hapmap]
rs4713562	0.89[JPT][hapmap]
rs4713577	0.89[JPT][hapmap]
rs4713579	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs471560	0.83[ASN][1000 genomes]
rs471752	0.84[ASN][1000 genomes]
rs478147	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs483637	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs490466	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[MEX][hapmap]
rs509971	0.81[ASN][1000 genomes]
rs513870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519140	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs524159	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs538808	0.83[ASN][1000 genomes]
rs539160	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs552681	0.83[ASN][1000 genomes]
rs554671	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs555034	0.84[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555742	0.80[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs566237	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs571683	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs573082	0.81[ASN][1000 genomes]
rs574254	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs581285	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs588062	0.82[CEU][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.81[EUR][1000 genomes]
rs594164	0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs598907	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs606402	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs628980	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs661055	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs663283	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs675565	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs678862	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs685384	0.80[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs687163	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6936326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs821443	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9348893	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357151	0.85[ASN][1000 genomes]
rs9368729	0.83[ASN][1000 genomes]
rs9380321	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394109	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs9394115	0.80[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394119	0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs620729	GCNT2	cis	cerebellum	SCAN

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

No data

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