Variant report

Variant	rs12663063
Chromosome Location	chr6:70900604-70900605
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10498871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1200569	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1200576	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1200577	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1210977	0.84[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16868632	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296007	0.90[EUR][1000 genomes]
rs2346212	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs3793056	0.85[MEX][hapmap]
rs3806036	0.84[CEU][hapmap]
rs3806058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828773	0.84[CEU][hapmap]
rs3828775	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707687	0.86[EUR][1000 genomes]
rs550152	0.90[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs555313	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs572716	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58042167	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583618	0.87[EUR][1000 genomes]
rs583619	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs58673424	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58701153	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622918	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62420159	0.83[EUR][1000 genomes]
rs62421668	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62421670	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624243	1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs633762	0.92[MEX][hapmap];0.80[AMR][1000 genomes]
rs658805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756657	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765390	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs809074	0.90[EUR][1000 genomes]
rs9454995	1.00[CEU][hapmap];0.90[EUR][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	nsv1026151	chr6:70621616-70946967	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv933674	chr6:70663616-70973112	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv830683	chr6:70743422-70941190	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1015807	chr6:70874416-70913489	Strong transcription Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12663063	C6orf57	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70875600-70919800	Weak transcription	GM12878-XiMat	blood
2	chr6:70885800-70901400	Strong transcription	Primary B cells from cord blood	blood
3	chr6:70886000-70904600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr6:70889600-70901800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:70900200-70901400	Enhancers	Fetal Lung	lung

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