Variant report

Variant	rs6690583
Chromosome Location	chr1:85466337-85466338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10443172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782534	0.86[YRI][hapmap]
rs10782537	0.87[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10873672	0.86[YRI][hapmap]
rs10873682	0.82[YRI][hapmap]
rs10873683	0.83[YRI][hapmap]
rs11161514	0.85[YRI][hapmap]
rs11588160	0.85[ASN][1000 genomes]
rs12024977	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs12030730	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs12030837	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs12037219	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs12042018	0.85[ASN][1000 genomes]
rs12042160	0.82[ASN][1000 genomes]
rs12042845	0.81[ASN][1000 genomes]
rs12042910	0.85[ASN][1000 genomes]
rs12045710	0.85[ASN][1000 genomes]
rs1371140	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1371143	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs1837329	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853776	0.85[ASN][1000 genomes]
rs2028304	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2083283	0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2083284	0.85[ASN][1000 genomes]
rs2304641	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2840050	0.93[CHB][hapmap]
rs55721024	0.86[ASN][1000 genomes]
rs589653	0.83[YRI][hapmap]
rs600536	0.88[YRI][hapmap]
rs61768850	0.86[ASN][1000 genomes]
rs61768852	0.86[ASN][1000 genomes]
rs61768853	0.86[ASN][1000 genomes]
rs61768854	0.90[ASN][1000 genomes]
rs61770879	0.82[ASN][1000 genomes]
rs632545	0.83[YRI][hapmap]
rs651916	0.86[YRI][hapmap]
rs6665436	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs6672362	0.84[CHB][hapmap];0.86[ASN][1000 genomes]
rs6679539	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs6680422	0.85[ASN][1000 genomes]
rs668860	0.83[YRI][hapmap]
rs6690464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699356	0.86[ASN][1000 genomes]
rs6699956	0.85[ASN][1000 genomes]
rs7522239	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[ASN][1000 genomes]
rs7547224	0.93[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7547317	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs893620	0.81[ASN][1000 genomes]
rs898036	1.00[CHB][hapmap];0.93[JPT][hapmap]

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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv470724	chr1:85334788-85585260	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv462383	chr1:85334788-85594466	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv546700	chr1:85334788-85594466	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv947434	chr1:85334915-85594135	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6690583	LOC339524	cis	parietal	SCAN
rs6690583	MCOLN2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85464200-85467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:85464400-85466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:85464800-85466800	Active TSS	GM12878-XiMat	blood
4	chr1:85465200-85467000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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