Variant report

Variant	rs6824615
Chromosome Location	chr4:167425316-167425317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10007851	0.83[EUR][1000 genomes]
rs10008481	0.80[EUR][1000 genomes]
rs10010173	0.82[EUR][1000 genomes]
rs10020655	0.83[EUR][1000 genomes]
rs10025831	0.83[EUR][1000 genomes]
rs10026453	0.83[EUR][1000 genomes]
rs10857381	0.83[EUR][1000 genomes]
rs10857383	0.83[EUR][1000 genomes]
rs11100654	0.83[EUR][1000 genomes]
rs1160586	0.82[EUR][1000 genomes]
rs1160587	0.81[EUR][1000 genomes]
rs12501140	0.84[EUR][1000 genomes]
rs12504728	0.84[EUR][1000 genomes]
rs12641852	0.83[EUR][1000 genomes]
rs1388885	0.82[EUR][1000 genomes]
rs1388886	0.83[EUR][1000 genomes]
rs1388887	0.83[EUR][1000 genomes]
rs1388888	0.83[EUR][1000 genomes]
rs1388889	0.83[EUR][1000 genomes]
rs1492527	0.81[AMR][1000 genomes]
rs1492528	0.80[AMR][1000 genomes]
rs1492536	0.85[JPT][hapmap];0.94[MEX][hapmap]
rs17518913	0.82[EUR][1000 genomes]
rs17597276	0.83[EUR][1000 genomes]
rs1988968	0.83[EUR][1000 genomes]
rs2029641	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2172319	0.83[EUR][1000 genomes]
rs28494733	0.82[EUR][1000 genomes]
rs28689804	0.81[EUR][1000 genomes]
rs28691004	0.81[EUR][1000 genomes]
rs28691761	0.82[EUR][1000 genomes]
rs4234899	0.83[EUR][1000 genomes]
rs4234900	0.83[EUR][1000 genomes]
rs4488904	0.81[EUR][1000 genomes]
rs4560359	0.82[EUR][1000 genomes]
rs4690848	0.83[EUR][1000 genomes]
rs4690849	0.83[EUR][1000 genomes]
rs4690850	0.83[EUR][1000 genomes]
rs4691288	0.82[EUR][1000 genomes]
rs4691289	0.83[EUR][1000 genomes]
rs6536968	0.80[AMR][1000 genomes]
rs6829635	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6844841	0.80[AMR][1000 genomes]
rs72695503	0.83[EUR][1000 genomes]
rs7658687	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7662181	0.83[EUR][1000 genomes]
rs7676309	0.84[EUR][1000 genomes]
rs970765	0.80[AMR][1000 genomes]
rs978229	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs978230	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs992020	0.83[EUR][1000 genomes]
rs992021	0.83[EUR][1000 genomes]
rs992022	0.83[EUR][1000 genomes]
rs9995641	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034421	chr4:166961339-167893289	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv537339	chr4:166961339-167893289	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv881405	chr4:167193885-167628013	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1023051	chr4:167304814-168211540	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv537340	chr4:167304814-168211540	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv881309	chr4:167377133-167500233	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv830143	chr4:167386232-167538014	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1017028	chr4:167420519-167697787	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6824615	C4orf39	cis	parietal	SCAN
rs6824615	TRIM60	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:167424000-167427200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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