Variant report

Variant	rs6562904
Chromosome Location	chr13:76093935-76093936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1050235	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11148993	0.87[CEU][hapmap]
rs12859594	0.80[EUR][1000 genomes]
rs12859711	0.80[EUR][1000 genomes]
rs12861744	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12861774	0.82[EUR][1000 genomes]
rs12865529	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12866747	0.80[EUR][1000 genomes]
rs12869081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12871445	0.82[EUR][1000 genomes]
rs17064647	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs2031234	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs34072684	0.80[EUR][1000 genomes]
rs34241221	0.80[EUR][1000 genomes]
rs34407556	0.80[EUR][1000 genomes]
rs34572351	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34949196	0.80[EUR][1000 genomes]
rs35132045	0.80[EUR][1000 genomes]
rs35132275	0.82[EUR][1000 genomes]
rs35352582	0.80[EUR][1000 genomes]
rs35556048	0.89[EUR][1000 genomes]
rs35596538	0.89[EUR][1000 genomes]
rs35631959	0.82[EUR][1000 genomes]
rs35680815	0.85[EUR][1000 genomes]
rs35853105	0.85[EUR][1000 genomes]
rs35901810	0.89[EUR][1000 genomes]
rs36043532	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885298	0.87[CEU][hapmap]
rs4885299	0.87[GIH][hapmap]
rs4885302	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885303	1.00[EUR][1000 genomes]
rs4885304	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4885310	0.85[EUR][1000 genomes]
rs4885311	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs4885315	0.80[EUR][1000 genomes]
rs4885327	0.80[EUR][1000 genomes]
rs6562905	0.83[CEU][hapmap]
rs6562910	0.80[EUR][1000 genomes]
rs66528354	0.99[EUR][1000 genomes]
rs66635712	0.80[EUR][1000 genomes]
rs66808557	0.85[EUR][1000 genomes]
rs67051742	0.89[EUR][1000 genomes]
rs67211435	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67270540	0.80[EUR][1000 genomes]
rs67532736	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67656352	0.80[EUR][1000 genomes]
rs68017902	0.80[EUR][1000 genomes]
rs68044755	0.82[EUR][1000 genomes]
rs68052366	0.80[EUR][1000 genomes]
rs71215998	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7321611	0.80[EUR][1000 genomes]
rs7324560	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7325969	0.83[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7337186	0.82[CEU][hapmap]
rs9530443	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9530444	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543938	0.81[CEU][hapmap]
rs9543943	0.87[CEU][hapmap]
rs9543950	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543952	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9543953	0.97[EUR][1000 genomes]
rs9543961	0.89[CEU][hapmap];1.00[EUR][1000 genomes]
rs9543962	0.88[EUR][1000 genomes]
rs9573581	0.83[CEU][hapmap]
rs9593081	0.80[CEU][hapmap]

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	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6562904	LMO7	cis	parietal	SCAN
rs6562904	UCHL3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76082600-76095400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:76089000-76099400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr13:76089000-76104800	Weak transcription	NHDF-Ad	bronchial
4	chr13:76089200-76099400	Weak transcription	Dnd41	blood
5	chr13:76093600-76109400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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