Variant report

Variant	rs10885867
Chromosome Location	chr10:117921732-117921733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:117904505..117907359-chr10:117920705..117922731,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10510016	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10749189	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10749190	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10749191	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10749194	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10749195	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10749196	0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10749197	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10787632	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10787633	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10787634	0.82[ASN][1000 genomes]
rs10885870	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11197563	0.92[ASN][1000 genomes]
rs11197570	0.87[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11197572	0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs11595700	0.83[ASN][1000 genomes]
rs12267789	0.92[ASN][1000 genomes]
rs12762746	0.83[ASN][1000 genomes]
rs2270181	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2420244	0.87[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2420245	0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2420246	0.83[ASN][1000 genomes]
rs3781535	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs3781536	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3781537	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3781538	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3781543	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3781544	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4495806	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4553287	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4751579	0.87[ASN][1000 genomes]
rs4751955	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7078730	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7080193	0.87[ASN][1000 genomes]
rs7080212	0.86[ASN][1000 genomes]
rs7087059	0.88[ASN][1000 genomes]
rs7096448	0.87[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7904057	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7914706	0.83[ASN][1000 genomes]
rs7915221	0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428568	chr10:117806874-117972993	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv3449389	chr10:117806874-118102404	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10885867	ATRNL1	cis	cerebellum	SCAN
rs10885867	C10orf82	cis	cerebellum	SCAN
rs10885867	GFRA1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:117915600-117924200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr10:117917600-117922600	Weak transcription	Brain Anterior Caudate	brain
3	chr10:117918400-117923200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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