Variant report

Variant	rs7427395
Chromosome Location	chr3:54399608-54399609
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	chr3:54398589..54400441-chr3:54403161..54405917,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11713798	0.92[CEU][hapmap];0.92[CHB][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11715872	0.89[EUR][1000 genomes]
rs11717967	0.92[CEU][hapmap]
rs1375517	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs1574200	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs17054035	0.84[CEU][hapmap]
rs1868505	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28499181	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55967821	0.80[AFR][1000 genomes]
rs56027715	0.89[EUR][1000 genomes]
rs59598269	0.87[EUR][1000 genomes]
rs6445649	0.91[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445650	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445652	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445654	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6445662	0.92[CEU][hapmap]
rs6807267	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs72988031	0.80[AFR][1000 genomes]
rs72988033	0.80[AFR][1000 genomes]
rs72988051	0.80[AFR][1000 genomes]
rs73841998	0.82[AFR][1000 genomes]
rs7431093	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7638153	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs9818236	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs9835975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7427395	APPL1	cis	cerebellum	SCAN
rs7427395	MAPKAPK3	cis	parietal	SCAN
rs7427395	SEMA3G	cis	parietal	SCAN
rs7427395	TEX264	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54392600-54410200	Weak transcription	Ovary	ovary
2	chr3:54393600-54400200	Weak transcription	Fetal Lung	lung
3	chr3:54395400-54407800	Weak transcription	Hela-S3	cervix
4	chr3:54395400-54409000	Weak transcription	Right Atrium	heart
5	chr3:54399600-54400800	Weak transcription	Fetal Brain Male	brain

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