Variant report

Variant	rs10888934
Chromosome Location	chr1:56033892-56033893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10493196	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs10789002	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10789003	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789004	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888931	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10888933	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206618	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11206620	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206622	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12044949	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12069408	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12086546	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12128185	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12128337	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12142554	0.86[EUR][1000 genomes]
rs12401977	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1392128	0.84[ASW][hapmap];0.87[TSI][hapmap]
rs1499658	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17112402	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs1875068	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4339898	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4927249	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61774741	0.95[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs61776360	0.86[EUR][1000 genomes]
rs6669248	0.85[EUR][1000 genomes]
rs6675850	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs72667832	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72667838	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72667846	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9436973	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9787362	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10888934	PRKAA2	cis	parietal	SCAN
rs10888934	TXNDC12	cis	cerebellum	SCAN
rs10888934	KTI12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56025800-56038400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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