Variant report

Variant	rs17546789
Chromosome Location	chr15:53611257-53611258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:53579873..53581442-chr15:53608994..53611608,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10152228	0.85[EUR][1000 genomes]
rs10152522	0.85[EUR][1000 genomes]
rs10152553	0.85[EUR][1000 genomes]
rs1027010	0.86[EUR][1000 genomes]
rs11070976	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11856300	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856514	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856604	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856856	0.85[EUR][1000 genomes]
rs12439589	0.85[EUR][1000 genomes]
rs12439627	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12442789	0.85[EUR][1000 genomes]
rs12592658	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904851	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12907341	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911558	0.85[EUR][1000 genomes]
rs12914787	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1386170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466597	0.85[EUR][1000 genomes]
rs1466598	0.85[EUR][1000 genomes]
rs1466599	0.85[EUR][1000 genomes]
rs1466600	0.85[EUR][1000 genomes]
rs1466601	0.85[EUR][1000 genomes]
rs1486556	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1486557	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1486558	0.82[EUR][1000 genomes]
rs1486559	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1486560	0.82[EUR][1000 genomes]
rs1486561	0.85[EUR][1000 genomes]
rs1486562	0.83[EUR][1000 genomes]
rs1486563	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1501071	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1552415	0.85[EUR][1000 genomes]
rs1552416	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17546957	0.85[EUR][1000 genomes]
rs2036356	0.83[EUR][1000 genomes]
rs2134002	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4143784	0.83[EUR][1000 genomes]
rs4143785	0.82[EUR][1000 genomes]
rs4776131	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776133	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55968066	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7162663	0.85[EUR][1000 genomes]
rs7173165	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs750485	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750486	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751175	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037429	0.86[EUR][1000 genomes]
rs972045	0.86[EUR][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	nsv1037630	chr15:53324645-53708925	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17546789	GNB5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53605400-53615200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:53605400-53617400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr15:53609000-53614800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:53609600-53615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:53610800-53611600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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